· Web viewaDept of Biosciences and Nutrition and Center for Innovative Medicine (CIMED), Karolinska Institutet (KI), Stockholm, Sweden, bOmics Science Center, RIKEN Yokohama Institute,

Persson et al.

ONLINE REPOSITORY TITLE PAGE

Supplementary Material

Transcriptome analysis of controlled and therapy-resistant childhood asthma reveals

distinct gene expression profiles

Helena Persson, PhD,a¶, Andrew T Kwon, PhD,b,c, Jordan A Ramilowski, PhD,b,c, Gilad

Silberberg, PhD,d, Cilla Söderhäll, PhD,a,e, Christina Orsmark-Pietras, PhD,a§, Björn

Nordlund, RN, PhD,e,f,g, Jon R Konradsen, MD, PhD,e,f,g, Michiel JL de Hoon, PhD,b,c, Erik

Melén, MD, PhD,e,h,i, Yoshihide Hayashizaki, MD, Profb,j, Gunilla Hedlin, MD, Profe,f,g, Juha

Kere, MD, Profa,e,k,l and Carsten O Daub, PhDa,b,c

aDept of Biosciences and Nutrition and Center for Innovative Medicine (CIMED), Karolinska

Institutet (KI), Stockholm, Sweden, bOmics Science Center, RIKEN Yokohama Institute,

Yokohama, Japan†, cDivision of Genomic Technologies, RIKEN Center for Life Science

Technologies, Yokohama, Japan, dUnit of Computational Medicine, Dept of Medicine, KI,

eCentre for Allergy Research, KI, fAstrid Lindgren Children’s Hospital, Karolinska University

Hospital, Stockholm, Sweden, gDept of Women’s and Children’s Health, KI, hInstitute of

Environmental Medicine, KI, iSachs’ Children’s Hospital, Stockholm, Sweden, jPreventive

Medicine and Diagnosis Innovation Program, RIKEN Research Cluster for Innovation, Wako,

Japan, kFolkhälsan Institute of Genetics, Helsinki, Finland, lResearch Programs Unit,

University of Helsinki, Helsinki, Finland.

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†RIKEN Omics Science Center ceased to exist as of April 1st, 2013, due to RIKEN

reorganization.

§Present address: Division of Oncology and Pathology, Dept of Clinical Sciences, Lund, Lund

University, Lund, Sweden.

¶Present address: Division of Clinical Genetics, Dept of Laboratory Medicine, Lund, Lund

University, Lund, Sweden.

Corresponding author

Prof Juha Kere

Karolinska Institutet

Dept of Biosciences and Nutrition

Hälsovägen 7-9

SE-141 83 Huddinge

Sweden

Tel: +46-8-524 810 57

Fax: +46-8-774 55 38

Email: [email protected]

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SUPPLEMENTARY METHODSChildren with controlled persistent asthma (CA, n = 15) and therapy-resistant asthma (SA, n =

15) were selected from the Swedish Search study, for which the details on inclusion criteria

and clinical examination procedures have been described previouslyE1, E2. Blood samples were

available for 25 out of 33 children with therapy-resistant asthma, and the 20 children with the

lowest scores (≤20) on the asthma control test (ACT) were selected for microarray analysisE2.

The Swedish Search study also included 39 children with controlled persistent asthma and 20

of these were used for microarray analysis. They were selected to have the highest ACT

scores (21-26) and match the age of the children with therapy-resistant asthma. Healthy

controls (CTRL, n = 19, whereof 10 used in this study) were recruited at Astrid Lindgren

Children’s Hospital, Stockholm, among children admitted for elective surgical procedures

unrelated to asthma. Blood samples were collected prior to the surgical procedure as

described previouslyE2. For the present study we selected samples with sufficient amounts of

remaining RNA and good quality microarray data, resulting in group sizes of 10 (CTRL), 15

(CA), and 15 (SA). After quality control of the CAGE data three samples were excluded,

leaving the sample numbers 9 (CTRL), 15 (CA), and 13 (SA). Informed consent was obtained

from all participating children and their parents and the study was approved by the local ethics

committee. For statistical analysis of clinical parameters, normally distributed data are

summarized by mean and standard deviation (sd) and compared using Student’s t-test. Non-

normally distributed data are presented as median and inter-quartile range (IQR), and

compared with the Mann-Whitney U test. Age- and sex-adjusted body mass index (BMI)

percentiles were calculated using the online BMI Percentile Calculator for Child and TeenE3.

RNA extraction and sequencing

The RNA had been extracted previouslyE2. Briefly, buffy coats were isolated by centrifugation

of whole blood and total RNA was extracted using the RiboPure-Blood Kit (Life

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Technologies) according to the manufacturer’s instructions. RNA quantity and quality were

assessed using NanoDrop 8000 and the Agilent 2100 Bioanalyzer. Sample preparation and

Heliscope CAGE sequencing were performed as described previouslyE4.

Sequence data processing

Reads were aligned to the human ribosomal DNA complete repeating unit using rRNAdust

(author T. Lassmann), an implementation of Myers’ bit parallel dynamic programming

algorithmE5. All reads with an edit distance smaller than or equal to 2 were discarded and the

remaining reads were mapped to the human genome (hg19) using Delve v 0.95E6. Mapped

reads were discarded if they had a Phred mapping quality below 20, mapped outside

chromosome boundaries or had a sequence identity below 85%. Remaining reads were

clustered using Paraclu 5E7 with a minimum tag count of 10 reads, a maximum cluster length

of 200 bp and a maximum density to baseline density ratio of 1 or greater. Tag clusters were

then annotated by based on GENCODE V10 transcript modelsE8 using custom-developed

scripts. The TSS tag cluster for hemoglobin, beta (HBB) was removed from the dataset; this

mRNA is highly expressed and specifically stabilized in erythrocytesE9 that contaminate buffy

coat preparations. On average 30% of sequencing reads mapped to the TSS for HBB, which

could skew the calculation of expression in tags per million reads (tpm) for all transcripts.

Final group sizes after quality control were CTRL: n = 9, CA: n = 15, and SA: n = 13.

Differential expression analysis

Differential expression analysis was done in R with edgeR 3.2.3E10 using tagwise dispersion

estimate and default parameters for all tag clusters expressed by at least 3 reads in at least 9

samples. A Benjamini-Hochberg false discovery rate (FDR) below 0.1 was used as the cut-off

for significantly differentially expressed tag clusters. A cut-off of p < 0.05 produced similar

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results but retained fewer genes for downstream enrichment analyses. For the generalized

linear model analysis, we used the following formula:

Ei=b0+b11¿

where

Ei = expression level (tag counts) for tag cluster i,

b0 = coefficient of expression for tag cluster i in CTRL

b1..2 = coefficients of expression in CA and SA, respectively, relative to CTRL,

b3..5 = slopes for the association between expression and cell counts,

[neutrophil] = neutrophil fractions of the total leukocyte counts,

[lymphocyte] = lymphocyte fractions of the total leukocyte counts,

[eosinophil] = eosinophil fractions of the total leukocyte counts,

ei = error term for tag cluster i

Cell fractions were calculated by dividing the cell counts by the total leukocyte counts for

each sample. Monocyte fraction was not used in the formula to avoid multicolinearity.

The databases for Gene Ontology (GO) version 2.9.0 and Kyoto Encyclopedia of Genes and

Genomes (KEGG) version 2.9.1 were obtained from BioconductorE11 and enrichment was

analyzed with GOseq 1.12.0E12 using default settings. Hierarchical clustering was done in R

using Spearman rank correlation and the heatmap produced with gplots 2.11.3. For power

calculations we applied the SSPAE13 package 2.4.0 from Bioconductor. The microarray

dataset for adult severe asthmaticsE14 was obtained from the Gene Expression OmnibusE15

(accession number GDS4425) and the Affymetrix Human Genome U133 Plus 2.0 probe

identifiers were converted to gene symbols using tables from Ensembl BioMartE16. Heatmaps

were produced as before but using Pearson correlation. Bootstrapping analysis of cluster

stability was done with the pvclust R packageE17.

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Identification and validation of novel transcription start sites

Novel transcription start sites (TSSs) were identified among differentially expressed tag

clusters without overlapping exonic annotation, i.e. intergenic, intronic and antisense tag

clusters. These were filtered for the presence of supporting publicly available mRNA and

expressed sequence tag (EST) data from the UCSC Genome BrowserE18. A high-confidence

set of novel TSSs supported by spliced ESTs was manually curated for experimental

validation by RT-PCR and Sanger sequencing. 800 ng DNase-treated RNA from two CTRL

samples was used for cDNA synthesis with the SuperScript III First-Strand cDNA Synthesis

kit (Life Technologies) according to the manufacturer’s instructions. Negative control

reactions with RNA but without reverse transcriptase (no RT) were run in parallel. The cDNA

was diluted 1:2 and 1 µl was used for PCR amplification with HotStarTaq Plus DNA

Polymerase (QIAGEN) in a 25 µl reaction using the temperature profile 95°C 5 min, followed

by 35 cycles of 94°C 30 s, 58°C 45 s, 72°C 1 min and a final elongation step at 72°C for 10

min. Primers are listed in Table E1 in the Online Repository. Products were visualized on 2%

agarose gels and purified with the QIAquick PCR Purification Kit, or where indicated in

Figure E5 (see the Online Repository), with the QIAquick Gel Extraction Kit (QIAGEN).

Purified PCR products were sequenced using both forward and reverse PCR primers.

Comparison of differentially expressed tag clusters to loci genetically associated with

asthma

HaploReg v2E19 was used to retrieve information for single nucleotide polymorphisms (SNPs)

in linkage disequilibrium (LD, r2 > 0.8 based on the 1000 Genomes Phase 1 European sample)

with 62 SNPs found to have genome-wide significant association with asthma collected from

17 studiesE20. LD blocks were defined as the interval from the first to the last SNP within LD

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from the query SNP (based on SNPs that are polymorphic in the European population).

Intersection and manipulation of genetic intervals was done with BEDToolsE21.

Motif activity response analysis (MARA)

The human genome (hg19) was scanned for SwissRegulon motif hits using MotEvoE22 and

motif activities were calculated as described previouslyE23. A reduced set of CAGE tag

clusters (n = 9,268) was selected to include only clusters differentially expressed between any

two phenotypes with unadjusted p-value < 0.1 and located in sense orientation within 500 bp

of a known TSS or in the 5' untranslated region (UTR) of a transcript. This filtered set was

used together with the tag clusters representing novel TSSs as input for motif activity

calculations. Two intervals surrounding each tag cluster were analyzed: -300 to +100 bp and -

1000 to +200 bp. We applied linear regression analysis based on Gaussian distribution to the

standard normal deviates of the motif activities (where the standardized motif activities were

divided by the associated standard deviations) and the cell count fractions. Weighted mean

motif activities were calculated for each disease group, which were then regularized by

adding the minimum mean activity to each value. Differences in the motif activities among

the disease groups were determined by log likelihood of the weighted mean activities.

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Table E1. Primers for validation of novel transcription start sites (TSSs) by RT-PCR and Sanger sequencing.

TSS Gene Forward primer Reverse primerAlternative TSSschr2:24714142(+) NCOA1 GGCTGAAATGCCTGTTCTTC TCTCACCTCATTTAAGGCCAATchr2:143828538(+) ARHGAP15 TCCTTGAAGCCAGCTACCAC TCTCATTTGCACAGCTCCTGchr4:148973914(+) ARHGAP10 GGAGGTCTAAGGGAGCTCAAA TGAGTTGGAGCTTGTTGTGGchr8:131370837(-) ASAP1 GTCAGCGCGTCTGAGGAG TCTGAAGGGCTGTTCTATCTTGchr9:117160251(-) AKNA/RP11-9M16.2 AGATTCGTTCACCCAGCAAC TGTGGAAGGGAAAACTGAGGchr13:46948966(-) KIAA0226L CAGGGACAGCATCATGTCAG CAGGGCTCCACAGGAGAATchr15:86087320(+) AKAP13 AAGCTTGCTCCTGCTAACCA TCGATGATGCCTCACAGAACchr16:90023689(+) DEF8 GCAGGTCAGGCTAGGAGCAC ACTCGGATGTTTGGCTCATCchr17:8316490(+) NDEL1 TCAGCTGAGGCCTGAGACAC GTGCCTCCAACTCTGCTTCTNovel transcriptschr6:105901520(+) lincRNA TGCCTATTTTTCCCTTTGAATC GCCAGCAATCCTTGGTATGTchr12:8605756(-) lincRNA GTTTCCAGTTCCCGTCAGAG CCCTTTGGTTGACATAGGAAAAntisense transcriptschr3:134314106(+) KY GCCGCCATGAGAAGAAGTAT CACGTCTCATGAGGTTCTGCchr14:95652012(+) CLMN/CTD-2240H23.2 GCAAGGCTCCACAGAGGAAT GAGACAGAGCAGCTTGACCA

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Table E2. Leukocyte counts (109 x L-1 blood) and sequencing library sizes from raw reads to the final dataset used for expression analysis (see Supplementary Methods in the Online repository for details on sequence data filtering including removal of the tag cluster corresponding to the transcription start site of hemoglobin, beta; HBB).

Sample WBC Neutrophils Eosinophils Lymphocytes Monocytes Raw reads Tagdust-filtered Single-mapping Ribosomal RNA HBB reads Used readsCTRL_136 5.7 2.5 0.2 2.6 0.4 41929091 36507811 11297347 799801 2060430 8437116CTRL_137 5.3 1.8 0.1 2.9 0.5 39439329 34498423 10089662 620701 1845282 7623679CTRL_138 5.2 2.3 0.1 2.4 0.4 36569638 31896470 9059613 340552 1764583 6954478CTRL_139 5.0 2.3 0.5 1.6 0.4 41358764 34775501 10840171 1091280 1726133 8022758CTRL_140 5.4 2.7 0.2 2.0 0.5 39750341 34853661 10276716 529912 1967784 7779020CTRL_141 6.0 2.4 0.9 2.2 0.3 38603448 33911862 10322656 442242 2908605 6971809CTRL_142 6.7 3.2 0.0 2.9 0.5 39307551 34171846 10900067 674615 1802162 8423290CTRL_143 7.4 3.3 0.2 3.3 0.5 41587193 35655824 11664788 759791 1666482 9238515CTRL_144 5.1 2.8 0.0 1.6 0.5 39460871 34583696 9389372 527139 1782885 7079348CA_145 4.4 1.9 0.2 1.9 0.4 30705525 26039110 7637725 343710 1394801 5899214CA_146 7.8 3.4 0.3 3.1 1.1 37251500 32361556 10098534 465291 1454372 8178871CA_147 5.6 2.1 0.5 2.6 0.4 31248188 26686495 7426827 357484 1542646 5526697CA_148 6.6 2.8 0.4 3.0 0.4 27540883 22920808 6719010 281639 1462439 4974932CA_149 3.2 1.1 0.1 1.8 0.2 35593298 30892797 8856120 471246 2230086 6154788CA_150 4.8 1.8 0.4 2.1 0.5 36767485 32135674 9091759 459152 1955120 6677487CA_151 9.0 3.7 0.2 4.3 0.7 41370710 36208108 11498074 1023503 2640684 7833887CA_152 8.2 3.3 0.6 3.5 0.7 40888613 35702105 10295012 664812 1782891 7847309CA_153 5.7 2.8 0.3 2.3 0.3 39314918 34412493 9179021 506841 1951400 6720780CA_154 5.3 2.1 0.1 2.7 0.3 36894042 32141608 8980126 454760 1403453 7121913CA_155 5.6 2.2 0.2 2.8 0.5 41579510 36599430 11165407 576750 1646091 8942566CA_156 4.7 1.7 0.0 2.5 0.4 38996385 33705917 8635752 345641 1233711 7056400CA_157 6.8 3.0 0.2 3.0 0.6 36579683 32251162 9068210 393988 1092152 7582070CA_158 5.5 2.5 0.2 2.4 0.4 36406385 32058579 8894748 436650 2385757 6072341CA_159 5.7 2.6 0.2 2.5 0.4 40518938 35241855 10625188 475423 1459557 8690208PSA_160 6.8 2.6 0.5 3.3 0.4 40175473 33509912 11462230 1166424 1698346 8597460PSA_161 9.5 5.9 0.3 2.8 0.3 29865095 25357932 7680526 383738 1290855 6005933PSA_162 9.2 4.6 0.5 3.6 0.5 37483512 32444148 11643412 713571 1231968 9697873PSA_164 6.8 3.8 0.4 2.1 0.4 35180876 30535939 7527584 380679 1092683 6054222PSA_165 6.5 3.9 0.4 1.8 0.4 35632175 30670582 9088163 326717 1431494 7329952PSA_166 6.4 3.4 0.4 2.1 0.5 24454614 20104132 5729018 193898 1416079 4119041PSA_167 6.5 3.9 0.2 2.0 0.4 34059952 29776921 9509636 441246 1242102 7826288PSA_168 11.4 6.8 0.4 3.7 0.2 27236973 22817399 6521704 221596 1534782 4765326PSA_169 5.1 2.3 0.5 1.9 0.4 38783421 33433617 11115169 476954 1297142 9341073PSA_171 4.1 2.1 0.0 1.6 0.3 38695589 33918035 10622287 425218 1870179 8326890PSA_172 4.2 1.8 0.1 1.6 0.6 37955413 33576259 10596080 450277 1447934 8697869PSA_173 4.4 2.2 0.1 1.8 0.3 41357566 36108407 11520521 654854 1329871 9535796PSA_174 5.7 2.0 0.2 3.0 0.4 33141756 28539899 8458145 411491 1252276 6794378

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Table E3. Differentially expressed tag clusters for CA vs CTRL.

TC logFC logCPM Adj. P Position Strand Annotation Transcript iD Gene symbol Description

chr10_+_35484802 1.87 3.29 5.22E-03 chr10:35484802-35484926 + TSS,SENST00000474931.1/ENST00000468236.1/ENST00000344351.5

CREM cAMP responsive element modulator

chr10_+_5136559 1.66 4.75 4.68E-05 chr10:5136559-5136636 + TSSregion500,S ENST00000480697.1 AKR1C3

aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)

chr10_+_70863831 -1.94 1.63 6.85E-02 chr10:70863831-70863845 + CDS_or_noncoding_last_exon,S

ENST00000242465.3/ENST00000462445.1 SRGN serglycin

chr10_+_89623808 -1.27 1.00 5.81E-02 chr10:89623808-89623866 + TSSregion500,S ENST00000462694.1/ENST00000487939.1 PTEN phosphatase and tensin

homolog

chr10_-_126849088 1.00 1.94 9.06E-02 chr10:126849088-126849149 - TSSregion500,SENST00000337195.5/ENST00000494626.2/ENST00000460976.1

CTBP2 C-terminal binding protein 2

chr10_-_64576013 -1.43 2.21 3.31E-02 chr10:64576013-64576175 - TSS,S ENST00000242480.3/ENST00000411732.1 EGR2 early growth response

2

chr10_-_72360161 1.36 3.64 3.55E-02 chr10:72360161-72360336 - CDS_or_noncoding_inner_exon,S

ENST00000373209.1/ENST00000318971.2/ENST00000441259.1

PRF1 perforin 1 (pore forming protein)



chr10_-_72362434 1.00 6.94 7.05E-02 chr10:72362434-72362546 - TSS,SENST00000373209.1/ENST00000318971.2/ENST00000441259.1


chr11_+_47412796 -1.41 0.79 8.29E-02 chr11:47412796-47412929 + CDS_or_noncoding_first_intron,AS ENST00000527426.1 RP11-750H9.5

chr11_+_71846707 -1.74 4.68 8.19E-02 chr11:71846707-71846814 + TSS,S

ENST00000445078.2/ENST00000456237.1/ENST00000442948.2/ENST00000325101.4

FOLR3 folate receptor 3 (gamma)

chr11_-_10821157 -2.00 -0.34 6.90E-02 chr11:10821157-10821275 - TSS,S ENST00000525606.1 EIF4G2eukaryotic translation initiation factor 4 gamma, 2

chr11_-_118081285 -1.71 3.46 1.11E-02 chr11:118081285-118081437 - CDS_or_noncoding_inner_exon,S

ENST00000356289.5/ENST00000292067.7/ENST00000533261.1/ENST00000526595.1/ENST00000526620.1/ENST00000537867.1/

AMICA1adhesion molecule, interacts with CXADR antigen 1

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ENST00000524477.1/ENST00000527877.1/ENST00000525565.1/ENST00000534294.1/ENST00000529164.1/ENST00000531536.1

chr11_-_3849257 -1.12 3.67 6.90E-02 chr11:3849257-3849449 - 5UTR_last_exon,S


RHOG ras homolog family member G


ENST00000378538.3/ENST00000227163.4/ENST00000533968.1

SPI1

spleen focus forming virus (SFFV) proviral integration oncogene spi1

chr11_-_85522024 0.84 4.57 5.20E-02 chr11:85522024-85522224 - TSS,S


SYTL2 synaptotagmin-like 2

chr12_+_90103535 -0.85 4.27 2.60E-02 chr12:90103535-90103643 + TSSregion500,AS ENST00000551310.1 ATP2B1ATPase, Ca++ transporting, plasma membrane 1

chr12_+_9795402 1.17 2.98 3.63E-02 chr12:9795402-9795522 + CDS_or_noncoding_first_exon,S ENST00000426641.2 GOT2P3

glutamic-oxaloacetic transaminase 2 pseudogene 3

chr12_-_106641666 -0.68 5.39 4.89E-02 chr12:106641666-106641802 - TSS,S ENST00000378026.4 CKAP4 cytoskeleton-associated protein 4

chr12_-_10875672 -1.67 2.99 3.48E-02 chr12:10875672-10875718 - TSSregion500,S


CSDA cold shock domain protein A

chr12_-_68845284 1.38 4.25 4.01E-02 chr12:68845284-68845483 - TSS,S ENST00000542875.1 RP11-81H14.2

chr12_-_89746177 -0.64 6.31 6.85E-02 chr12:89746177-89746298 - TSS,S ENST00000308385.6/ENST00000548755.1 DUSP6 dual specificity

phosphatase 6

chr13_-_110438835 -0.78 6.57 9.06E-02 chr13:110438835-110439007 - TSS,S ENST00000375856.3 IRS2 insulin receptor substrate 2

chr14_+_22918582 1.36 3.80 9.06E-02 chr14:22918582-22918654 + CDS_or_noncoding_last_intron,AS ENST00000514473.2 AE000661.37



chr14_+_22925528 0.99 4.84 6.62E-02 chr14:22925528-22925713 + CDS_or_noncoding_first_exon,S ENST00000390475.1 TRDJ2 T cell receptor delta

joining 2

chr14_+_60716312 -1.90 2.92 3.66E-02 chr14:60716312-60716356 + TSSregion500,S ENST00000395076.4/ENST00000325658.3/ PPM1A protein phosphatase,

Mg2+/Mn2+ dependent,

1414

Persson et al.

ENST00000528241.2 1A

chr14_+_75745753 -1.30 2.24 8.92E-02 chr14:75745753-75745763 + TSSregion500,S ENST00000556324.1 FOSFBJ murine osteosarcoma viral oncogene homolog


ENST00000303562.4/ENST00000535987.1/ENST00000555686.1/ENST00000555672.1/ENST00000555347.1

FOSFBJ murine osteosarcoma viral oncogene homolog

chr14_-_25103344 1.29 8.44 3.63E-02 chr14:25103344-25103520 - TSS,S

ENST00000415355.3/ENST00000216341.4/ENST00000382539.2/ENST00000382542.1/ENST00000382540.1/ENST00000532263.1/ENST00000554242.1/ENST00000530830.1/ENST00000526004.1

GZMB

granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)

chr14_-_35872416 -1.65 2.93 3.11E-03 chr14:35872416-35872424 - TSSregion500,S ENST00000555371.1/ENST00000556664.1 NFKBIA

nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha

chr14_-_35873848 -1.13 7.18 2.15E-03 chr14:35873848-35873985 - TSS,S

ENST00000216797.5/ENST00000554001.1/ENST00000557140.1/ENST00000553342.1/ENST00000557100.1/ENST00000557459.1/ENST00000555629.1

NFKBIA


chr15_+_31664212 -1.55 1.73 4.70E-02 chr15:31664212-31664310 + 5UTR_last_exon,S ENST00000558844.1 KLF13 Kruppel-like factor 13

chr15_+_43478001 -1.39 0.75 9.06E-02 chr15:43478001-43478164 + TSS,S ENST00000444658.2 CCNDBP1 cyclin D-type binding-protein 1

chr15_+_58430571 -1.15 3.42 4.66E-02 chr15:58430571-58430584 + TSS,S ENST00000536493.1 AQP9 aquaporin 9

chr16_+_3096707 -1.46 1.70 7.01E-03 chr16:3096707-3096711 + TSSregion500,S ENST00000336577.3 MMP25 matrix metallopeptidase 25

chr16_+_57681338 1.80 1.42 9.06E-02 chr16:57681338-57681375 + 5UTR_first_intron,SENST00000544297.1/ENST00000456916.1/ENST00000388812.4

GPR56 G protein-coupled receptor 56

chr16_-_405193 1.19 3.49 3.63E-02 chr16:405193-405380 - intergenic intergenic NA NAchr17_+_34227367 1.89 0.63 7.53E-02 chr17:34227367-34227501 + intergenic intergenic NA NA

chr17_+_37865774 1.57 3.42 2.60E-02 chr17:37865774-37865959 + CDS_or_noncoding_first_intron,S ENST00000445658.2 ERBB2

v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)

chr17_+_72462527 1.20 4.96 6.21E-03 chr17:72462527-72462548 + TSSregion500,S ENST00000361933.2/ CD300A CD300a molecule

1515

Persson et al.

ENST00000360141.3/ENST00000392625.3/ENST00000310828.5

chr17_-_68165434 -1.68 0.12 7.05E-02 chr17:68165434-68165544 - TSSregion500,AS ENST00000243457.2 KCNJ2potassium inwardly-rectifying channel, subfamily J, member 2


ENST00000254806.3/ENST00000344296.4/ENST00000416574.2

WBP2 WW domain binding protein 2

chr19_+_12902551 -1.11 3.38 4.99E-02 chr19:12902551-12902614 + TSSregion500,S ENST00000302754.4 JUNB jun B proto-oncogene

chr19_+_39897475 -0.73 10.54 3.11E-03 chr19:39897475-39897519 + TSS,S ENST00000248673.3 ZFP36zinc finger protein 36, C3H type, homolog (mouse)

chr19_+_39898433 -1.15 2.26 2.77E-02 chr19:39898433-39898475 + CDS_or_noncoding_last_exon,S ENST00000248673.3 ZFP36

zinc finger protein 36, C3H type, homolog (mouse)







chr19_+_45971244 -1.62 5.61 1.22E-03 chr19:45971244-45971289 + TSS,S


FOSBFBJ murine osteosarcoma viral oncogene homolog B

chr19_+_45971668 -1.89 0.81 9.06E-02 chr19:45971668-45971768 + TSSregion500,S



chr19_+_47823182 -2.40 -0.66 9.06E-02 chr19:47823182-47823190 + CDS_or_noncoding_last_exon,S ENST00000355085.2 C5AR1

complement component 5a receptor 1

chr19_+_51890311 1.61 2.50 3.93E-02 chr19:51890311-51890438 + CDS_or_noncoding_inner_exon,AS ENST00000221973.2 LIM2 lens intrinsic membrane

protein 2, 19kDachr19_+_7437754 -1.83 -0.14 4.38E-02 chr19:7437754-7437912 + intergenic intergenic NA NA


ENST00000543343.1/ENST00000309311.5 EEF2 eukaryotic translation

elongation factor 2

chr1_+_118165763 -2.13 0.10 8.19E-02 chr1:118165763-118165766 + CDS_or_noncoding_last_exon,S ENST00000369448.3 FAM46C family with sequence

similarity 46, member C

chr1_+_145440653 -1.05 3.67 7.05E-02 chr1:145440653-145440758 + TSSregion500,S ENST00000486597.1 TXNIP cDNA FLJ61424, highly similar to Homo

1616

Persson et al.

sapiens thioredoxin interacting protein (TXNIP), mRNA

chr1_+_209849199 -1.50 3.39 7.30E-02 chr1:209849199-209849309 + CDS_or_noncoding_last_exon,S ENST00000367029.4 G0S2 G0/G1switch 2

chr1_+_45265972 -0.80 6.24 1.80E-02 chr1:45265972-45266161 + TSS,S ENST00000543983.1/ENST00000465443.1 PLK3 polo-like kinase 3

chr1_+_51702289 -1.29 4.09 3.63E-02 chr1:51702289-51702327 + TSSregion500,S ENST00000242719.3/ENST00000494873.1 RNF11 ring finger protein 11

chr1_+_55273150 1.94 1.62 4.89E-02 chr1:55273150-55273328 + CDS_or_noncoding_inner_exon,S

ENST00000358193.3/ENST00000371273.3 C1ORF177 NA


SH2D2A SH2 domain containing 2A


SH2D1B SH2 domain containing 1B

chr1_-_167409896 1.96 -0.15 7.05E-02 chr1:167409896-167410008 - CDS_or_noncoding_inner_exon,S

ENST00000362089.5/ENST00000392122.3/ENST00000483825.1

CD247 CD247 molecule

chr20_+_30193050 -3.41 1.67 2.15E-03 chr20:30193050-30193211 + TSS,S ENST00000376112.3/ENST00000376105.3 ID1

inhibitor of DNA binding 1, dominant negative helix-loop-helix protein

chr20_+_37707484 1.97 0.54 7.69E-02 chr20:37707484-37707551 + intergenic intergenic NA NA

chr20_-_47361555 -1.69 -0.08 9.15E-02 chr20:47361555-47361687 - CDS_or_noncoding_inner_exon,S

ENST00000371941.3/ENST00000396220.1 PREX1

phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1

chr20_-_4804243 -0.64 3.98 6.00E-02 chr20:4804243-4804288 - TSSregion500,S ENST00000379400.3/ENST00000474232.1 RASSF2

Ras association (RalGDS/AF-6) domain family member 2

chr21_+_40177842 -0.61 5.83 6.62E-02 chr21:40177842-40177909 + TSS,S ENST00000432278.1 ETS2v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)


MLC1megalencephalic leukoencephalopathy with subcortical cysts 1

chr2_+_120687240 0.84 6.11 4.38E-02 chr2:120687240-120687438 + TSS,S ENST00000544261.1 PTPN4

protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)

chr2_+_143718820 2.10 -0.17 8.58E-02 chr2:143718820-143718872 + CDS_or_noncoding_inner_intron,S

ENST00000264170.4/ENST00000375773.2/ENST00000409512.1

KYNU kynureninase

chr2_+_158290873 -2.25 -0.89 6.62E-02 chr2:158290873-158290905 + 5UTR_inner_exon,AS

ENST00000540637.1/ENST00000418920.1 CYTIP cytohesin 1 interacting

proteinchr2_+_237897693 -3.39 1.23 7.24E-03 chr2:237897693-237897808 + intergenic intergenic NA NA

1717

Persson et al.

chr2_+_7865810 1.02 4.89 7.01E-03 chr2:7865810-7865995 + TSS,S ENST00000417930.1 AC092580.4

chr2_+_98329970 2.40 -0.58 8.29E-02 chr2:98329970-98329976 + TSSregion500,S ENST00000264972.5/ENST00000483781.1 ZAP70

zeta-chain (TCR) associated protein kinase 70kDa

chr2_-_235404769 1.47 1.14 7.05E-02 chr2:235404769-235404842 - CDS_or_noncoding_first_exon,S

ENST00000390645.2/ENST00000339728.3 ARL4C ADP-ribosylation factor-

like 4C

chr2_-_238600408 -1.02 1.64 9.06E-02 chr2:238600408-238600593 - TSSregion500,AS


LRRFIP1leucine rich repeat (in FLII) interacting protein 1

chr2_-_37898705 -0.56 7.00 7.05E-02 chr2:37898705-37898841 - TSSregion500,S ENST00000295324.3 CDC42EP3CDC42 effector protein (Rho GTPase binding) 3

chr2_-_47387476 2.61 0.28 3.93E-02 chr2:47387476-47387641 - CDS_or_noncoding_last_exon,S ENST00000460218.1 CALM2

calmodulin 2 (phosphorylase kinase, delta)

chr4_+_40201115 -1.70 -0.33 9.06E-02 chr4:40201115-40201251 + 5UTR_first_intron,S


RHOH ras homolog family member H

chr4_+_74853663 2.44 0.74 7.69E-02 chr4:74853663-74853715 + CDS_or_noncoding_first_exon,AS ENST00000296028.3 PPBP

pro-platelet basic protein (chemokine (C-X-C motif) ligand 7)

chr4_-_154605156 -1.60 1.12 3.63E-02 chr4:154605156-154605348 - intergenic intergenic NA NAchr4_-_48116463 1.43 3.67 4.22E-02 chr4:48116463-48116595 - TSS,S ENST00000506073.1 TXK TXK tyrosine kinase

chr5_+_137801158 -2.20 5.91 6.99E-03 chr5:137801158-137801179 + TSS,SENST00000411801.2/ENST00000535792.1/ENST00000239938.4

EGR1 early growth response 1

chr5_+_137801300 -2.89 1.63 2.15E-03 chr5:137801300-137801415 + TSSregion500,SENST00000411801.2/ENST00000535792.1/ENST00000239938.4


chr5_+_137802453 -2.98 1.17 3.11E-03 chr5:137802453-137802597 + CDS_or_noncoding_inner_exon,S

ENST00000411801.2/ENST00000535792.1 EGR1 early growth response

1

chr5_+_177027101 -0.69 3.78 8.44E-02 chr5:177027101-177027237 + TSS,S


B4GALT7xylosylprotein beta 1,4-galactosyltransferase, polypeptide 7

chr6_+_114178493 -0.57 8.66 6.53E-02 chr6:114178493-114178688 + TSS,S ENST00000368635.4 MARCKSmyristoylated alanine-rich protein kinase C substrate

chr6_+_114178781 -0.83 3.51 6.90E-02 chr6:114178781-114178932 + TSSregion500,S ENST00000368635.4 MARCKSmyristoylated alanine-rich protein kinase C substrate

chr6_+_14117860 -1.08 5.19 4.99E-02 chr6:14117860-14118039 + TSS,S ENST00000379153.3 CD83 CD83 molecule

chr6_+_154566797 -2.42 0.45 3.93E-02 chr6:154566797-154566904 + CDS_or_noncoding_last_intron,S ENST00000337049.4 OPRM1 opioid receptor, mu 1

1818

Persson et al.

chr6_+_89790868 -2.22 1.36 1.80E-02 chr6:89790868-89790877 + 5UTR_last_intron,S ENST00000369472.1 PNRC1 proline-rich nuclear receptor coactivator 1

chr6_-_31560676 0.80 5.26 3.63E-02 chr6:31560676-31560808 - TSS,S


NCR3 natural cytotoxicity triggering receptor 3

chr7_+_100271340 -0.46 6.82 7.69E-02 chr7:100271340-100271519 + TSS,S


GNB2

guanine nucleotide binding protein (G protein), beta polypeptide 2



STARD3NL STARD3 N-terminal like

chr7_-_36763798 0.98 4.42 8.44E-02 chr7:36763798-36763855 - TSSregion500,S


AOAH acyloxyacyl hydrolase (neutrophil)

chr7_-_38344997 1.83 1.33 8.86E-02 chr7:38344997-38345194 - intergenic intergenic NA NA


SLC25A37

solute carrier family 25 (mitochondrial iron transporter), member 37


chr8_-_22550924 -1.22 3.57 3.29E-02 chr8:22550924-22551044 - TSSregion500,S ENST00000317216.2/ENST00000519492.1 EGR3 early growth response

3


ENST00000481739.1/ENST00000356384.4 RXRA retinoid X receptor,

alpha

chr9_+_4662265 -0.91 2.60 9.06E-02 chr9:4662265-4662424 + TSS,S ENST00000381883.2/ENST00000537542.1 PPAPDC2

phosphatidic acid phosphatase type 2 domain containing 2

chr9_-_34126465 -1.73 3.28 8.44E-02 chr9:34126465-34126514 - TSSregion500,S ENST00000361264.3 DCAF12 DDB1 and CUL4 associated factor 12

chr9_-_74979780 -1.35 2.74 4.38E-02 chr9:74979780-74979938 - TSS,S ENST00000487330.1 ZFAND5 zinc finger, AN1-type domain 5

chr9_-_94173418 -1.43 2.05 8.44E-02 chr9:94173418-94173492 - 5UTR_first_intron,S ENST00000375724.1/ENST00000297689.2 NFIL3 nuclear factor,

interleukin 3 regulated

chrM_+_811 -1.42 4.54 3.31E-02 chrM:811-814 + intergenic intergenic NA NAchrX_-_106957871 -1.35 2.29 4.99E-02 chrX:106957871-106957983 - CDS_or_noncoding

_last_exon,SENST00000372390.4/ENST00000372397.2/ENST00000315660.4/

TSC22D3 TSC22 domain family, member 3

1919

Persson et al.


chrX_-_106960136 -0.68 9.24 3.31E-02 chrX:106960136-106960300 - TSS,S ENST00000503515.1 TSC22D3 TSC22 domain family, member 3

2020

230

Persson et al.

Table E4. Differentially expressed tag clusters for SA vs CTRL.


chr10_+_114206949 0.54 5.88 7.91E-02 chr10:114206949-114207088 + TSS,S


VTI1A

vesicle transport through interaction with t-SNAREs homolog 1A (yeast)

chr10_+_12615851 1.68 -0.07 4.08E-02 chr10:12615851-12615975 +CDS_or_noncoding_inner_intron,S

ENST00000378847.3/ENST00000378845.1 CAMK1D

calcium/calmodulin-dependent protein kinase ID

chr10_+_135044125 -1.43 0.67 3.25E-02 chr10:135044125-135044239 + CDS_or_noncoding_first_exon,S ENST00000304477.2 UTF1

undifferentiated embryonic cell transcription factor 1

chr10_+_20105533 0.76 3.80 3.93E-02 chr10:20105533-20105573 + TSSregion500,S


PLXDC2 plexin domain containing 2



chr10_+_87802049 -0.62 4.03 9.08E-02 chr10:87802049-87802059 +CDS_or_noncoding_inner_intron,AS

ENST00000327946.7/ENST00000464741.1 GRID1 glutamate receptor,

ionotropic, delta 1

chr10_+_89705229 -0.56 9.31 7.86E-02 chr10:89705229-89705246 + TSSregion500,S ENST00000395256.2 RP11-380G5.3



chr10_-_15902420 0.63 4.58 4.68E-02 chr10:15902420-15902532 - TSS,S ENST00000277632.3/ENST00000477891.1 FAM188A

family with sequence similarity 188, member A

chr10_-_31288304 0.72 4.22 4.54E-02 chr10:31288304-31288498 - TSS,S ENST00000538351.1 ZNF438 zinc finger protein 438

chr10_-_64576013 -1.28 2.27 3.66E-02 chr10:64576013-64576175 - TSS,S ENST00000242480.3/ENST00000411732.1 EGR2 early growth response

2

chr11_+_108094041 0.56 4.65 6.96E-02 chr11:108094041-108094204 + TSSregion500,S ENST00000530958.1/ENST00000526567.1 ATM ataxia telangiectasia

mutated


FAR1 fatty acyl CoA reductase 1

chr11_+_44939434 1.07 3.11 3.22E-02 chr11:44939434-44939570 + TSSregion500,S ENST00000520245.1 TSPAN18 tetraspanin 18

chr11_+_60237271 -2.06 -0.63 6.21E-02 chr11:60237271-60237456 + 3UTR_last_exon,S

ENST00000345732.4/ENST00000532073.1/ENST00000534668.1/

MS4A1membrane-spanning 4-domains, subfamily A, member 1

2121

231232

Persson et al.

ENST00000389939.2

chr11_+_65190259 0.98 9.47 7.82E-03 chr11:65190259-65190323 + TSS,S ENST00000501122.2 NEAT1nuclear paraspeckle assembly transcript 1 (non-protein coding)

chr11_+_65190530 1.05 4.15 2.07E-02 chr11:65190530-65190557 + TSSregion500,S ENST00000499732.1/ENST00000501122.2 NEAT1

nuclear paraspeckle assembly transcript 1 (non-protein coding)

chr11_+_65195912 2.16 -0.12 9.10E-02 chr11:65195912-65195956 + CDS_or_noncoding_first_exon,S ENST00000501122.2 NEAT1


chr11_+_65198184 1.87 1.14 5.66E-02 chr11:65198184-65198284 + CDS_or_noncoding_first_exon,S ENST00000501122.2 NEAT1






chr11_+_65269313 -1.55 3.74 6.21E-02 chr11:65269313-65269322 + TSSregion500,S ENST00000508832.1 MALAT1

metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)

chr11_+_65269367 -1.89 4.63 3.74E-02 chr11:65269367-65269381 + TSSregion500,S ENST00000508832.1 MALAT1


chr11_+_65271341 -2.71 2.31 8.68E-02 chr11:65271341-65271343 + CDS_or_noncoding_first_exon,S ENST00000534336.1 MALAT1









RPLP2 ribosomal protein, large, P2

chr11_+_8704273 -0.45 7.55 2.72E-02 chr11:8704273-8704391 + TSS,SENST00000531978.1/ENST00000524496.1/ENST00000534599.1/

RPL27A ribosomal protein L27a

2222

Persson et al.


chr11_-_10315600 0.74 5.95 5.33E-03 chr11:10315600-10315799 - TSS,S ENST00000256190.8 SBF2 SET binding factor 2

chr11_-_46142520 0.62 4.70 1.77E-02 chr11:46142520-46142695 - TSS,S


PHF21A PHD finger protein 21A

chr11_-_85522024 0.77 4.48 9.88E-02 chr11:85522024-85522224 - TSS,S



chr11_-_85779972 0.59 8.60 9.14E-03 chr11:85779972-85780172 - TSS,S


PICALMphosphatidylinositol binding clathrin assembly protein

chr12_+_1018011 -1.92 1.59 8.60E-02 chr12:1018011-1018098 + CDS_or_noncoding_last_exon,S ENST00000540885.1 WNK1 WNK lysine deficient

protein kinase 1

chr12_+_104895602 2.37 0.19 5.90E-02 chr12:104895602-104895791 + CDS_or_noncoding_first_intron,S

ENST00000549260.1/ENST00000303694.5 CHST11

carbohydrate (chondroitin 4) sulfotransferase 11

chr12_+_105064229 1.19 2.85 9.16E-02 chr12:105064229-105064419 + CDS_or_noncoding_last_intron,S

ENST00000549260.1/ENST00000303694.5/ENST00000549016.1

CHST11carbohydrate (chondroitin 4) sulfotransferase 11


LRMP lymphoid-restricted membrane protein


ENST00000548553.1/ENST00000332160.4 METTL7A methyltransferase like

7Achr12_+_5632862 -1.19 1.41 8.73E-02 chr12:5632862-5632873 + intergenic intergenic NA NA



chr12_-_11324071 0.75 5.00 5.08E-02 chr12:11324071-11324256 - TSS,S


PRR4 proline rich 4 (lacrimal)

chr12_-_26986078 0.67 5.11 3.66E-02 chr12:26986078-26986222 - TSS,S ENST00000381340.3 ITPR2inositol 1,4,5-trisphosphate receptor, type 2

chr12_-_57039668 -0.39 8.08 1.77E-02 chr12:57039668-57039866 - TSS,S ENST00000262030.3/ENST00000552919.1/ ATP5B ATP synthase, H+

transporting,

2323

Persson et al.


mitochondrial F1 complex, beta polypeptide


chr12_-_90102557 0.61 4.95 4.07E-02 chr12:90102557-90102575 - TSSregion500,S ENST00000428670.3 ATP2B1ATPase, Ca++ transporting, plasma membrane 1

chr13_+_23969117 -0.99 4.21 8.11E-03 chr13:23969117-23969132 +CDS_or_noncoding_first_intron,AS

ENST00000382292.3 SACSspastic ataxia of Charlevoix-Saguenay (sacsin)



FRY furry homolog (Drosophila)

chr13_+_42031563 -0.59 5.64 4.54E-02 chr13:42031563-42031753 + TSS,S ENST00000379359.3 C13ORF15 NA

chr13_-_46728936 -1.41 -0.03 9.88E-02 chr13:46728936-46729040 -CDS_or_noncoding_inner_exon,S

ENST00000323076.2/ENST00000398576.1/ENST00000416500.1

LCP1 lymphocyte cytosolic protein 1 (L-plastin)

chr13_-_46948851 0.94 4.72 6.21E-02 chr13:46948851-46949006 - 5UTR_first_intron,S

ENST00000378787.3/ENST00000534925.1/ENST00000417405.1

KIAA0226L KIAA0226-like

chr14_+_64228282 0.99 4.50 2.48E-02 chr14:64228282-64228403 + TSSregion500,S ENST00000554348.1 RP11-804M7.2



SRSF5 serine/arginine-rich splicing factor 5

chr14_+_71374383 0.59 5.77 9.30E-02 chr14:71374383-71374451 + TSS,S ENST00000554292.1 PCNX pecanex homolog (Drosophila)

chr14_+_71787776 0.81 4.90 8.69E-03 chr14:71787776-71787875 + TSSregion500,S ENST00000557151.1 SIPA1L1signal-induced proliferation-associated 1 like 1

chr14_-_107259747 -1.17 4.67 9.55E-02 chr14:107259747-107259848 - TSSregion500,S ENST00000450948.1 IGHV5-78immunoglobulin heavy variable 5-78 (pseudogene)

chr14_-_23771335 -1.80 -0.01 3.25E-02 chr14:23771335-23771340 - 5UTR_inner_intron,AS ENST00000553824.1 BCL2L2 BCL2-like 2

chr14_-_92852982 1.27 0.91 5.96E-02 chr14:92852982-92853172 - 5UTR_inner_intron,AS ENST00000318079.5 SLC24A4

solute carrier family 24 (sodium/potassium/calcium exchanger), member 4

chr14_-_94856827 0.90 4.34 5.49E-02 chr14:94856827-94856836 - TSSregion500,SENST00000440909.1/ENST00000448921.1/ENST00000437397.1/

SERPINA1serpin peptidase inhibitor, clade A (alpha-1 antiproteinase,

2424

Persson et al.

ENST00000355814.4/ENST00000393088.4/ENST00000404814.4/ENST00000449399.3/ENST00000557492.1/ENST00000556955.1/ENST00000553327.1/ENST00000557118.1/ENST00000555289.1/ENST00000557361.1/ENST00000557093.1

antitrypsin), member 1

chr14_-_99737975 -0.67 3.04 8.64E-02 chr14:99737975-99738161 - TSSregion500,SENST00000357195.3/ENST00000345514.2/ENST00000443726.2

BCL11B B-cell CLL/lymphoma 11B (zinc finger protein)


chr15_+_50646398 -0.90 1.47 7.39E-02 chr15:50646398-50646470 + 5UTR_first_intron,AS

ENST00000380877.3/ENST00000220429.8/ENST00000543881.1/ENST00000429662.2/ENST00000396464.3/ENST00000359031.4/ENST00000560825.1/ENST00000558970.1

GABPB1GA binding protein transcription factor, beta subunit 1

chr15_+_55611346 0.98 1.97 7.34E-02 chr15:55611346-55611380 + TSSregion500,S ENST00000164305.4/ENST00000539642.1 PIGB

phosphatidylinositol glycan anchor biosynthesis, class B

chr15_+_78462578 -1.01 2.11 3.25E-02 chr15:78462578-78462718 + CDS_or_noncoding_last_exon,S ENST00000558535.1 IDH3A

isocitrate dehydrogenase 3 (NAD+) alpha

chr15_+_86087291 0.78 5.07 7.46E-02 chr15:86087291-86087325 + 5UTR_inner_intron,S ENST00000426424.2 AKAP13 A kinase (PRKA)

anchor protein 13

chr15_+_86266304 1.40 0.15 9.10E-02 chr15:86266304-86266465 +CDS_or_noncoding_inner_exon,S


AKAP13 A kinase (PRKA) anchor protein 13

chr15_+_94774580 0.99 3.05 2.48E-02 chr15:94774580-94774633 + TSSregion500,SENST00000543482.1/ENST00000456504.1/ENST00000556363.1

MCTP2 multiple C2 domains, transmembrane 2

chr15_+_94774756 0.51 6.38 8.68E-02 chr15:94774756-94774839 + TSS,S ENST00000543482.1/ENST00000556363.1 MCTP2 multiple C2 domains,

transmembrane 2

2525

Persson et al.

chr15_+_98503887 -0.71 4.14 4.68E-02 chr15:98503887-98504027 + TSS,S ENST00000268042.6 ARRDC4 arrestin domain containing 4


ENST00000268035.6/ENST00000558762.1/ENST00000559925.1

IGF1R insulin-like growth factor 1 receptor

chr15_-_34729924 0.94 4.66 4.65E-02 chr15:34729924-34730078 - 5UTR_inner_intron,S ENST00000543376.1 GOLGA8A golgin A8 family,

member A

chr15_-_61133380 1.09 2.14 1.84E-02 chr15:61133380-61133539 - CDS_or_noncoding_first_intron,S


RORA RAR-related orphan receptor A

chr16_+_2014895 -0.84 3.92 2.41E-02 chr16:2014895-2015093 + TSS,S ENST00000531523.1 SNHG9small nucleolar RNA host gene 9 (non-protein coding)

chr16_+_23890834 2.80 -0.56 4.92E-02 chr16:23890834-23890850 + CDS_or_noncoding_first_intron,S ENST00000498739.1 PRKCB protein kinase C, beta

chr16_+_23914220 2.13 0.42 2.48E-02 chr16:23914220-23914337 + CDS_or_noncoding_first_intron,S ENST00000498739.1 PRKCB protein kinase C, beta

chr16_+_29817622 -0.46 4.88 5.09E-02 chr16:29817622-29817713 + TSSregion500,S ENST00000219782.5/ENST00000322945.5 MAZ

MYC-associated zinc finger protein (purine-binding transcription factor)

chr16_+_31539532 -0.95 2.80 7.03E-02 chr16:31539532-31539539 +CDS_or_noncoding_inner_exon,S

ENST00000302312.4 AHSP alpha hemoglobin stabilizing protein

chr16_+_67876183 -0.44 4.82 5.41E-02 chr16:67876183-67876240 + TSS,S ENST00000303596.1 THAP11 THAP domain containing 11

chr16_+_69599832 0.59 5.57 8.30E-02 chr16:69599832-69599959 + TSS,S ENST00000354436.2 NFAT5nuclear factor of activated T-cells 5, tonicity-responsive


ENST00000539778.1/ENST00000537098.1 CMIP c-Maf inducing protein

chr16_+_85833176 -0.41 8.25 1.77E-02 chr16:85833176-85833356 + TSS,S ENST00000253452.2 COX4I1 cytochrome c oxidase subunit IV isoform 1

chr16_+_89627047 -0.44 9.36 5.41E-02 chr16:89627047-89627147 + TSS,S


RPL13 ribosomal protein L13


chr16_-_2827235 -0.55 5.93 2.78E-02 chr16:2827235-2827321 - TSS,S ENST00000409906.3/ENST00000262306.7 TCEB2

transcription elongation factor B (SIII), polypeptide 2 (18kDa, elongin B)

2626

Persson et al.

chr16_-_68056996 -0.76 3.59 1.53E-02 chr16:68056996-68057147 - 5UTR_first_exon,S ENST00000332395.5 DDX28

DEAD (Asp-Glu-Ala-Asp) box polypeptide 28

chr17_+_26794788 -0.63 8.46 5.99E-02 chr17:26794788-26794814 + TSS,S ENST00000393464.3 RPS7P1 ribosomal protein S7 pseudogene 1


chr17_+_38482580 0.76 3.98 6.10E-02 chr17:38482580-38482732 + 5UTR_first_intron,S

ENST00000254066.4/ENST00000425707.2/ENST00000394089.1

RARA retinoic acid receptor, alpha

chr17_+_41150408 -0.41 6.26 9.10E-02 chr17:41150408-41150495 + TSS,S ENST00000253788.4 RPL27 ribosomal protein L27

chr17_+_47293900 1.90 -0.18 7.61E-02 chr17:47293900-47294035 +CDS_or_noncoding_inner_exon,S

ENST00000225941.1/ENST00000419580.2 ABI3 ABI family, member 3



CD300A CD300a molecule

chr17_+_7789501 1.61 0.10 7.33E-02 chr17:7789501-7789570 + CDS_or_noncoding_first_intron,S ENST00000380358.4 CHD3 chromodomain helicase

DNA binding protein 3chr17_+_8316388 0.61 7.28 2.28E-02 chr17:8316388-8316578 + intergenic intergenic NA NA

chr17_-_40491329 1.34 1.09 5.58E-02 chr17:40491329-40491428 -CDS_or_noncoding_inner_exon,S

ENST00000264657.4/ENST00000389272.3/ENST00000404395.3

STAT3

signal transducer and activator of transcription 3 (acute-phase response factor)

chr17_-_44249394 1.23 1.57 8.03E-02 chr17:44249394-44249584 - TSSregion500,S ENST00000432791.1 KIAA1267 NA

chr17_-_48943666 -0.64 5.76 8.68E-02 chr17:48943666-48943746 - TSS,S ENST00000499247.2/ENST00000509385.1 TOB1 transducer of ERBB2, 1

chr17_-_5342333 -0.35 6.52 8.73E-02 chr17:5342333-5342501 - TSS,S ENST00000225698.3 C1QBP

complement component 1, q subcomponent binding protein


chr17_-_7745491 -1.54 0.12 5.47E-02 chr17:7745491-7745551 - 5UTR_first_intron,AS

ENST00000448097.1/ENST00000254846.4 KDM6B lysine (K)-specific

demethylase 6B

chr18_+_2655680 0.48 8.35 9.10E-02 chr18:2655680-2655741 + TSSregion500,S ENST00000261598.8/ENST00000320876.5 SMCHD1

structural maintenance of chromosomes flexible hinge domain containing 1


ENST00000261598.8/ENST00000320876.5 SMCHD1


chr18_+_32650149 2.26 -0.70 8.03E-02 chr18:32650149-32650248 + 5UTR_inner_exon,S ENST00000413393.1 MAPRE2

microtubule-associated protein, RP/EB family, member 2

chr18_+_3594053 0.59 3.75 6.43E-02 chr18:3594053-3594120 + TSS,S ENST00000317114.1 AP002478.1 NAchr19_+_12848278 -0.49 5.64 2.48E-02 chr19:12848278-12848408 + TSS,S ENST00000357332.3 ASNA1 arsA arsenite

2727

Persson et al.

transporter, ATP-binding, homolog 1 (bacterial)


ENST00000397661.1/ENST00000360105.3/ENST00000358552.3

NFIXnuclear factor I/X (CCAAT-binding transcription factor)

chr19_+_16254473 0.53 7.12 2.48E-02 chr19:16254473-16254655 + TSS,S ENST00000535834.1 HSH2D hematopoietic SH2 domain containing


ENST00000253680.6/ENST00000397372.4/ENST00000535834.1

HSH2D hematopoietic SH2 domain containing

chr19_+_1905326 -0.43 4.75 6.98E-02 chr19:1905326-1905429 + TSS,S


SCAMP4 secretory carrier membrane protein 4

chr19_+_3094285 -1.10 1.42 4.93E-02 chr19:3094285-3094411 + TSS,S ENST00000078429.3 GNA11

guanine nucleotide binding protein (G protein), alpha 11 (Gq class)

chr19_+_41812977 -1.32 1.38 8.68E-02 chr19:41812977-41813005 + 3UTR_last_exon,S

ENST00000352456.2/ENST00000392006.2/ENST00000378215.3

HNRNPUL1heterogeneous nuclear ribonucleoprotein U-like 1

chr19_+_42300425 0.47 7.75 8.68E-02 chr19:42300425-42300581 + TSS,S


CEACAM3carcinoembryonic antigen-related cell adhesion molecule 3

chr19_+_45542746 1.06 2.70 4.65E-02 chr19:45542746-45542832 + TSS,S ENST00000544944.1 CLASRPCLK4-associating serine/arginine rich protein

chr19_+_45971244 -1.49 5.70 4.52E-03 chr19:45971244-45971289 + TSS,S



chr19_+_49999627 -0.43 9.54 4.88E-02 chr19:49999627-49999702 + TSS,S ENST00000270625.1 RPS11 ribosomal protein S11chr19_-_12904278 -1.44 -0.23 6.76E-02 chr19:12904278-12904290 - intergenic intergenic NA NA

chr19_-_2041076 -1.38 1.28 8.64E-02 chr19:2041076-2041204 -CDS_or_noncoding_inner_exon,S


MKNK2MAP kinase interacting serine/threonine kinase 2

chr19_-_29704012 -0.47 6.14 3.39E-02 chr19:29704012-29704147 - TSS,S ENST00000304863.3 UQCRFS1ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1

2828

Persson et al.


ENST00000316763.2/ENST00000377011.1/ENST00000424804.2

VRK3 vaccinia related kinase 3

chr1_+_113711575 -0.76 3.36 5.41E-02 chr1:113711575-113711613 + TSSregion500,S ENST00000457967.1 RP11-389O22.4

chr1_+_153963219 -0.48 10.68 9.88E-02 chr1:153963219-153963285 + TSS,S


RPS27 ribosomal protein S27

chr1_+_153968064 -0.43 6.59 9.08E-02 chr1:153968064-153968083 + TSSregion500,S ENST00000431295.1 RP11-422P24.9

chr1_+_167737047 1.72 -0.16 9.10E-02 chr1:167737047-167737075 + CDS_or_noncoding_first_intron,S

ENST00000367853.3/ENST00000474729.1 MPZL1 myelin protein zero-like

1

chr1_+_174188243 1.18 2.51 6.46E-02 chr1:174188243-174188403 + TSS,S ENST00000367692.3 RABGAP1L RAB GTPase activating protein 1-like

chr1_+_174389237 2.34 0.05 2.48E-02 chr1:174389237-174389359 +CDS_or_noncoding_inner_intron,S

ENST00000251507.4/ENST00000367692.3 RABGAP1L RAB GTPase activating

protein 1-like


CDC73

cell division cycle 73, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)


ENST00000418674.1/ENST00000427110.2/ENST00000391970.3

PTPRCprotein tyrosine phosphatase, receptor type, C


ENST00000391959.3/ENST00000367270.4 PPP1R12B protein phosphatase 1,

regulatory subunit 12Bchr1_+_228675040 -0.56 6.55 3.25E-02 chr1:228675040-228675163 + TSSregion500,S ENST00000305943.7 RNF187 ring finger protein 187

chr1_+_236030422 -1.16 1.08 8.03E-02 chr1:236030422-236030615 + TSSregion500,AS

ENST00000389794.3/ENST00000389793.2/ENST00000468626.1

LYST lysosomal trafficking regulator


chr1_+_40854389 -0.96 2.51 2.48E-02 chr1:40854389-40854414 + CDS_or_noncoding_first_intron,S

ENST00000372718.3/ENST00000372708.1 SMAP2 small ArfGAP2

chr1_+_47845938 1.93 -0.02 4.07E-02 chr1:47845938-47845953 + intergenic intergenic NA NA

chr1_+_59762630 0.71 3.05 8.09E-02 chr1:59762630-59762796 + TSS,S


FGGYFGGY carbohydrate kinase domain containing

2929

Persson et al.

chr1_+_97187205 0.70 4.72 1.50E-02 chr1:97187205-97187402 + TSS,S


PTBP2 polypyrimidine tract binding protein 2

chr1_-_115053701 0.49 6.18 4.54E-02 chr1:115053701-115053873 - TSS,S ENST00000358465.2/ENST00000369543.2 TRIM33 tripartite motif

containing 33

chr1_-_155112964 -0.71 3.14 8.86E-02 chr1:155112964-155113043 - TSS,S ENST00000368400.4 DPM3dolichyl-phosphate mannosyltransferase polypeptide 3


ENST00000362089.5/ENST00000392122.3/ENST00000483825.1


chr1_-_173446127 0.80 2.65 6.41E-02 chr1:173446127-173446327 - TSS,S ENST00000421168.2 AL645568.1 NA

chr1_-_176176231 0.61 6.26 1.02E-02 chr1:176176231-176176427 - TSS,S ENST00000367665.3/ENST00000436424.1 RFWD2

ring finger and WD repeat domain 2, E3 ubiquitin protein ligase

chr1_-_182763979 0.96 1.97 5.58E-02 chr1:182763979-182764106 - 5UTR_first_intron,AS

ENST00000367551.3/ENST00000445965.2/ENST00000367554.3

NPL

N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)

chr1_-_234745882 -0.56 5.83 4.06E-02 chr1:234745882-234745972 - upstream1000,S ENST00000366609.3/ENST00000366610.3 IRF2BP2

interferon regulatory factor 2 binding protein 2

chr1_-_235292089 -0.53 6.59 1.68E-02 chr1:235292089-235292278 - TSS,S ENST00000366607.4 TOMM20

translocase of outer mitochondrial membrane 20 homolog (yeast)

chr1_-_27816117 2.09 -0.59 5.49E-02 chr1:27816117-27816310 - 5UTR_first_intron,S

ENST00000430629.2/ENST00000536657.1 WASF2 WAS protein family,

member 2



PTP4A2protein tyrosine phosphatase type IVA, member 2

chr1_-_98386462 0.68 8.05 1.62E-03 chr1:98386462-98386637 - TSS,S


DPYD dihydropyrimidine dehydrogenase




3030

Persson et al.



C20ORF43 NA

chr20_+_60962089 -0.51 9.45 9.65E-02 chr20:60962089-60962193 + TSS,S





PLCB1phospholipase C, beta 1 (phosphoinositide-specific)

chr20_-_1350022 -2.06 -0.35 4.53E-02 chr20:1350022-1350071 - 3UTR_last_exon,S ENST00000400137.4 FKBP1A FK506 binding protein

1A, 12kDa


RALGAPA2Ral GTPase activating protein, alpha subunit 2 (catalytic)

chr20_-_46376071 1.28 0.47 9.24E-02 chr20:46376071-46376265 - CDS_or_noncoding_first_intron,S ENST00000474450.1 SULF2 sulfatase 2


ENST00000547341.1/ENST00000547595.1/ENST00000548700.1

KCNJ15potassium inwardly-rectifying channel, subfamily J, member 15

chr22_+_19414171 -1.11 2.77 1.48E-02 chr22:19414171-19414187 + 5UTR_first_intron,AS ENST00000541063.1 HIRA

HIR histone cell cycle regulation defective homolog A (S. cerevisiae)

chr22_+_30353172 1.78 0.21 9.88E-02 chr22:30353172-30353266 + 5UTR_first_intron,S ENST00000445401.1 MTMR3 myotubularin related

protein 3

chr22_+_44584298 -0.87 3.29 4.28E-02 chr22:44584298-44584310 + CDS_or_noncoding_first_exon,S ENST00000468564.1 PARVG parvin, gamma

chr22_-_31682123 -1.94 0.07 3.74E-02 chr22:31682123-31682203 - CDS_or_noncoding_last_intron,S


PIK3IP1phosphoinositide-3-kinase interacting protein 1

chr22_-_31688334 -0.42 7.36 8.93E-02 chr22:31688334-31688531 - TSS,S




ENST00000396821.3/ENST00000444597.1/ENST00000381633.3

DDX17 DEAD (Asp-Glu-Ala-Asp) box helicase 17

3131

Persson et al.

chr22_-_39715561 -0.47 7.60 5.41E-02 chr22:39715561-39715684 - TSS,S



chr2_+_102353931 1.87 1.02 3.25E-02 chr2:102353931-102353966 + CDS_or_noncoding_first_intron,S ENST00000417294.1 MAP4K4

mitogen-activated protein kinase kinase kinase kinase 4

chr2_+_103034997 0.81 5.35 4.93E-02 chr2:103034997-103035149 + TSS,S ENST00000264260.2 IL18RAP interleukin 18 receptor accessory protein

chr2_+_130939729 -0.58 5.85 6.21E-02 chr2:130939729-130939893 + TSS,S ENST00000409255.1/ENST00000455239.1 MZT2B mitotic spindle

organizing protein 2Bchr2_+_136890097 -1.62 1.12 4.67E-02 chr2:136890097-136890205 + intergenic intergenic NA NA

chr2_+_139259327 0.51 4.65 7.16E-02 chr2:139259327-139259395 + TSS,S ENST00000280098.4 SPOPL speckle-type POZ protein-like


chr2_+_143886870 0.54 8.23 4.57E-02 chr2:143886870-143887014 + TSS,S ENST00000295095.6/ENST00000552641.1 ARHGAP15 Rho GTPase activating

protein 15


ENST00000295095.6/ENST00000552641.1/ENST00000469117.1

ARHGAP15 Rho GTPase activating protein 15


ENST00000295095.6/ENST00000552641.1/ENST00000469117.1



ENST00000295095.6/ENST00000552641.1/ENST00000469117.1


chr2_+_192543694 0.95 3.15 3.93E-02 chr2:192543694-192543736 + TSS,S ENST00000435931.1 OBFC2A NAchr2_+_199716837 -0.76 4.96 5.66E-02 chr2:199716837-199716853 + intergenic intergenic NA NA

chr2_+_20646808 0.51 5.88 9.83E-02 chr2:20646808-20646871 + TSS,S ENST00000272233.4 RHOB ras homolog family member B

chr2_+_217363518 -0.55 10.32 5.99E-02 chr2:217363518-217363623 + TSS,S



chr2_+_223725685 0.45 5.58 9.10E-02 chr2:223725685-223725816 + TSS,S ENST00000535678.1 ACSL3acyl-CoA synthetase long-chain family member 3

3232

Persson et al.

chr2_+_231110481 2.78 -0.95 6.76E-02 chr2:231110481-231110613 +CDS_or_noncoding_inner_exon,S


SP140 SP140 nuclear body protein

chr2_+_237897693 -3.13 1.41 5.41E-02 chr2:237897693-237897808 + intergenic intergenic NA NA


ENST00000338315.4/ENST00000406420.3/ENST00000495018.1

MFSD2Bmajor facilitator superfamily domain containing 2B

chr2_+_43453937 -0.95 1.58 9.10E-02 chr2:43453937-43454014 + TSSregion500,AS ENST00000282388.3 ZFP36L2 zinc finger protein 36,

C3H type-like 2

chr2_+_68478597 1.09 2.08 8.68E-02 chr2:68478597-68478795 + TSSregion500,AS ENST00000409377.1 PPP3R1

protein phosphatase 3, regulatory subunit B, alpha




chr2_+_69043406 1.28 1.06 9.55E-02 chr2:69043406-69043496 + TSSregion500,S ENST00000479844.1 ARHGAP25 Rho GTPase activating protein 25


chr2_+_98329970 2.42 -0.57 5.57E-02 chr2:98329970-98329976 + TSSregion500,S ENST00000264972.5/ENST00000483781.1 ZAP70


chr2_-_136893762 -1.10 2.46 9.08E-02 chr2:136893762-136893918 - intergenic intergenic NA NA

chr2_-_160472897 0.59 5.90 5.90E-02 chr2:160472897-160473078 - TSS,S


BAZ2Bbromodomain adjacent to zinc finger domain, 2B


GALNT3

UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)

chr2_-_198175391 0.46 7.03 9.65E-02 chr2:198175391-198175567 - TSS,S


ANKRD44 ankyrin repeat domain 44

3333

Persson et al.

chr2_-_40679155 0.75 4.53 3.25E-02 chr2:40679155-40679298 - TSS,S ENST00000406785.1 SLC8A1solute carrier family 8 (sodium/calcium exchanger), member 1

chr2_-_8464701 1.68 2.00 8.68E-02 chr2:8464701-8464864 - TSS,S ENST00000430192.1 LINC00299 long intergenic non-protein coding RNA 299


EPHB1 EPH receptor B1

chr3_+_134514064 1.53 1.61 9.92E-02 chr3:134514064-134514224 + TSS,S ENST00000482618.1/ENST00000398015.3 EPHB1 EPH receptor B1

chr3_+_134920041 -0.96 2.55 5.22E-02 chr3:134920041-134920045 +CDS_or_noncoding_inner_intron,S

ENST00000398015.3/ENST00000493838.1 EPHB1 EPH receptor B1

chr3_+_14076729 -0.90 3.41 5.90E-02 chr3:14076729-14076747 + 5UTR_first_intron,S


TPRXL tetra-peptide repeat homeobox-like



MBNL1 muscleblind-like splicing regulator 1


FNDC3B fibronectin type III domain containing 3B

chr3_+_174094991 -0.42 8.22 7.42E-02 chr3:174094991-174095018 + TSSregion500,S ENST00000435269.1 RP11-393N4.2



LPPLIM domain containing preferred translocation partner in lipoma

chr3_+_197677027 -0.45 7.77 2.72E-02 chr3:197677027-197677103 + TSS,S




ENST00000431569.1 FAM157Afamily with sequence similarity 157, member A

3434

Persson et al.


ENST00000396671.2/ENST00000356447.4/ENST00000416420.1/ENST00000413780.1/ENST00000415021.1/ENST00000447875.1/ENST00000453729.2/ENST00000431815.1/ENST00000447414.1/ENST00000416811.2/ENST00000428492.1/ENST00000418247.1

THRB thyroid hormone receptor, beta

chr3_+_32433154 -0.50 3.91 8.30E-02 chr3:32433154-32433197 + TSS,S ENST00000334983.5/ENST00000349718.4 CMTM7

CKLF-like MARVEL transmembrane domain containing 7

chr3_+_39448179 -0.44 8.21 7.07E-02 chr3:39448179-39448255 + TSS,S


RPSA ribosomal protein SA


chr3_+_42641962 1.62 -0.12 7.91E-02 chr3:42641962-42641993 + TSSregion500,S


NKTR natural killer-tumor recognition sequence

chr3_+_51428637 -0.61 4.38 3.74E-02 chr3:51428637-51428755 + TSS,S ENST00000323686.4 RBM15B RNA binding motif protein 15B

chr3_+_63850179 1.11 1.14 6.76E-02 chr3:63850179-63850271 + TSS,S


ATXN7 ataxin 7

chr3_+_72128314 -1.48 -0.21 7.26E-02 chr3:72128314-72128352 +CDS_or_noncoding_first_intron,AS

ENST00000470712.1 RP11-398A8.3

chr3_-_119813135 0.50 6.17 6.10E-02 chr3:119813135-119813335 - TSS,S ENST00000264235.8 GSK3B glycogen synthase kinase 3 beta

chr3_-_13009094 -0.93 4.54 7.92E-02 chr3:13009094-13009256 - TSS,S ENST00000273221.4 IQSEC1 IQ motif and Sec7 domain 1

3535

Persson et al.


SLC9A9

solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9


chr3_-_169482780 -0.61 3.75 9.65E-02 chr3:169482780-169482971 - TSS,S ENST00000363312.1 TERC telomerase RNA component

chr3_-_42003514 0.70 3.72 5.90E-02 chr3:42003514-42003686 - TSS,S


ULK4 unc-51-like kinase 4 (C. elegans)

chr3_-_47125367 0.90 2.88 4.65E-02 chr3:47125367-47125509 - TSS,S ENST00000492397.1 SETD2 SET domain containing 2

chr4_+_113218425 0.61 6.87 1.77E-02 chr4:113218425-113218601 + TSS,S

ENST00000458497.1/ENST00000309610.6/ENST00000177648.9/ENST00000504176.2/ENST00000509722.1/ENST00000505127.1/ENST00000515330.1/ENST00000515106.1/ENST00000505176.1/ENST00000502366.1/ENST00000509688.1/ENST00000426472.2/ENST00000504488.1

ALPK1 alpha-kinase 1

chr4_+_119199844 -0.91 6.12 8.69E-02 chr4:119199844-119199924 + TSS,S ENST00000500560.1 SNHG8 NAchr4_+_123012762 -1.93 -0.58 7.69E-02 chr4:123012762-123012763 + intergenic intergenic NA NA


FAM160A1family with sequence similarity 160, member A1

chr4_+_37912620 2.28 0.20 1.48E-02 chr4:37912620-37912799 + 5UTR_first_intron,S ENST00000454732.2 TBC1D1

TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1



PRDM5 PR domain containing 5


ELF2E74-like factor 2 (ets domain transcription factor)

3636

Persson et al.

chr4_-_38858350 0.68 5.25 4.57E-02 chr4:38858350-38858530 - TSS,S


TLR1 toll-like receptor 1

chr4_-_48116463 1.38 3.62 3.66E-02 chr4:48116463-48116595 - TSS,S ENST00000506073.1 TXK TXK tyrosine kinase

chr4_-_48908707 -0.53 4.29 5.49E-02 chr4:48908707-48908834 - TSS,S


OCIAD2 OCIA domain containing 2



WDFY3 WD repeat and FYVE domain containing 3

chr5_+_100239472 1.06 2.32 7.35E-02 chr5:100239472-100239541 + upstream1000,AS

ENST00000231461.4/ENST00000451528.2/ENST00000523381.1

ST8SIA4ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 4

chr5_+_109257711 -1.89 -0.49 3.25E-02 chr5:109257711-109257856 + intergenic intergenic NA NAchr5_+_115898212 -0.80 6.25 1.28E-03 chr5:115898212-115898282 + TSS,S ENST00000478778.1 CTB-118N6.1


ENST00000411801.2/ENST00000535792.1 EGR1 early growth response

1

chr5_+_139487359 0.93 2.59 5.41E-02 chr5:139487359-139487434 + TSS,S ENST00000505703.1 PURA purine-rich element binding protein A


protein 26


ENST00000378004.3/ENST00000274498.4/ENST00000378013.2





chr5_+_145838658 1.19 1.56 9.30E-02 chr5:145838658-145838847 + TSS,S ENST00000513298.1 TCERG1 transcription elongation regulator 1



TNIP1 TNFAIP3 interacting protein 1

3737

Persson et al.

chr5_+_177027101 -0.86 3.75 3.09E-02 chr5:177027101-177027237 + TSS,S



chr5_+_32221993 -0.58 4.36 5.58E-02 chr5:32221993-32222026 + TSSregion500,S ENST00000477507.1 CTD-2186M15.1


ENST00000381286.3/ENST00000523039.1 IL6ST

interleukin 6 signal transducer (gp130, oncostatin M receptor)

chr5_+_60628054 0.73 5.49 7.28E-03 chr5:60628054-60628105 + TSS,S ENST00000252744.5 ZSWIM6 zinc finger, SWIM-type containing 6

chr5_+_76878154 -0.86 1.92 8.68E-02 chr5:76878154-76878177 + TSSregion500,S ENST00000493874.1 RP11-526L22.1



ZFYVE16 zinc finger, FYVE domain containing 16

chr5_+_79703805 0.60 5.06 1.48E-02 chr5:79703805-79703925 + TSS,S





VCAN versican

chr5_+_85913712 -0.51 8.21 8.90E-02 chr5:85913712-85913905 + TSS,S


COX7C cytochrome c oxidase subunit VIIc


ENST00000502934.1/ENST00000507217.1 RP11-348J24.2



CCNJL cyclin J-like

3838

Persson et al.

chr5_-_18746175 0.99 2.61 3.42E-02 chr5:18746175-18746329 - TSS,S ENST00000512978.1 CTD-2023M8.1

chr5_-_6378521 -0.47 4.67 9.13E-02 chr5:6378521-6378707 - TSS,S ENST00000255764.3/ENST00000504058.1 MED10 mediator complex

subunit 10

chr5_-_79946714 -2.52 2.21 8.68E-02 chr5:79946714-79946867 - 5UTR_first_intron,S ENST00000504396.1 DHFR dihydrofolate reductase


FAM172Afamily with sequence similarity 172, member A

chr5_-_94417257 0.52 6.55 2.48E-02 chr5:94417257-94417377 - TSS,S



chr6_+_108880957 -0.58 5.95 4.47E-02 chr6:108880957-108881031 + TSSregion500,S ENST00000343882.6 FOXO3 forkhead box O3chr6_+_13289737 -1.55 0.83 5.41E-02 chr6:13289737-13289823 + intergenic intergenic NA NA

chr6_+_138188328 -1.09 6.83 2.48E-02 chr6:138188328-138188507 + TSS,S ENST00000421450.1/ENST00000420009.1 TNFAIP3 tumor necrosis factor,

alpha-induced protein 3chr6_+_144606710 1.06 3.88 8.82E-04 chr6:144606710-144606829 + TSSregion500,S ENST00000433557.1 UTRN utrophinchr6_+_144665236 0.63 7.36 8.03E-02 chr6:144665236-144665413 + TSS,S ENST00000421035.1 UTRN utrophin


chr6_+_21593931 -0.74 4.20 4.28E-02 chr6:21593931-21594047 + TSS,S ENST00000244745.1 SOX4 SRY (sex determining region Y)-box 4

chr6_+_21597506 -1.71 -0.12 8.99E-02 chr6:21597506-21597656 + 3UTR_first_exon,S ENST00000244745.1 SOX4 SRY (sex determining

region Y)-box 4chr6_+_26204717 -0.47 9.24 6.10E-02 chr6:26204717-26204861 + TSS,S ENST00000360441.4 HIST1H4E histone cluster 1, H4echr6_+_26240544 -0.59 6.39 6.80E-02 chr6:26240544-26240740 + TSS,S ENST00000377745.2 HIST1H4F histone cluster 1, H4f

chr6_+_29910526 2.18 1.73 8.60E-02 chr6:29910526-29910551 + 5UTR_inner_exon,S ENST00000536480.1 HLA-A

HLA class I histocompatibility antigen, A-1 alpha chain variant

chr6_+_31601762 -1.14 1.72 2.48E-02 chr6:31601762-31601777 + TSSregion500,S ENST00000460302.1/ENST00000484787.1 PRRC2A proline-rich coiled-coil

2A

chr6_+_43603551 -0.54 3.45 8.73E-02 chr6:43603551-43603610 + TSS,S ENST00000372171.4/ENST00000508232.1 MAD2L1BP MAD2L1 binding

protein



SENP6 SUMO1/sentrin specific peptidase 6


ENST00000463016.1/ENST00000460913.1 CDK19 cyclin-dependent

kinase 19

chr6_-_116600964 -0.39 5.96 6.71E-02 chr6:116600964-116601122 - TSS,S ENST00000368608.3/ENST00000545830.1 TSPYL1 TSPY-like 1

3939

Persson et al.

chr6_-_133035018 1.08 5.34 8.73E-02 chr6:133035018-133035204 - TSS,S ENST00000367928.4 VNN1 vanin 1



VNN2 vanin 2

chr6_-_16761542 0.54 6.04 8.68E-02 chr6:16761542-16761737 - TSS,S


ATXN1Ataxin 1, isoform CRA_a; Uncharacterized protein

chr6_-_43197089 -0.55 3.47 8.64E-02 chr6:43197089-43197245 - TSS,SENST00000230431.6/ENST00000509253.1/ENST00000393987.2

C6ORF108 NA

chr6_-_84937306 0.80 2.45 6.76E-02 chr6:84937306-84937410 - TSS,S


KIAA1009 KIAA1009

chr7_+_131012587 0.47 6.71 3.66E-02 chr7:131012587-131012732 + TSS,S


MKLN1muskelin 1, intracellular mediator containing kelch motifs

chr7_+_139586200 1.32 1.80 3.25E-02 chr7:139586200-139586214 + CDS_or_noncoding_first_intron,S ENST00000462275.1 TBXAS1 thromboxane A

synthase 1 (platelet)



CREB5cAMP responsive element binding protein 5

4040

Persson et al.

chr7_+_37723315 0.74 5.36 1.48E-02 chr7:37723315-37723483 + TSS,S





IKZF1 IKAROS family zinc finger 1 (Ikaros)

chr7_+_77166493 0.66 5.23 4.09E-02 chr7:77166493-77166664 + TSS,S ENST00000248594.6 PTPN12protein tyrosine phosphatase, non-receptor type 12

chr7_+_90225935 1.23 2.98 6.36E-03 chr7:90225935-90226005 + TSSregion500,S ENST00000380050.3 CDK14 cyclin-dependent kinase 14

chr7_-_105905967 0.88 4.63 9.08E-02 chr7:105905967-105905969 -CDS_or_noncoding_inner_intron,S

ENST00000222553.3/ENST00000354289.4 NAMPT

nicotinamide phosphoribosyltransferase


DOCK4 dedicator of cytokinesis 4

chr7_-_130794642 0.88 2.93 5.58E-02 chr7:130794642-130794706 - TSSregion500,S ENST00000451786.1 AC058791.2

chr7_-_142247565 -0.61 4.23 7.69E-02 chr7:142247565-142247650 - TSS,S ENST00000390361.3 TRBV7-3 T cell receptor beta variable 7-3

chr7_-_142511011 -0.72 3.55 4.06E-02 chr7:142511011-142511184 - TSS,S ENST00000417977.2 TRBV30T cell receptor beta variable 30 (gene/pseudogene)

chr7_-_2883845 -0.80 4.67 2.48E-02 chr7:2883845-2884045 - TSS,S ENST00000275364.3 GNA12guanine nucleotide binding protein (G protein) alpha 12



VPS13B vacuolar protein sorting 13 homolog B (yeast)




4141

Persson et al.





PVT1 Pvt1 oncogene (non-protein coding)

chr8_+_142726317 -1.44 -0.22 7.71E-02 chr8:142726317-142726327 + intergenic intergenic NA NA

chr8_+_23424071 -0.87 3.86 5.90E-02 chr8:23424071-23424155 + TSSregion500,S ENST00000522164.1/ENST00000521637.1 SLC25A37


chr8_+_23430115 -1.88 -0.62 4.65E-02 chr8:23430115-23430150 + TSSregion500,S ENST00000399967.3 AC051642.1

chr8_+_25042178 0.51 6.75 9.10E-02 chr8:25042178-25042326 + TSS,S ENST00000410074.1/ENST00000481100.1 DOCK5 dedicator of cytokinesis

5chr8_+_7380136 -1.23 1.80 3.74E-02 chr8:7380136-7380152 + intergenic intergenic NA NAchr8_+_8777573 0.90 2.56 8.73E-02 chr8:8777573-8777660 + intergenic intergenic NA NA


PGCP NA

chr8_-_123683573 0.87 4.74 4.54E-02 chr8:123683573-123683766 - 5UTR_inner_intron,S ENST00000521608.1 RP11-973F15.1

chr8_-_133772746 0.54 7.42 3.59E-02 chr8:133772746-133772920 - TSS,S


TMEM71 transmembrane protein 71

chr8_-_71316022 0.75 2.76 5.99E-02 chr8:71316022-71316077 - TSS,S ENST00000452400.2 NCOA2 nuclear receptor coactivator 2



ENST00000435485.1 RP11-308N19.1

chr9_+_111389046 -0.64 6.30 1.48E-02 chr9:111389046-111389163 + TSS,S ENST00000306634.3 RP11-220D10.1

chr9_+_127420623 1.22 2.34 5.58E-02 chr9:127420623-127420808 + TSS,S ENST00000429139.1 MIR181A2HG MIR181A2 host gene (non-protein coding)

chr9_+_134510921 1.63 1.23 5.90E-02 chr9:134510921-134511065 + 5UTR_inner_intron,AS


RAPGEF1Rap guanine nucleotide exchange factor (GEF) 1

chr9_+_141107496 0.84 3.41 8.03E-02 chr9:141107496-141107541 + TSS,S ENST00000446912.1 FAM157B family with sequence

4242

Persson et al.

similarity 157, member B

chr9_+_33993703 -1.24 0.39 8.73E-02 chr9:33993703-33993710 + 5UTR_inner_intron,AS ENST00000379239.4 UBAP2 ubiquitin associated

protein 2


ENST00000539801.1/ENST00000381652.3/ENST00000544510.1

JAK2 Janus kinase 2

chr9_+_74204443 -0.55 8.21 8.30E-02 chr9:74204443-74204473 + TSSregion500,S ENST00000437667.1 RP11-563H8.2chr9_+_92142178 1.64 0.68 2.48E-02 chr9:92142178-92142376 + intergenic intergenic NA NA


ABCA1ATP-binding cassette, sub-family A (ABC1), member 1

chr9_-_127624192 -0.39 9.01 5.96E-02 chr9:127624192-127624274 - TSS,S



chr9_-_140100023 -0.51 3.86 9.65E-02 chr9:140100023-140100137 - TSS,S ENST00000343666.5/ENST00000537254.1 TMEM203 transmembrane protein

203

chr9_-_73028820 -0.85 3.58 6.10E-02 chr9:73028820-73028894 - 5UTR_first_exon,S ENST00000377126.2 KLF9 Kruppel-like factor 9

chr9_-_80646818 0.59 4.39 8.31E-02 chr9:80646818-80646920 - TSSregion500,S ENST00000286548.4 GNAQguanine nucleotide binding protein (G protein), q polypeptide

chrM_+_11718 -1.64 3.77 7.62E-02 chrM:11718-11724 + intergenic intergenic NA NAchrM_+_11848 -0.83 6.24 3.66E-02 chrM:11848-11913 + intergenic intergenic NA NAchrM_+_13003 -1.81 0.24 6.61E-02 chrM:13003-13004 + intergenic intergenic NA NAchrM_+_13053 -1.03 3.81 5.24E-02 chrM:13053-13056 + intergenic intergenic NA NAchrM_+_8635 -0.57 5.94 5.08E-02 chrM:8635-8670 + intergenic intergenic NA NAchrM_+_9303 -0.92 3.35 9.92E-02 chrM:9303-9314 + intergenic intergenic NA NA

chrX_+_17024264 0.61 5.77 8.95E-02 chrX:17024264-17024436 + 5UTR_inner_exon,S ENST00000380064.4 REPS2

RALBP1 associated Eps domain containing 2

chrX_+_70520082 -0.74 3.80 5.57E-02 chrX:70520082-70520265 + TSSregion500,S ENST00000536900.1 AL590762.1

chrX_+_71320933 0.55 7.12 8.75E-02 chrX:71320933-71321070 + CDS_or_noncoding_first_intron,S ENST00000540800.1 NHSL2 NHS-like 2

chrX_+_77166100 0.44 5.65 5.49E-02 chrX:77166100-77166283 + TSS,S


ATP7AATPase, Cu++ transporting, alpha polypeptide


4343

233

Persson et al.

Table E5. Differentially expressed tag clusters for SA vs CA.


chr10_+_105200035 -1.90 -0.45 2.25E-02 chr10:105200035-105200135 + CDS_or_noncoding_inner_exon,S ENST00000369797.3 PDCD11 programmed cell death

11

chr10_+_11207376 0.36 9.13 2.50E-02 chr10:11207376-11207492 + TSS,S ENST00000537122.1 CELF2 CUGBP, Elav-like family member 2



PDCD4programmed cell death 4 (neoplastic transformation inhibitor)

chr10_+_12391541 0.49 6.04 9.46E-02 chr10:12391541-12391739 + TSS,S ENST00000378845.1/ENST00000487696.1 CAMK1D


chr10_+_129845769 0.24 8.11 9.74E-02 chr10:129845769-129845961 + TSS,S


PTPREprotein tyrosine phosphatase, receptor type, E

chr10_+_134351254 0.38 5.53 9.43E-02 chr10:134351254-134351434 + TSS,S


INPP5A inositol polyphosphate-5-phosphatase, 40kDa

chr10_+_17271838 1.63 2.01 2.28E-02 chr10:17271838-17271880 + TSSregion500,S ENST00000469543.1 VIM vimentin

chr10_+_20105327 0.45 5.37 6.46E-02 chr10:20105327-20105379 + TSS,S ENST00000536022.1 PLXDC2 plexin domain containing 2




chr10_+_20105824 0.58 4.38 7.10E-02 chr10:20105824-20105907 + TSSregion500,S ENST00000536022.1 PLXDC2 plexin domain containing 2

chr10_+_20179628 1.31 0.31 6.30E-02 chr10:20179628-20179708 + 5UTR_first_intron,S ENST00000377238.1 PLXDC2 plexin domain containing

2

chr10_+_20290746 1.22 0.46 8.58E-02 chr10:20290746-20290917 + 5UTR_inner_exon,S ENST00000377238.1 PLXDC2 plexin domain containing

2chr10_+_26727248 0.42 7.65 2.82E-02 chr10:26727248-26727340 + TSS,S ENST00000490118.1 APBB1IP amyloid beta (A4)

precursor protein-

4444

234235

Persson et al.

binding, family B, member 1 interacting protein



APBB1IP

amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein


ENST00000445780.1/ENST00000376236.4/ENST00000490118.1

APBB1IP

amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein

chr10_+_31608115 0.45 5.24 9.00E-02 chr10:31608115-31608212 + TSS,S


ZEB1 zinc finger E-box binding homeobox 1

chr10_+_45869611 0.48 7.80 1.24E-02 chr10:45869611-45869730 + TSS,S ENST00000542434.1/ENST00000374391.2 ALOX5 arachidonate 5-

lipoxygenase


ENST00000542434.1/ENST00000374391.2 ALOX5 arachidonate 5-

lipoxygenase


ENST00000542434.1/ENST00000374391.2/ENST00000483623.1

ALOX5 arachidonate 5-lipoxygenase

chr10_+_51489182 0.83 2.29 9.99E-02 chr10:51489182-51489285 + CDS_or_noncoding_inner_intron,S ENST00000429265.2 TIMM23B

translocase of inner mitochondrial membrane 23 homolog B (yeast)

chr10_+_51581267 0.71 2.90 5.52E-02 chr10:51581267-51581327 + 5UTR_inner_exon,S ENST00000414907.2 NCOA4 nuclear receptor

coactivator 4


ENST00000452682.1/ENST00000438493.1/ENST00000430396.2/ENST00000330923.6/ENST00000374087.4/ENST00000414907.2/ENST00000344348.6/ENST00000374082.1/

NCOA4 nuclear receptor coactivator 4

4545

Persson et al.

ENST00000431200.1/ENST00000443446.1/ENST00000498586.1


PFKFB36-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3

chr10_+_69644740 2.38 -0.43 4.55E-02 chr10:69644740-69644833 + TSSregion500,SENST00000432464.1/ENST00000497639.1/ENST00000473922.1

SIRT1 sirtuin 1

chr10_+_70502121 1.19 -0.23 9.43E-02 chr10:70502121-70502272 + 5UTR_inner_exon,S

ENST00000536012.1/ENST00000540807.1 CCAR1 cell division cycle and

apoptosis regulator 1

chr10_+_70856830 0.86 3.69 9.78E-03 chr10:70856830-70856963 + CDS_or_noncoding_inner_exon,S ENST00000242465.3 SRGN serglycin

chr10_+_70863631 0.77 4.83 5.06E-02 chr10:70863631-70863772 + CDS_or_noncoding_last_exon,S






chr10_+_73949655 -1.16 -0.25 6.46E-02 chr10:73949655-73949668 + TSSregion500,S ENST00000416278.1 RP11-570G20.1

chr10_+_79793558 -0.55 11.46 8.75E-02 chr10:79793558-79793664 + TSS,S



chr10_+_89623109 0.85 1.21 7.80E-02 chr10:89623109-89623131 + TSSregion500,S ENST00000371953.3 PTEN phosphatase and tensin homolog

chr10_+_89624021 1.08 1.80 3.01E-02 chr10:89624021-89624152 + TSSregion500,S ENST00000462694.1/ENST00000487939.1 PTEN phosphatase and tensin

homolog

chr10_+_89636687 0.80 4.08 5.52E-02 chr10:89636687-89636701 + CDS_or_noncoding_first_intron,S ENST00000371953.3 PTEN phosphatase and tensin

homolog

4646

Persson et al.

chr10_+_93624834 -1.69 -0.09 2.54E-02 chr10:93624834-93624994 + 3UTR_last_exon,S ENST00000371627.4 TNKS2

tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase 2



ENTPD1ectonucleoside triphosphate diphosphohydrolase 1

chr10_+_97599434 1.51 -0.37 7.43E-02 chr10:97599434-97599565 + TSSregion500,S ENST00000461927.1 ENTPD1ectonucleoside triphosphate diphosphohydrolase 1

chr10_-_120514416 0.42 6.51 4.06E-02 chr10:120514416-120514574 - TSS,S ENST00000369156.1 C10ORF46 NA

chr10_-_125851860 0.46 6.86 3.65E-02 chr10:125851860-125851976 - TSS,S ENST00000346248.5/ENST00000546346.1 CHST15

carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15

chr10_-_125852195 0.89 2.14 1.79E-02 chr10:125852195-125852264 - TSSregion500,S ENST00000346248.5/ENST00000546346.1 CHST15

carbohydrate (N-acetylgalactosamine 4-sulfate 6-O) sulfotransferase 15

chr10_-_30024715 0.60 4.95 4.67E-03 chr10:30024715-30024904 - TSS,S ENST00000375400.3/ENST00000375398.2 SVIL supervillin

chr10_-_30025861 0.76 3.50 1.26E-02 chr10:30025861-30025981 - TSSregion500,S ENST00000465422.1 SVIL supervillinchr10_-_31288304 0.64 4.17 2.50E-02 chr10:31288304-31288498 - TSS,S ENST00000538351.1 ZNF438 zinc finger protein 438

chr10_-_60027618 0.59 5.29 1.24E-02 chr10:60027618-60027815 - TSS,S ENST00000373935.3 IPMK inositol polyphosphate multikinase



PSAP prosaposin

chr10_-_81930578 1.03 2.32 3.56E-02 chr10:81930578-81930669 - 5UTR_inner_exon,S

ENST00000424188.1/ENST00000537102.1/ENST00000372219.3

ANXA11 annexin A11

chr10_-_89822167 1.28 -0.15 5.01E-02 chr10:89822167-89822320 - intergenic intergenic NA NAchr10_-_89864066 0.59 6.31 1.90E-02 chr10:89864066-89864238 - intergenic intergenic NA NA


ENST00000412050.2/ENST00000265997.4 CPEB3

cytoplasmic polyadenylation element binding protein 3

4747

Persson et al.



AMPD3adenosine monophosphate deaminase 3

chr11_+_108199813 -1.77 -0.32 4.15E-02 chr11:108199813-108199973 + CDS_or_noncoding_inner_exon,S


ATM ataxia telangiectasia mutated

chr11_+_118224886 -1.24 1.22 5.75E-02 chr11:118224886-118224969 + 3UTR_last_exon,S ENST00000532917.1 CD3G CD3g molecule, gamma (CD3-TCR complex)

chr11_+_120929046 1.37 -0.45 9.89E-02 chr11:120929046-120929160 + CDS_or_noncoding_inner_exon,S


TBCEL tubulin folding cofactor E-like

chr11_+_121322776 0.46 8.14 1.91E-02 chr11:121322776-121322875 + TSSregion500,S ENST00000260197.6/ENST00000532451.1 SORL1

sortilin-related receptor, L(DLR class) A repeats containing

chr11_+_121323063 0.52 3.31 7.31E-02 chr11:121323063-121323073 + TSSregion500,S ENST00000532451.1 SORL1sortilin-related receptor, L(DLR class) A repeats containing


ENST00000260197.6/ENST00000532451.1 SORL1



ENST00000260197.6/ENST00000532451.1 SORL1


chr11_+_124616984 -1.73 0.23 5.58E-02 chr11:124616984-124617056 + 3UTR_last_exon,SENST00000284292.5/ENST00000412681.1/ENST00000526916.1

NRGNneurogranin (protein kinase C substrate, RC3)



FLI1 Friend leukemia virus integration 1

chr11_+_13371485 1.48 -0.19 4.33E-02 chr11:13371485-13371589 + TSS,S ENST00000485918.2 ARNTL aryl hydrocarbon receptor nuclear

4848

Persson et al.

translocator-like




chr11_+_288122 0.91 3.76 1.26E-02 chr11:288122-288140 + TSSregion500,S ENST00000534742.1/ENST00000525217.1 RP11-326C3.2

chr11_+_33279252 0.80 1.62 6.58E-02 chr11:33279252-33279279 + TSSregion500,S ENST00000379016.3/ENST00000303296.4 HIPK3

homeodomain interacting protein kinase 3

chr11_+_33279821 0.50 5.09 8.56E-02 chr11:33279821-33279926 + TSS,S ENST00000531504.1/ENST00000456517.1 HIPK3

homeodomain interacting protein kinase 3

chr11_+_35201810 0.74 4.88 5.01E-02 chr11:35201810-35201931 + TSS,S ENST00000531873.1/ENST00000525209.1 CD44 CD44 molecule (Indian

blood group)

chr11_+_35251775 -0.76 2.95 2.67E-02 chr11:35251775-35251785 + 3UTR_last_exon,S ENST00000263398.6 CD44 CD44 molecule (Indian blood group)

chr11_+_47600559 -0.35 5.59 8.02E-02 chr11:47600559-47600652 + TSS,S


NDUFS3

NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzyme Q reductase)

chr11_+_58385890 -1.35 0.63 6.39E-02 chr11:58385890-58386064 + 3UTR_last_exon,S ENST00000316059.6 ZFP91 zinc finger protein 91 homolog (mouse)

chr11_+_58992270 1.41 -0.35 7.48E-02 chr11:58992270-58992452 + intergenic intergenic NA NA

chr11_+_59522809 0.57 5.83 1.06E-02 chr11:59522809-59522964 + TSS,S


STX3 syntaxin 3

chr11_+_59554499 1.16 1.13 4.84E-02 chr11:59554499-59554611 + TSS,S ENST00000528805.1 STX3 syntaxin 3




chr11_+_63606809 1.14 1.55 1.02E-02 chr11:63606809-63606977 + TSSregion500,S ENST00000402010.2/ MARK2 MAP/microtubule affinity-

4949

Persson et al.


regulating kinase 2



SYVN1 synovial apoptosis inhibitor 1, synoviolin

chr11_+_65088131 1.98 -0.28 8.01E-02 chr11:65088131-65088171 + 5UTR_last_exon,SENST00000279249.2/ENST00000533419.1/ENST00000544348.1

CDC42EP2 CDC42 effector protein (Rho GTPase binding) 2




chr11_+_65267556 1.05 3.66 7.47E-02 chr11:65267556-65267563 + CDS_or_noncoding_first_exon,S

ENST00000544868.1/ENST00000534336.1 MALAT1


chr11_+_65268354 -0.99 3.76 3.65E-02 chr11:65268354-65268357 + CDS_or_noncoding_first_exon,S

ENST00000544868.1/ENST00000534336.1 MALAT1



ENST00000544868.1/ENST00000534336.1 MALAT1






5050

Persson et al.

chr11_+_65348659 1.12 0.01 9.60E-02 chr11:65348659-65348813 + TSSregion500,S ENST00000526990.1 EHBP1L1 EH domain binding protein 1-like 1

chr11_+_66888724 1.19 0.10 9.37E-02 chr11:66888724-66888808 + 5UTR_inner_exon,S

ENST00000398645.2/ENST00000529006.1 KDM2A lysine (K)-specific

demethylase 2A

chr11_+_71846707 1.51 4.85 1.34E-02 chr11:71846707-71846814 + TSS,S


FOLR3 folate receptor 3 (gamma)

chr11_+_74459865 0.37 5.74 5.52E-02 chr11:74459865-74460016 + TSS,S ENST00000299563.4 RNF169 ring finger protein 169



chr11_+_755864 1.17 2.59 4.02E-02 chr11:755864-755976 + TSSregion500,S ENST00000533796.1 TALDO1 transaldolase 1

chr11_+_78138980 1.67 -0.51 4.32E-02 chr11:78138980-78139180 + CDS_or_noncoding_last_intron,S ENST00000534168.1 RP11-

452H21.1

chr11_+_82600510 0.77 2.33 3.45E-02 chr11:82600510-82600619 + 5UTR_first_intron,AS


PRCP prolylcarboxypeptidase (angiotensinase C)

chr11_+_82870140 -1.80 -0.31 2.61E-02 chr11:82870140-82870164 + CDS_or_noncoding_first_intron,S

ENST00000298281.4/ENST00000530660.1/ENST00000530304.1

PCF11

PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)


chr11_-_10627666 0.75 4.62 7.15E-03 chr11:10627666-10627849 - CDS_or_noncoding_first_intron,S ENST00000531706.1 LYVE1

lymphatic vessel endothelial hyaluronan receptor 1

chr11_-_10821157 1.69 -0.47 8.56E-02 chr11:10821157-10821275 - TSS,S ENST00000525606.1 EIF4G2eukaryotic translation initiation factor 4 gamma, 2


ENST00000356289.5/ENST00000292067.7/ENST00000533261.1/ENST00000526595.1/ENST00000526620.1/ENST00000537867.1/ENST00000524477.1/ENST00000527877.1/ENST00000525565.1/

AMICA1adhesion molecule, interacts with CXADR antigen 1

5151

Persson et al.

ENST00000534294.1/ENST00000529164.1/ENST00000531536.1

chr11_-_122930413 1.14 1.59 2.85E-02 chr11:122930413-122930534 - TSSregion500,S ENST00000524552.1 HSPA8 heat shock 70kDa protein 8


chr11_-_3849257 1.24 3.78 1.02E-02 chr11:3849257-3849449 - 5UTR_last_exon,S


RHOG ras homolog family member G

chr11_-_46142520 0.43 4.70 2.89E-02 chr11:46142520-46142695 - TSS,S




ENST00000378538.3/ENST00000227163.4/ENST00000533968.1

SPI1

spleen focus forming virus (SFFV) proviral integration oncogene spi1


chr11_-_61187421 1.37 0.11 5.17E-02 chr11:61187421-61187582 - TSSregion500,S ENST00000544147.1 CPSF7cleavage and polyadenylation specific factor 7, 59kDa

chr11_-_72437805 1.55 -0.54 8.24E-02 chr11:72437805-72437849 - CDS_or_noncoding_first_exon,S ENST00000455638.2 ARAP1

ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1

chr11_-_72525050 0.44 5.02 8.68E-02 chr11:72525050-72525145 - TSSregion500,AS


ATG16L2 autophagy related 16-like 2 (S. cerevisiae)



FCHSD2 FCH and double SH3 domains 2

5252

Persson et al.

chr11_-_73387523 -1.19 0.76 8.45E-02 chr11:73387523-73387649 - 3UTR_last_exon,SENST00000310653.5/ENST00000336083.3/ENST00000393571.4

RAB6A RAB6A, member RAS oncogene family

chr11_-_77122859 0.38 7.59 5.52E-02 chr11:77122859-77123054 - TSS,S


PAK1p21 protein (Cdc42/Rac)-activated kinase 1

chr11_-_77531732 0.60 3.33 4.15E-02 chr11:77531732-77531738 - TSSregion500,S ENST00000467567.1/ENST00000530604.1 RSF1 remodeling and spacing

factor 1


ENST00000340149.2/ENST00000361507.4 GAB2 GRB2-associated

binding protein 2



GAB2 GRB2-associated binding protein 2

chr11_-_78128806 0.58 5.82 6.06E-03 chr11:78128806-78129004 - TSS,S



chr11_-_85779796 1.67 1.42 1.63E-03 chr11:85779796-85779902 - TSS,S ENST00000356360.5/ENST00000534412.1 PICALM

phosphatidylinositol binding clathrin assembly protein

chr11_-_85779972 0.56 8.53 6.40E-04 chr11:85779972-85780172 - TSS,S



chr12_+_10374491 0.94 1.85 2.75E-02 chr12:10374491-10374585 + 3UTR_last_exon,S


GABARAPL1 GABA(A) receptor-associated protein like 1

5353

Persson et al.

chr12_+_105064122 1.35 -0.29 6.88E-02 chr12:105064122-105064142 + CDS_or_noncoding_last_intron,S

ENST00000549260.1/ENST00000303694.5/ENST00000549016.1

CHST11carbohydrate (chondroitin 4) sulfotransferase 11

chr12_+_119442508 -1.19 1.13 3.58E-02 chr12:119442508-119442521 + CDS_or_noncoding_first_intron,S ENST00000267260.4 SRRM4 serine/arginine repetitive

matrix 4



RNF10 ring finger protein 10


chr12_+_14518558 0.40 5.98 8.33E-02 chr12:14518558-14518670 + TSS,S


ATF7IPactivating transcription factor 7 interacting protein

chr12_+_1863418 1.68 -0.35 4.37E-02 chr12:1863418-1863609 + 5UTR_inner_exon,S ENST00000357103.4 ADIPOR2 adiponectin receptor 2



chr12_+_31882124 0.53 4.74 4.97E-02 chr12:31882124-31882302 + TSSregion500,AS


AMN1antagonist of mitotic exit network 1 homolog (S. cerevisiae)


ENST00000540924.1/ENST00000312561.4/ENST00000541981.1/ENST00000535596.1/

C12ORF35 NA

5454

Persson et al.

ENST00000397578.3/ENST00000535606.1

chr12_+_32112314 0.40 8.75 3.92E-02 chr12:32112314-32112394 + TSS,S


C12ORF35 NA



C12ORF35 NA


ENST00000312561.4/ENST00000381054.3 C12ORF35 NA

chr12_+_32638822 0.56 6.45 1.67E-02 chr12:32638822-32639001 + TSS,S ENST00000531134.1 FGD4 FYVE, RhoGEF and PH domain containing 4

chr12_+_40618750 0.53 7.05 1.40E-02 chr12:40618750-40618945 + TSS,S ENST00000343742.2/ENST00000298910.7 LRRK2 leucine-rich repeat

kinase 2


ENST00000416796.1/ENST00000343742.2/ENST00000298910.7

LRRK2 leucine-rich repeat kinase 2

chr12_+_4410650 -1.13 1.50 8.84E-03 chr12:4410650-4410657 + 3UTR_last_exon,S ENST00000261254.3 CCND2 cyclin D2



SCAF11 SR-related CTD-associated factor 11


ENST00000455310.1/ENST00000301180.5/ENST00000549620.1

DIP2BDIP2 disco-interacting protein 2 homolog B (Drosophila)

chr12_+_51324884 -1.45 0.04 4.37E-02 chr12:51324884-51324894 + 3UTR_last_exon,S ENST00000548553.1/ENST00000332160.4 METTL7A methyltransferase like

7A

chr12_+_51634115 1.60 2.60 7.15E-03 chr12:51634115-51634214 + 5UTR_inner_exon,S ENST00000551313.1 DAZAP2 DAZ associated protein

2

chr12_+_57870607 0.46 3.77 7.09E-02 chr12:57870607-57870697 + TSSregion500,AS ENST00000552953.1/ENST00000547200.1 ARHGAP9 Rho GTPase activating

protein 9

5555

Persson et al.

chr12_+_57916472 0.35 5.96 7.88E-02 chr12:57916472-57916668 + TSS,S


MBD6 methyl-CpG binding domain protein 6


ENST00000549623.1/ENST00000300263.6 MBD6 methyl-CpG binding

domain protein 6

chr12_+_57919133 1.08 0.99 6.30E-02 chr12:57919133-57919236 + 5UTR_inner_exon,S ENST00000300263.6 MBD6 methyl-CpG binding

domain protein 6

chr12_+_62654125 0.31 8.82 9.23E-02 chr12:62654125-62654251 + TSS,S

ENST00000280377.5/ENST00000393654.3/ENST00000549523.1/ENST00000312635.6/ENST00000549237.1/ENST00000550632.1/ENST00000548524.1/ENST00000546718.1/ENST00000551206.1/ENST00000537297.2

USP15 ubiquitin specific peptidase 15

chr12_+_65004199 0.35 7.79 5.37E-02 chr12:65004199-65004303 + TSS,S


RASSF3Ras association (RalGDS/AF-6) domain family member 3

chr12_+_66582670 1.34 -0.02 7.20E-02 chr12:66582670-66582716 + TSSregion500,SENST00000261233.4/ENST00000545837.1/ENST00000457197.2

IRAK3 interleukin-1 receptor-associated kinase 3

chr12_+_66582922 0.64 5.44 4.09E-02 chr12:66582922-66583121 + TSS,S ENST00000545837.1/ENST00000457197.2 IRAK3 interleukin-1 receptor-

associated kinase 3

chr12_+_69747044 -1.33 0.82 2.90E-02 chr12:69747044-69747052 + CDS_or_noncoding_last_exon,S ENST00000549690.1 LYZ lysozyme


ENST00000542848.1/ENST00000399448.1/ENST00000447931.2/ENST00000538715.1/ENST00000318974.9/ENST00000456013.1/ENST00000535462.1/ENST00000541698.1/ENST00000542462.1/

PTPN6protein tyrosine phosphatase, non-receptor type 6

5656

Persson et al.


chr12_+_70671903 2.40 -0.59 6.41E-02 chr12:70671903-70672057 + TSS,S


CNOT2 CCR4-NOT transcription complex, subunit 2

chr12_+_81331585 1.01 1.51 4.95E-02 chr12:81331585-81331643 + TSS,S ENST00000549175.1 ACSS3acyl-CoA synthetase short-chain family member 3

chr12_+_862837 1.08 2.76 5.52E-02 chr12:862837-862940 + 5UTR_first_exon,S ENST00000252477.7 WNK1 WNK lysine deficient

protein kinase 1chr12_+_94542345 0.55 6.49 1.13E-02 chr12:94542345-94542539 + TSS,S ENST00000258526.4 PLXNC1 plexin C1

chr12_+_94543401 0.88 3.58 1.55E-02 chr12:94543401-94543537 + CDS_or_noncoding_first_exon,S ENST00000258526.4 PLXNC1 plexin C1


UHRF1BP1L UHRF1 binding protein 1-like

chr12_-_10282695 0.31 8.48 6.06E-02 chr12:10282695-10282895 - TSS,S


CLEC7A C-type lectin domain family 7, member A

chr12_-_109017534 0.88 1.83 9.46E-02 chr12:109017534-109017578 - CDS_or_noncoding_last_exon,S

ENST00000388962.3/ENST00000550948.1/ENST00000228463.6

SELPLG selectin P ligand

chr12_-_120652665 1.13 0.88 1.94E-02 chr12:120652665-120652806 - 5UTR_inner_exon,S ENST00000331257.5 PXN paxillin

chr12_-_53931191 1.19 0.95 1.40E-02 chr12:53931191-53931346 - CDS_or_noncodin ENST00000420353.1/ ATF7 activating transcription

5757

Persson et al.

g_inner_exon,S


factor 7



CD63 CD63 molecule

chr12_-_57870518 1.07 0.19 7.73E-02 chr12:57870518-57870566 - TSSregion500,S ENST00000552953.1/ENST00000547200.1 ARHGAP9 Rho GTPase activating

protein 9

chr12_-_72003949 -1.11 0.79 8.27E-02 chr12:72003949-72004144 - CDS_or_noncoding_last_exon,S ENST00000550963.1 ZFC3H1 zinc finger, C3H1-type

containing


ZFC3H1 zinc finger, C3H1-type containing


NINJ2 ninjurin 2



chr12_-_95044208 0.48 5.65 8.99E-02 chr12:95044208-95044398 - TSS,S ENST00000261226.4 TMCC3transmembrane and coiled-coil domain family 3

chr12_-_95397402 -0.37 6.23 6.30E-02 chr12:95397402-95397552 - TSS,S


NDUFA12NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12

chr12_-_96390067 0.59 5.16 6.49E-03 chr12:96390067-96390149 - TSS,S


HAL histidine ammonia-lyase

chr13_+_108930765 0.98 1.08 8.36E-02 chr13:108930765-108930901 + CDS_or_noncoding_first_intron,S ENST00000479435.1 TNFSF13B

tumor necrosis factor (ligand) superfamily, member 13b

5858

Persson et al.

chr13_+_113439463 1.54 0.34 9.89E-02 chr13:113439463-113439528 + TSS,S ENST00000418678.1/ENST00000432166.1 ATP11A ATPase, class VI, type

11A

chr13_+_28712826 0.75 1.88 8.01E-02 chr13:28712826-28712853 + TSSregion500,S ENST00000399613.1/ENST00000503791.1 PAN3

PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)








chr13_+_48807461 0.91 3.78 4.19E-02 chr13:48807461-48807514 + TSSregion500,S ENST00000378565.4/ENST00000378549.5 ITM2B integral membrane

protein 2B

chr13_+_52411185 1.79 -0.36 7.49E-03 chr13:52411185-52411221 + CDS_or_noncoding_inner_intron,AS ENST00000501205.1 LINC00282 NA

chr13_+_96329340 0.30 6.39 8.36E-02 chr13:96329340-96329492 + TSS,S ENST00000376795.5 DNAJC3 DnaJ (Hsp40) homolog, subfamily C, member 3

chr13_-_46756212 0.85 1.03 8.84E-02 chr13:46756212-46756231 - 5UTR_first_intron,S ENST00000323076.2 LCP1 lymphocyte cytosolic

protein 1 (L-plastin)

chr13_-_50699516 0.47 6.28 7.86E-02 chr13:50699516-50699707 - TSSregion500,S ENST00000425586.1 DLEU2deleted in lymphocytic leukemia 2 (non-protein coding)

chr14_+_102289617 -1.91 -0.32 3.13E-02 chr14:102289617-102289651 + TSSregion500,S ENST00000556493.1 PPP2R5Cprotein phosphatase 2, regulatory subunit B', gamma


ENST00000359520.7/ENST00000558678.1/ENST00000380088.4

TECPR2 tectonin beta-propeller repeat containing 2

chr14_+_103058922 0.41 5.90 3.72E-02 chr14:103058922-103059063 + TSS,S ENST00000262241.5 RCOR1 REST corepressor 1

chr14_+_23020933 -0.99 1.16 5.72E-02 chr14:23020933-23021055 + 3UTR_last_exon,S ENST00000478163.2 TRAC T cell receptor alpha constant

chr14_+_37334414 -1.22 -0.13 5.83E-02 chr14:37334414-37334419 + CDS_or_noncoding_inner_intron,AS

ENST00000555449.1/ENST00000331299.5 SLC25A21

solute carrier family 25 (mitochondrial oxoadipate carrier), member 21

chr14_+_39736548 0.38 5.60 6.41E-02 chr14:39736548-39736636 + TSS,S ENST00000556148.1/ENST00000348007.3 CTAGE5 CTAGE family, member

5

5959

Persson et al.

chr14_+_50361184 -0.57 4.50 7.87E-02 chr14:50361184-50361203 + 3UTR_last_exon,S ENST00000298316.5 ARF6 ADP-ribosylation factor 6

chr14_+_52327110 1.09 1.11 4.41E-02 chr14:52327110-52327166 + TSS,S ENST00000335281.4 GNG2guanine nucleotide binding protein (G protein), gamma 2

chr14_+_56585010 0.57 5.37 2.72E-02 chr14:56585010-56585204 + TSS,S ENST00000267460.4 PELI2pellino E3 ubiquitin protein ligase family member 2

chr14_+_57877726 -1.90 -0.77 3.76E-02 chr14:57877726-57877798 + 3UTR_last_exon,SENST00000556492.1/ENST00000395257.2/ENST00000298406.6

NAA30N(alpha)-acetyltransferase 30, NatC catalytic subunit

chr14_+_58765185 0.46 5.63 5.79E-02 chr14:58765185-58765381 + TSS,S


ARID4A AT rich interactive domain 4A (RBP1-like)

chr14_+_65171091 0.46 5.76 8.84E-02 chr14:65171091-65171207 + TSS,S ENST00000247226.7 PLEKHG3

pleckstrin homology domain containing, family G (with RhoGef domain) member 3



PCNX pecanex homolog (Drosophila)

chr14_+_71374383 0.62 5.67 5.23E-03 chr14:71374383-71374451 + TSS,S ENST00000554292.1 PCNX pecanex homolog (Drosophila)

chr14_+_71787138 0.56 5.48 1.13E-02 chr14:71787138-71787226 + TSS,S


SIPA1L1signal-induced proliferation-associated 1 like 1



ENST00000381232.3/ENST00000555818.1/ENST00000358550.2


chr14_+_75745753 1.31 2.36 1.55E-02 chr14:75745753-75745763 + TSSregion500,S ENST00000556324.1 FOSFBJ murine osteosarcoma viral oncogene homolog

chr14_+_75747250 0.85 2.41 8.17E-02 chr14:75747250-75747309 + TSSregion500,S ENST00000555347.1 FOS FBJ murine

6060

Persson et al.

osteosarcoma viral oncogene homolog



FOSFBJ murine osteosarcoma viral oncogene homolog

chr14_+_90871925 -1.21 2.03 1.26E-02 chr14:90871925-90871935 + 3UTR_last_exon,S ENST00000356978.4/ENST00000553630.1 CALM1


chr14_+_90872381 -0.78 3.78 4.37E-02 chr14:90872381-90872505 + 3UTR_last_exon,S ENST00000356978.4 CALM1calmodulin 1 (phosphorylase kinase, delta)

chr14_+_95651943 0.52 4.27 3.92E-02 chr14:95651943-95652076 + TSSregion500,AS ENST00000556796.1 CTD-2240H23.2



BAZ1A bromodomain adjacent to zinc finger domain, 1A

chr14_-_50698260 0.47 5.47 2.00E-02 chr14:50698260-50698451 - TSS,S ENST00000216373.5 SOS2 son of sevenless homolog 2 (Drosophila)

chr14_-_51297798 0.39 6.64 7.80E-02 chr14:51297798-51297940 - TSS,S


NIN ninein (GSK3B interacting protein)

chr14_-_51411077 0.42 7.62 3.62E-02 chr14:51411077-51411249 - TSS,S


PYGL phosphorylase, glycogen, liver

chr14_-_65543047 -0.82 3.64 5.37E-02 chr14:65543047-65543184 - CDS_or_noncoding_last_exon,S ENST00000555932.1 MAX MYC associated factor X


ENST00000336440.3/ENST00000435246.2 ZFP36L1 zinc finger protein 36,

C3H type-like 1



SLC8A3solute carrier family 8 (sodium/calcium exchanger), member 3

6161

Persson et al.

chr14_-_73930276 0.48 6.99 1.62E-02 chr14:73930276-73930387 - TSS,S


NUMB numb homolog (Drosophila)

chr14_-_94849358 1.48 0.50 2.50E-02 chr14:94849358-94849361 - 5UTR_first_intron,S ENST00000554720.1 SERPINA1

serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1

chr14_-_94849388 0.97 4.75 1.15E-02 chr14:94849388-94849586 - TSS,S ENST00000489769.1 SERPINA1



ENST00000440909.1/ENST00000448921.1/ENST00000437397.1/ENST00000355814.4/ENST00000393088.4/ENST00000404814.4/ENST00000449399.3/ENST00000557492.1/ENST00000556955.1/ENST00000553327.1/ENST00000557118.1/ENST00000555289.1/ENST00000557361.1/ENST00000557093.1

SERPINA1


chr14_-_94856845 0.40 10.00 6.88E-02 chr14:94856845-94857039 - TSS,S


SERPINA1


6262

Persson et al.



DICER1 dicer 1, ribonuclease type III

chr14_-_95786136 0.77 3.02 5.67E-02 chr14:95786136-95786275 - TSS,S ENST00000298912.3/ENST00000553733.1 CLMN calmin (calponin-like,

transmembrane)

chr14_-_99636882 -1.01 1.89 8.01E-02 chr14:99636882-99637006 - 3UTR_last_exon,S ENST00000357195.3/ENST00000345514.2 BCL11B B-cell CLL/lymphoma

11B (zinc finger protein)

chr14_-_99639178 -2.09 0.37 7.33E-02 chr14:99639178-99639289 - 3UTR_last_exon,S ENST00000357195.3/ENST00000345514.2 BCL11B B-cell CLL/lymphoma

11B (zinc finger protein)

chr15_+_31664212 1.77 1.89 8.19E-03 chr15:31664212-31664310 + 5UTR_last_exon,S ENST00000558844.1 KLF13 Kruppel-like factor 13


B2M beta-2-microglobulin

chr15_+_45951117 1.20 0.67 8.56E-02 chr15:45951117-45951315 + 5UTR_inner_exon,S ENST00000260324.6 SQRDL sulfide quinone

reductase-like (yeast)chr15_+_49170484 1.99 0.50 4.84E-02 chr15:49170484-49170492 + TSSregion500,S ENST00000441252.2 AC012379.1chr15_+_57212073 1.86 -0.40 8.59E-02 chr15:57212073-57212127 + TSSregion500,S ENST00000561152.1 TCF12 transcription factor 12

chr15_+_58430379 0.44 8.26 2.03E-02 chr15:58430379-58430489 + TSS,S ENST00000219919.4/ENST00000559443.1 AQP9 aquaporin 9


AQP9 aquaporin 9


ENST00000558772.1/ENST00000219919.4/ENST00000536493.1

AQP9 aquaporin 9

chr15_+_59280340 0.53 3.11 5.52E-02 chr15:59280340-59280403 + TSSregion500,S ENST00000557998.1 RNF111 ring finger protein 111

chr15_+_65133305 -0.84 2.85 6.99E-02 chr15:65133305-65133312 + upstream1000,S


AC069368.3 Uncharacterized protein

6363

Persson et al.

chr15_+_65134073 0.38 6.94 3.56E-02 chr15:65134073-65134200 + TSS,S


PLEKHO2pleckstrin homology domain containing, family O member 2



PLEKHO2pleckstrin homology domain containing, family O member 2

chr15_+_68584927 -1.52 -0.05 8.83E-02 chr15:68584927-68585004 + 3UTR_last_exon,S ENST00000306917.4 FEM1B fem-1 homolog b (C. elegans)



CSK c-src tyrosine kinase

chr15_+_75498963 1.31 2.48 5.75E-02 chr15:75498963-75499009 + 5UTR_first_intron,S ENST00000446981.2 C15ORF39 NA

chr15_+_77287685 0.45 5.92 2.75E-02 chr15:77287685-77287751 + TSS,S ENST00000560621.1/ENST00000560377.1 PSTPIP1

proline-serine-threonine phosphatase interacting protein 1

chr15_+_78462578 -0.80 2.05 7.00E-02 chr15:78462578-78462718 + CDS_or_noncoding_last_exon,S ENST00000558535.1 IDH3A

isocitrate dehydrogenase 3 (NAD+) alpha


ENST00000558332.1/ENST00000394656.3 IL16 interleukin 16

chr15_+_85291780 0.47 5.50 3.29E-02 chr15:85291780-85291862 + TSSregion500,S ENST00000560079.1 ZNF592 zinc finger protein 592

chr15_+_86087073 0.52 4.50 9.46E-02 chr15:86087073-86087147 + TSSregion500,S ENST00000558166.1 AKAP13 A kinase (PRKA) anchor protein 13

chr15_+_86087291 0.63 5.03 4.95E-02 chr15:86087291-86087325 + 5UTR_inner_intron,S ENST00000426424.2 AKAP13 A kinase (PRKA) anchor

protein 13

chr15_+_86098560 0.40 5.69 9.97E-02 chr15:86098560-86098700 + TSS,S ENST00000558811.1 AKAP13 A kinase (PRKA) anchor protein 13


ENST00000352732.4/ENST00000355100.3 ABHD2 abhydrolase domain

containing 2


chr15_+_90969336 1.11 2.42 7.86E-03 chr15:90969336-90969500 + TSS,S ENST00000559682.1 IQGAP1IQ motif containing GTPase activating protein 1


MAN2A2 mannosidase, alpha, class 2A, member 2

6464

Persson et al.

chr15_+_92396921 0.48 5.24 3.56E-02 chr15:92396921-92397081 + TSS,S ENST00000318445.6/ENST00000553653.1 SLCO3A1

solute carrier organic anion transporter family, member 3A1



chr15_+_94774756 0.39 6.37 8.80E-02 chr15:94774756-94774839 + TSS,S ENST00000543482.1/ENST00000556363.1 MCTP2 multiple C2 domains,

transmembrane 2

chr15_+_94858765 1.47 -0.41 9.77E-02 chr15:94858765-94858840 + 5UTR_inner_exon,S ENST00000331706.4 MCTP2 multiple C2 domains,

transmembrane 2

chr15_+_99797728 1.20 0.63 7.77E-02 chr15:99797728-99797876 + TSS,S ENST00000559111.1 HSP90B2Pheat shock protein 90kDa beta (Grp94), member 2, pseudogene


MTMR10 myotubularin related protein 10

chr15_-_34628631 1.36 -0.18 5.19E-02 chr15:34628631-34628738 - 5UTR_inner_exon,S


SLC12A6solute carrier family 12 (potassium/chloride transporters), member 6

chr15_-_34629882 0.61 5.47 1.63E-03 chr15:34629882-34629989 - TSS,S


SLC12A6solute carrier family 12 (potassium/chloride transporters), member 6

chr15_-_42783207 0.47 4.90 7.43E-02 chr15:42783207-42783393 - TSS,S ENST00000434903.2 ZFP106 zinc finger protein 106 homolog (mouse)



NEDD4

neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase

chr15_-_70015654 0.76 1.75 8.99E-02 chr15:70015654-70015790 - intergenic intergenic NA NAchr15_-_70047854 0.72 2.92 5.75E-02 chr15:70047854-70047963 - intergenic intergenic NA NA

6565

Persson et al.

chr15_-_83777291 0.62 3.11 3.86E-02 chr15:83777291-83777486 - CDS_or_noncoding_first_intron,AS


TM6SF1 transmembrane 6 superfamily member 1

chr15_-_90349741 0.82 2.07 4.02E-02 chr15:90349741-90349875 - 5UTR_inner_exon,S ENST00000300060.6 ANPEP alanyl (membrane)

aminopeptidase


ANPEP alanyl (membrane) aminopeptidase

chr16_+_11770394 1.17 1.22 5.42E-02 chr16:11770394-11770479 + 3UTR_last_exon,S ENST00000329565.5 SNN stannin

chr16_+_22448315 0.77 3.83 1.04E-02 chr16:22448315-22448383 + TSS,S ENST00000446662.1 RP11-368J21.1 NA

chr16_+_23847250 0.42 8.64 5.90E-02 chr16:23847250-23847376 + TSS,S ENST00000321728.7/ENST00000303531.7 PRKCB protein kinase C, beta

chr16_+_23847533 1.09 3.50 1.12E-02 chr16:23847533-23847598 + TSSregion500,S ENST00000498058.1 PRKCB protein kinase C, betachr16_+_24043443 1.16 0.27 8.01E-02 chr16:24043443-24043539 + TSSregion500,S ENST00000486868.1 PRKCB protein kinase C, beta



IL4R interleukin 4 receptor

chr16_+_2807770 0.87 1.68 9.33E-02 chr16:2807770-2807917 + 5UTR_inner_exon,S ENST00000544933.1 SRRM2 serine/arginine repetitive

matrix 2



SRRM2 serine/arginine repetitive matrix 2



LAT linker for activation of T cells

chr16_+_29676225 -1.40 0.57 7.80E-02 chr16:29676225-29676360 + 5UTR_first_intron,S ENST00000449759.1 QPRT

quinolinate phosphoribosyltransferase

6666

Persson et al.



MAZ



ENST00000356798.4/ENST00000358164.4/ENST00000454514.2

ITGAL

integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)

chr16_+_30774437 1.87 -0.19 5.92E-02 chr16:30774437-30774561 + TSS,S ENST00000452273.2 RNF40 ring finger protein 40, E3 ubiquitin protein ligase

chr16_+_3096303 0.53 4.28 7.87E-02 chr16:3096303-3096357 + TSSregion500,S ENST00000336577.3 MMP25 matrix metallopeptidase 25




ENST00000336577.3/ENST00000325800.10

MMP25 matrix metallopeptidase 25

chr16_+_31885055 0.35 6.83 4.99E-02 chr16:31885055-31885248 + TSS,S ENST00000300870.8/ENST00000394846.2 ZNF267 zinc finger protein 267




CYLD cylindromatosis (turban tumor syndrome)

chr16_+_56510326 -1.80 0.03 1.47E-02 chr16:56510326-56510425 + 3UTR_last_exon,S ENST00000336111.4/ENST00000540727.1 OGFOD1

2-oxoglutarate and iron-dependent oxygenase domain containing 1


solute carrier family 12 (sodium/chloride transporters), member 3



chr16_+_57713105 1.27 0.02 8.21E-02 chr16:57713105-57713271 + 5UTR_inner_exon,S ENST00000327655.6 GPR97 G protein-coupled

receptor 97

chr16_+_81685807 1.06 1.50 7.04E-02 chr16:81685807-81685971 + 5UTR_inner_exon,S ENST00000542097.1 CMIP c-Maf inducing protein

chr16_+_81812843 0.42 6.78 2.60E-02 chr16:81812843-81813003 + TSS,S ENST00000359376.2 PLCG2 phospholipase C, gamma 2

6767

Persson et al.

(phosphatidylinositol-specific)

chr16_+_84628259 0.57 2.65 6.78E-02 chr16:84628259-84628316 + CDS_or_noncoding_inner_intron,AS ENST00000262428.4 COTL1 coactosin-like 1

(Dictyostelium)

chr16_+_84872037 2.00 -0.12 5.87E-02 chr16:84872037-84872167 + 5UTR_inner_exon,S ENST00000262424.4 CRISPLD2

cysteine-rich secretory protein LCCL domain containing 2


chr16_+_88643712 1.34 0.02 3.51E-02 chr16:88643712-88643756 + CDS_or_noncoding_first_exon,S ENST00000545404.1 ZC3H18 zinc finger CCCH-type

containing 18

chr16_+_90023630 0.43 5.12 4.43E-02 chr16:90023630-90023756 + CDS_or_noncoding_inner_intron,S

ENST00000268676.7/ENST00000418391.2 DEF8

differentially expressed in FDCP 8 homolog (mouse)



ENST00000339430.4/ENST00000413364.1/ENST00000381810.3

LITAF lipopolysaccharide-induced TNF factor


ENST00000381774.3/ENST00000433677.2/ENST00000261660.4

CPPED1calcineurin-like phosphoesterase domain containing 1

chr16_-_2097788 -0.67 2.18 4.55E-02 chr16:2097788-2097919 - TSS,S ENST00000219066.1 NTHL1 nth endonuclease III-like 1 (E. coli)

chr16_-_28223170 0.34 7.29 4.94E-02 chr16:28223170-28223355 - TSS,S ENST00000304658.5 XPO6 exportin 6



chr16_-_3929873 0.82 2.62 3.29E-02 chr16:3929873-3930071 - TSSregion500,S ENST00000323508.4/ENST00000382070.2 CREBBP CREB binding protein

chr16_-_84623743 0.98 3.01 6.11E-02 chr16:84623743-84623880 - CDS_or_noncoding_inner_exon,S ENST00000262428.4 COTL1 coactosin-like 1

(Dictyostelium)


ENST00000261650.5/ENST00000541285.1/ENST00000490106.1

ALKBH5 alkB, alkylation repair homolog 5 (E. coli)



MYO18A myosin XVIIIA


6868

Persson et al.

chr17_+_29421882 0.48 4.13 6.30E-02 chr17:29421882-29422019 + TSS,S


NF1 neurofibromin 1


ENST00000325874.7/ENST00000394744.1 RAB11FIP4 RAB11 family interacting

protein 4 (class II)

chr17_+_30808489 -0.86 2.71 5.41E-02 chr17:30808489-30808581 + 3UTR_last_exon,S ENST00000261712.2 PSMD11proteasome (prosome, macropain) 26S subunit, non-ATPase, 11


chr17_+_34430978 -1.18 2.57 5.36E-02 chr17:34430978-34430985 + TSSregion500,S ENST00000250151.3/ENST00000394495.1 CCL4 chemokine (C-C motif)

ligand 4

chr17_+_36884506 -1.55 -0.50 5.48E-02 chr17:36884506-36884655 + 3UTR_last_exon,S ENST00000325718.7 MLLT6

myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6



LASP1 LIM and SH3 protein 1

chr17_+_37360783 -1.63 1.19 8.35E-02 chr17:37360783-37360909 + CDS_or_noncoding_last_exon,S ENST00000225430.4 RPL19 ribosomal protein L19

chr17_+_38375497 0.41 4.66 8.24E-02 chr17:38375497-38375692 + TSS,S


WIPF2 WAS/WASL interacting protein family, member 2

chr17_+_38512925 -1.01 2.25 7.43E-02 chr17:38512925-38513027 + CDS_or_noncoding_last_exon,S ENST00000319149.8 RARA retinoic acid receptor,

alpha

chr17_+_40610859 0.44 5.57 4.94E-02 chr17:40610859-40610959 + TSS,S


ATP6V0A1ATPase, H+ transporting, lysosomal V0 subunit a1

chr17_+_41338256 1.31 1.23 3.62E-02 chr17:41338256-41338433 + 5UTR_inner_exon,S ENST00000537493.1 NBR1 neighbor of BRCA1 gene

1

6969

Persson et al.


ENST00000540306.1/ENST00000262415.2 DHX8 DEAH (Asp-Glu-Ala-His)

box polypeptide 8

chr17_+_42398805 -1.45 0.95 6.96E-02 chr17:42398805-42398899 + CDS_or_noncoding_inner_exon,AS

ENST00000377095.4/ENST00000225308.8/ENST00000537904.1

SLC25A39 solute carrier family 25, member 39


ENST00000053867.2/ENST00000393566.2/ENST00000357351.4

GRN granulin


ENST00000331495.2/ENST00000328118.3 FMNL1 formin-like 1

chr17_+_45390148 -1.83 0.76 2.34E-02 chr17:45390148-45390334 + CDS_or_noncoding_inner_intron,S

ENST00000435993.2/ENST00000560629.1 ITGB3 Integrin beta

chr17_+_45734221 1.34 0.06 8.56E-02 chr17:45734221-45734401 + TSS,S ENST00000537679.1 KPNB1 karyopherin (importin) beta 1



ARRB2 arrestin, beta 2










7070

Persson et al.


ENST00000506533.1/ENST00000503935.2/ENST00000435742.2

KAT7 K(lysine) acetyltransferase 7



RABEP1 rabaptin, RAB GTPase binding effector protein 1

chr17_+_57842316 1.00 1.55 8.21E-02 chr17:57842316-57842469 + 5UTR_inner_exon,S ENST00000539763.1 VMP1 vacuole membrane

protein 1

chr17_+_65822192 1.04 1.85 3.19E-02 chr17:65822192-65822354 + TSS,S ENST00000544778.1 BPTF bromodomain PHD finger transcription factor

chr17_+_66287449 0.60 3.17 6.65E-02 chr17:66287449-66287530 + 5UTR_first_intron,S ENST00000452479.1 ARSG arylsulfatase G

chr17_+_67498362 0.74 3.70 4.56E-02 chr17:67498362-67498560 + CDS_or_noncoding_first_intron,S ENST00000359094.2 MAP2K6 mitogen-activated

protein kinase kinase 6

chr17_+_72322334 -1.26 1.47 8.31E-03 chr17:72322334-72322401 + TSS,S


KIF19 kinesin family member 19




chr17_+_72764279 0.97 1.44 8.21E-02 chr17:72764279-72764345 + CDS_or_noncoding_inner_exon,S ENST00000262613.4 SLC9A3R1

solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 1



SEC14L1 SEC14-like 1 (S. cerevisiae)

7171

Persson et al.



SEC14L1 SEC14-like 1 (S. cerevisiae)

chr17_+_76374689 0.37 5.93 6.05E-02 chr17:76374689-76374847 + TSS,S ENST00000262764.5/ENST00000329897.7 PGS1 phosphatidylglycerophos

phate synthase 1

chr17_+_78261646 2.36 0.19 2.85E-02 chr17:78261646-78261713 + TSSregion500,S ENST00000559070.1 RNF213 ring finger protein 213chr17_+_8316388 0.68 7.17 4.38E-04 chr17:8316388-8316578 + intergenic intergenic NA NA


ENST00000544865.1/ENST00000263073.4 SMG6

smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)

chr17_-_2295637 1.20 0.19 4.95E-02 chr17:2295637-2295724 - CDS_or_noncoding_inner_intron,S

ENST00000174618.4/ENST00000404961.2 MNT MNT, MAX dimerization

protein

chr17_-_27901164 -1.76 -0.73 8.17E-02 chr17:27901164-27901323 - CDS_or_noncoding_last_exon,S ENST00000473217.1 GIT1

G protein-coupled receptor kinase interacting ArfGAP 1


ENST00000269033.3/ENST00000540801.1/ENST00000394848.1

SSH2 slingshot homolog 2 (Drosophila)

chr17_-_28088305 0.41 7.91 5.52E-02 chr17:28088305-28088499 - TSSregion500,S ENST00000324677.6 SSH2 slingshot homolog 2 (Drosophila)

chr17_-_29641018 0.31 9.79 8.56E-02 chr17:29641018-29641142 - TSS,S ENST00000330927.3/ENST00000544462.1 EVI2B ecotropic viral integration

site 2B

chr17_-_36981460 0.38 5.73 7.85E-02 chr17:36981460-36981640 - TSS,S ENST00000225428.3/ENST00000536127.1 CWC25

CWC25 spliceosome-associated protein homolog (S. cerevisiae)

chr17_-_37915713 -1.75 0.47 3.22E-02 chr17:37915713-37915906 - 3UTR_last_exon,S ENST00000488188.1 IKZF3 IKAROS family zinc finger 3 (Aiolos)

chr17_-_38474193 0.99 0.78 5.01E-02 chr17:38474193-38474374 - TSSregion500,AS ENST00000425707.2/ENST00000394089.1 RARA retinoic acid receptor,

alpha


ENST00000361523.3/ENST00000438274.2/ENST00000543382.1

BECN1 beclin 1, autophagy related

chr17_-_43482339 0.97 0.93 7.36E-02 chr17:43482339-43482485 - TSSregion500,S ENST00000532667.1 ARHGAP27 Rho GTPase activating protein 27

chr17_-_44249394 1.09 1.50 3.57E-02 chr17:44249394-44249584 - TSSregion500,S ENST00000432791.1 KIAA1267 NA

7272

Persson et al.

chr17_-_49198086 0.52 5.78 1.15E-02 chr17:49198086-49198263 - TSS,S


SPAG9 sperm associated antigen 9



NLRP1 NLR family, pyrin domain containing 1


ENST00000316881.3/ENST00000537230.1 TRIM25 tripartite motif containing

25

chr17_-_56081124 -1.27 1.55 2.00E-02 chr17:56081124-56081282 - 3UTR_last_exon,S ENST00000258962.3 SRSF1 serine/arginine-rich splicing factor 1

chr17_-_58469333 0.44 5.71 4.15E-02 chr17:58469333-58469508 - TSS,S ENST00000393003.2 USP32 ubiquitin specific peptidase 32


ENST00000540698.1/ENST00000450599.1/ENST00000225792.4

DDX5 DEAD (Asp-Glu-Ala-Asp) box helicase 5

chr17_-_73842724 0.75 3.60 1.55E-02 chr17:73842724-73842872 - CDS_or_noncoding_inner_exon,S ENST00000431190.1 WBP2 WW domain binding

protein 2


ENST00000254806.3/ENST00000344296.4/ENST00000416574.2

WBP2 WW domain binding protein 2

chr17_-_76698235 1.51 -0.03 4.95E-02 chr17:76698235-76698326 - 5UTR_inner_exon,S ENST00000392453.3 CYTH1 cytohesin 1

chr17_-_76921332 0.46 7.27 6.51E-02 chr17:76921332-76921501 - TSS,S ENST00000262768.5 TIMP2 TIMP metallopeptidase inhibitor 2

chr17_-_7760495 -0.45 3.71 5.38E-02 chr17:7760495-7760593 - CDS_or_noncoding_first_exon,S ENST00000333775.4 LSMD1 LSM domain containing

1


ENST00000326724.4/ENST00000374792.1 AATK apoptosis-associated

tyrosine kinase

chr17_-_8868952 0.28 7.24 6.58E-02 chr17:8868952-8869080 - TSS,S ENST00000447110.1 PIK3R5phosphoinositide-3-kinase, regulatory subunit 5



chr18_+_2655873 0.40 5.72 5.56E-02 chr18:2655873-2655931 + TSS,S ENST00000261598.8/ENST00000320876.5 SMCHD1 structural maintenance

of chromosomes flexible

7373

Persson et al.

hinge domain containing 1




ENST00000261598.8/ENST00000320876.5 SMCHD1



ENST00000261598.8/ENST00000320876.5 SMCHD1



ENST00000217652.3/ENST00000536605.1 MYL12A

myosin, light chain 12A, regulatory, non-sarcomeric

chr18_+_3603609 1.58 -0.33 6.46E-02 chr18:3603609-3603737 + TSS,S ENST00000445581.2 AP002478.2 NA


SMAD4 SMAD family member 4


ENST00000398130.2/ENST00000256858.5 KIAA1468 KIAA1468


ENST00000397790.2/ENST00000545796.1 NFATC1

nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1


ENST00000400556.3/ENST00000400555.3/ENST00000285124.7

PPP4R1 protein phosphatase 4, regulatory subunit 1

chr19_+_11435147 1.45 -0.06 4.15E-02 chr19:11435147-11435341 + 3UTR_last_exon,AS ENST00000222120.2 RAB3D RAB3D, member RAS

oncogene familychr19_+_12902551 1.04 3.39 2.75E-02 chr19:12902551-12902614 + TSSregion500,S ENST00000302754.4 JUNB jun B proto-oncogene


ENST00000316448.4/ENST00000539083.1 CALR calreticulin

chr19_+_15751541 0.58 4.76 5.06E-02 chr19:15751541-15751731 + TSS,S ENST00000538865.1/ENST00000221307.6 CYP4F3

cytochrome P450, family 4, subfamily F, polypeptide 3

chr19_+_16244231 -0.74 3.23 2.67E-02 chr19:16244231-16244280 + 3UTR_last_exon,S ENST00000300935.2 RAB8A RAB8A, member RAS oncogene family

chr19_+_16437841 0.75 2.49 6.62E-02 chr19:16437841-16437881 + CDS_or_noncoding_last_exon,S ENST00000248071.4 KLF2 Kruppel-like factor 2

(lung)

7474

Persson et al.

chr19_+_18226300 -1.06 2.72 1.32E-02 chr19:18226300-18226313 + CDS_or_noncoding_inner_intron,S ENST00000262811.4 MAST3

microtubule associated serine/threonine kinase 3

chr19_+_19627009 -0.35 6.35 5.37E-02 chr19:19627009-19627117 + TSS,S


CTC-260F20.3 NA

chr19_+_2282242 0.84 1.15 8.60E-02 chr19:2282242-2282397 + TSSregion500,AS ENST00000342063.2 C19ORF35 NA

chr19_+_33203301 -0.91 1.85 4.34E-02 chr19:33203301-33203314 + 3UTR_last_exon,S ENST00000397061.2 NUDT19nudix (nucleoside diphosphate linked moiety X)-type motif 19


ENST00000433627.3/ENST00000544216.2/ENST00000540746.1

LSM14ALSM14A, SCD6 homolog A (S. cerevisiae)


ENST00000433627.3/ENST00000544216.2/ENST00000540746.1






HMG20B high mobility group 20B


ENST00000246551.3/ENST00000437550.1 HCST hematopoietic cell signal

transducer

chr19_+_39898433 0.94 2.20 3.86E-02 chr19:39898433-39898475 + CDS_or_noncoding_last_exon,S ENST00000248673.3 ZFP36






chr19_+_39898819 1.51 1.93 9.88E-03 chr19:39898819-39898828 + CDS_or_noncodin ENST00000248673.3 ZFP36 zinc finger protein 36,

7575

Persson et al.

g_last_exon,S C3H type, homolog (mouse)



SUPT5H suppressor of Ty 5 homolog (S. cerevisiae)


ENST00000291842.4/ENST00000446701.2 SHKBP1 SH3KBP1 binding

protein 1


HNRNPUL1heterogeneous nuclear ribonucleoprotein U-like 1

chr19_+_42300425 0.59 7.64 6.73E-03 chr19:42300425-42300581 + TSS,S



chr19_+_45251849 1.63 -0.62 5.52E-02 chr19:45251849-45251853 + TSSregion500,S ENST00000164227.5 BCL3 B-cell CLL/lymphoma 3


chr19_+_46029415 2.09 -0.88 6.10E-02 chr19:46029415-46029447 + CDS_or_noncoding_last_exon,S ENST00000245932.5 VASP vasodilator-stimulated

phosphoprotein

chr19_+_47823067 1.06 1.89 6.01E-02 chr19:47823067-47823117 + CDS_or_noncoding_last_exon,S ENST00000355085.2 C5AR1 complement component

5a receptor 1

chr19_+_47823182 2.52 -0.47 2.61E-02 chr19:47823182-47823190 + CDS_or_noncoding_last_exon,S ENST00000355085.2 C5AR1 complement component

5a receptor 1

chr19_+_47823341 1.09 0.80 8.56E-02 chr19:47823341-47823372 + CDS_or_noncoding_last_exon,S ENST00000355085.2 C5AR1 complement component

5a receptor 1


ENST00000246802.4/ENST00000325566.11/ENST00000446535.2

GLTSCR2 glioma tumor suppressor candidate region gene 2



MED25 mediator complex subunit 25

7676

Persson et al.

chr19_+_50985483 1.19 0.24 5.42E-02 chr19:50985483-50985561 + CDS_or_noncoding_inner_exon,S ENST00000376920.3 C19ORF63 NA



LILRA2

leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2

chr19_+_7437754 1.51 -0.26 5.17E-02 chr19:7437754-7437912 + intergenic intergenic NA NAchr19_+_7741934 0.57 4.35 4.76E-02 chr19:7741934-7742008 + TSS,S ENST00000333598.2 C19ORF59 NA


ENST00000438103.1/ENST00000361757.2/ENST00000250872.3

SBNO2 strawberry notch homolog 2 (Drosophila)

chr19_-_11446162 1.20 -0.14 6.41E-02 chr19:11446162-11446230 - CDS_or_noncoding_inner_exon,S ENST00000222120.2 RAB3D RAB3D, member RAS

oncogene family


ENST00000455140.1/ENST00000248070.5/ENST00000535753.1

EPS15L1epidermal growth factor receptor pathway substrate 15-like 1

chr19_-_18390851 -1.03 4.79 6.61E-02 chr19:18390851-18390917 - 3UTR_first_exon,S ENST00000252818.3 JUND jun D proto-oncogene

chr19_-_18632817 0.46 6.25 4.97E-02 chr19:18632817-18632938 - TSS,S ENST00000262809.3 ELL elongation factor RNA polymerase II

chr19_-_19754354 0.35 7.15 4.97E-02 chr19:19754354-19754491 - TSS,S ENST00000203556.3/ENST00000445806.2 GMIP GEM interacting protein

chr19_-_2078564 1.31 0.30 8.01E-02 chr19:2078564-2078670 - 5UTR_inner_exon,S ENST00000357066.2 MOB3A MOB kinase activator 3A

chr19_-_2085245 0.31 7.46 8.84E-02 chr19:2085245-2085433 - 5UTR_inner_exon,S ENST00000357066.2 MOB3A MOB kinase activator 3A

chr19_-_21751973 1.10 4.01 4.22E-02 chr19:21751973-21752084 - intergenic intergenic NA NAchr19_-_2950620 1.12 0.18 6.99E-02 chr19:2950620-2950696 - intergenic intergenic NA NA

chr19_-_3053158 -1.35 0.35 5.98E-02 chr19:3053158-3053209 - 3UTR_last_exon,S ENST00000327141.3/ENST00000221561.7 AES amino-terminal enhancer

of split

chr19_-_39322000 1.87 -0.16 7.73E-02 chr19:39322000-39322159 - CDS_or_noncoding_inner_exon,S ENST00000221418.3 ECH1 enoyl CoA hydratase 1,

peroxisomal



elongation factor 2

chr19_-_42133332 0.56 6.73 2.34E-02 chr19:42133332-42133491 - TSS,S ENST00000221954.2/ENST00000472081.1 CEACAM4

carcinoembryonic antigen-related cell adhesion molecule 4

7777

Persson et al.

chr19_-_42305662 0.96 1.83 8.21E-02 chr19:42305662-42305842 - CDS_or_noncoding_inner_intron,AS



chr19_-_4539957 0.46 7.19 3.29E-02 chr19:4539957-4540131 - TSS,S ENST00000306390.4/ENST00000538589.1 LRG1 leucine-rich alpha-2-

glycoprotein 1

chr19_-_52250183 1.43 1.59 2.90E-02 chr19:52250183-52250252 - 5UTR_last_exon,S ENST00000304748.3 FPR1 formyl peptide receptor 1

chr19_-_54824359 0.45 6.35 7.32E-02 chr19:54824359-54824495 - TSS,S


LILRA5

chr19_-_59065458 1.35 1.62 2.00E-02 chr19:59065458-59065616 - 5UTR_inner_exon,S ENST00000312547.1 CHMP2A charged multivesicular

body protein 2A


ENST00000305795.6/ENST00000338257.6 MYO1F myosin IF



UBE4B ubiquitination factor E4B


KIF1B kinesin family member 1B

chr1_+_10738533 1.70 0.31 3.71E-02 chr1:10738533-10738547 + CDS_or_noncoding_first_intron,AS ENST00000478728.2 CASZ1 castor zinc finger 1

chr1_+_110168930 2.49 -0.40 9.78E-03 chr1:110168930-110169018 + TSSregion500,S ENST00000534144.1 AMPD2adenosine monophosphate deaminase 2

chr1_+_116519121 0.70 2.26 6.70E-02 chr1:116519121-116519164 + TSSregion500,S ENST00000369503.4/ENST00000369502.1 SLC22A15 solute carrier family 22,

member 15

chr1_+_118167048 -0.90 4.47 9.97E-02 chr1:118167048-118167197 + 3UTR_last_exon,S ENST00000369448.3 FAM46C family with sequence similarity 46, member C

chr1_+_118167622 -1.03 4.60 5.52E-02 chr1:118167622-118167741 + 3UTR_last_exon,S ENST00000369448.3 FAM46C family with sequence similarity 46, member C

7878

Persson et al.


ENST00000400863.3/ENST00000376259.3/ENST00000492361.1

TNFRSF1Btumor necrosis factor receptor superfamily, member 1B

chr1_+_145438929 1.59 0.46 6.39E-02 chr1:145438929-145438932 + TSSregion500,S ENST00000425134.1 TXNIP

cDNA FLJ61424, highly similar to Homo sapiens thioredoxin interacting protein (TXNIP), mRNA

chr1_+_145440653 0.91 3.61 8.59E-02 chr1:145440653-145440758 + TSSregion500,S ENST00000486597.1 TXNIP

cDNA FLJ61424, highly similar to Homo sapiens thioredoxin interacting protein (TXNIP), mRNA

chr1_+_15045198 -1.45 -0.15 7.85E-02 chr1:15045198-15045205 + CDS_or_noncoding_first_intron,S

ENST00000376030.2/ENST00000422387.2/ENST00000491547.1

KAZN kazrin, periplakin interacting protein

chr1_+_151584479 0.43 6.03 2.51E-02 chr1:151584479-151584677 + TSS,S


SNX27 sorting nexin family member 27

chr1_+_153963219 -0.41 10.70 6.06E-02 chr1:153963219-153963285 + TSS,S




IL6R interleukin 6 receptor

chr1_+_154401669 1.73 -0.22 7.33E-02 chr1:154401669-154401846 + TSS,S ENST00000476006.1 IL6R interleukin 6 receptor

chr1_+_156783987 -1.44 0.41 5.72E-02 chr1:156783987-156784186 + TSSregion500,AS ENST00000468744.1 SH2D2A SH2 domain containing 2A


ENST00000375980.4/ENST00000375975.4/ENST00000445566.1

EFHD2 EF-hand domain family, member D2

chr1_+_158813119 0.72 3.80 1.27E-02 chr1:158813119-158813171 + CDS_or_noncoding_inner_exon,S ENST00000368141.4 MNDA myeloid cell nuclear

differentiation antigen


ENST00000367972.4/ENST00000271450.6/ENST00000467525.1

FCGR2AFc fragment of IgG, low affinity IIa, receptor (CD32)

7979

Persson et al.

chr1_+_167190109 0.46 3.83 6.41E-02 chr1:167190109-167190173 + TSS,S


POU2F1 POU class 2 homeobox 1

chr1_+_168213964 -1.94 -0.24 4.15E-02 chr1:168213964-168214114 + intergenic intergenic NA NAchr1_+_168220751 -1.48 -0.46 8.36E-02 chr1:168220751-168220948 + intergenic intergenic NA NA



PRRC2C proline-rich coiled-coil 2C


PADI4 peptidyl arginine deiminase, type IV

chr1_+_17668433 1.59 0.78 2.52E-03 chr1:17668433-17668588 + CDS_or_noncoding_inner_exon,S ENST00000375448.4 PADI4 peptidyl arginine

deiminase, type IV


RGS18 regulator of G-protein signaling 18


ENST00000235382.5/ENST00000464302.1/ENST00000487236.1

RGS2 regulator of G-protein signaling 2, 24kDa

chr1_+_192780102 0.68 3.72 9.38E-02 chr1:192780102-192780239 + CDS_or_noncoding_inner_exon,S ENST00000235382.5 RGS2 regulator of G-protein

signaling 2, 24kDa

chr1_+_192780771 1.40 0.72 5.83E-02 chr1:192780771-192780786 + 3UTR_last_exon,S ENST00000235382.5 RGS2 regulator of G-protein signaling 2, 24kDa

chr1_+_203276397 1.09 2.17 8.17E-03 chr1:203276397-203276438 + CDS_or_noncoding_inner_exon,S ENST00000475157.1 BTG2 BTG family, member 2

chr1_+_204524120 -1.49 0.16 9.38E-02 chr1:204524120-204524273 + 3UTR_last_exon,S ENST00000367182.3 MDM4 Mdm4 p53 binding protein homolog (mouse)

8080

Persson et al.



CD55

CD55 molecule, decay accelerating factor for complement (Cromer blood group)



CD55

CD55 molecule, decay accelerating factor for complement (Cromer blood group)

chr1_+_207669486 0.50 4.93 5.54E-02 chr1:207669486-207669633 + TSS,S


CR1complement component (3b/4b) receptor 1 (Knops blood group)

chr1_+_209849199 1.52 3.44 2.63E-02 chr1:209849199-209849309 + CDS_or_noncoding_last_exon,S ENST00000367029.4 G0S2 G0/G1switch 2



TRAF3IP3 TRAF3 interacting protein 3

8181

Persson et al.


ENST00000361395.2/ENST00000366938.2 ESRRG estrogen-related

receptor gamma

chr1_+_21835839 0.57 6.26 6.76E-02 chr1:21835839-21835964 + TSS,S


ALPL alkaline phosphatase, liver/bone/kidney



ALPL alkaline phosphatase, liver/bone/kidney

chr1_+_220960195 0.76 4.65 1.02E-02 chr1:220960195-220960282 + TSSregion500,S ENST00000366910.5 MOSC1 NAchr1_+_228333714 1.51 -0.26 5.69E-02 chr1:228333714-228333737 + TSS,S ENST00000470155.1 GUK1 guanylate kinase 1chr1_+_228675040 -0.41 6.51 7.81E-02 chr1:228675040-228675163 + TSSregion500,S ENST00000305943.7 RNF187 ring finger protein 187

chr1_+_231762403 0.74 3.52 1.24E-02 chr1:231762403-231762591 + TSS,S


DISC1 disrupted in schizophrenia 1


ENST00000407071.2/ENST00000366518.3/ENST00000413001.1

KIF26B kinesin family member 26B

chr1_+_246729735 0.55 2.58 7.83E-02 chr1:246729735-246729760 + TSS,S ENST00000366513.4/ENST00000483271.1 CNST consortin, connexin

sorting protein




ENST00000324856.7/ENST00000457599.2 ARID1A AT rich interactive

domain 1A (SWI-like)

8282

Persson et al.

chr1_+_27153156 0.37 7.86 4.15E-02 chr1:27153156-27153248 + TSS,S ENST00000374142.3 ZDHHC18 zinc finger, DHHC-type containing 18

chr1_+_27153466 0.75 3.40 1.67E-02 chr1:27153466-27153577 + CDS_or_noncoding_first_exon,S ENST00000374142.3 ZDHHC18 zinc finger, DHHC-type

containing 18

chr1_+_27155427 0.86 1.93 9.36E-02 chr1:27155427-27155490 + CDS_or_noncoding_first_intron,S ENST00000374142.3 ZDHHC18 zinc finger, DHHC-type

containing 18chr1_+_28203084 0.87 3.13 4.95E-02 chr1:28203084-28203220 + TSS,S ENST00000482828.1 C1ORF38 NA

chr1_+_28293927 1.38 -0.03 6.02E-02 chr1:28293927-28293989 + 3UTR_last_exon,S ENST00000373884.5 XKR8XK, Kell blood group complex subunit-related family, member 8

chr1_+_29444273 -1.44 2.25 1.49E-02 chr1:29444273-29444361 + CDS_or_noncoding_last_exon,S ENST00000460378.1 EPB41

erythrocyte membrane protein band 4.1 (elliptocytosis 1, RH-linked)

chr1_+_29445644 -0.99 1.67 8.21E-02 chr1:29445644-29445798 + CDS_or_noncoding_last_exon,S ENST00000460378.1 EPB41



ENST00000429533.2/ENST00000530729.1 MAP7D1 MAP7 domain containing

1


ENST00000354618.5/ENST00000469141.2/ENST00000478853.1

THRAP3thyroid hormone receptor associated protein 3



ENST00000372797.3/ENST00000372802.1/ENST00000449311.1/ENST00000421589.1/ENST00000414893.1/ENST00000414281.1/ENST00000420216.1/ENST00000372792.2/ENST00000538246.1/ENST00000372798.1/ENST00000340450.3/ENST00000372805.3/ENST00000435719.1/ENST00000372794.2/ENST00000427843.1/ENST00000417287.1/ENST00000424977.1/ENST00000446031.1

CAP1CAP, adenylate cyclase-associated protein 1 (yeast)

chr1_+_40840055 1.43 1.48 2.34E-02 chr1:40840055-40840132 + TSSregion500,S ENST00000372708.1 SMAP2 small ArfGAP2

8383

Persson et al.

chr1_+_41157630 1.06 2.68 9.78E-03 chr1:41157630-41157686 + TSS,S ENST00000534399.1/ENST00000372653.1 NFYC nuclear transcription

factor Y, gamma

chr1_+_76540373 0.68 3.06 8.73E-02 chr1:76540373-76540543 + TSS,S ENST00000394994.3/ENST00000328299.3 ST6GALNAC3

ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3

chr1_+_85236844 -1.13 1.16 7.06E-02 chr1:85236844-85236854 + intergenic intergenic NA NAchr1_+_88012617 -0.71 3.18 8.61E-02 chr1:88012617-88012624 + intergenic intergenic NA NA


PKN2 protein kinase N2



CSDE1cold shock domain containing E1, RNA-binding

chr1_-_115292733 1.56 1.44 3.36E-02 chr1:115292733-115292841 - TSS,S ENST00000438362.2 CSDE1cold shock domain containing E1, RNA-binding


ENST00000271638.2/ENST00000478109.1 S100A11 S100 calcium binding

protein A11

chr1_-_154573958 0.71 3.13 2.75E-02 chr1:154573958-154574098 - CDS_or_noncoding_first_exon,S ENST00000529168.1 ADAR adenosine deaminase,

RNA-specificchr1_-_159046537 0.58 3.02 7.35E-02 chr1:159046537-159046735 - TSS,S ENST00000368130.4 AIM2 absent in melanoma 2

chr1_-_160654751 1.44 1.41 7.50E-03 chr1:160654751-160654816 - CDS_or_noncoding_inner_exon,S ENST00000368046.3 CD48 CD48 molecule

chr1_-_169555626 0.64 4.66 1.38E-02 chr1:169555626-169555796 - TSS,S ENST00000546081.1 F5coagulation factor V (proaccelerin, labile factor)

chr1_-_176175769 0.87 1.44 5.34E-02 chr1:176175769-176175878 - TSS,S ENST00000367667.1 RFWD2ring finger and WD repeat domain 2, E3 ubiquitin protein ligase



8484

Persson et al.

chr1_-_182763979 0.89 1.90 1.93E-02 chr1:182763979-182764106 - 5UTR_first_intron,AS

ENST00000367551.3/ENST00000445965.2/ENST00000367554.3

NPL

N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)


NCF2 neutrophil cytosolic factor 2

chr1_-_184943554 0.45 7.34 2.34E-02 chr1:184943554-184943673 - TSSregion500,S ENST00000367511.3 FAM129A family with sequence similarity 129, member A

chr1_-_202910139 -1.28 2.59 4.99E-02 chr1:202910139-202910222 - CDS_or_noncoding_last_exon,S ENST00000495562.1 ADIPOR1 adiponectin receptor 1

chr1_-_21616907 0.56 3.93 6.33E-02 chr1:21616907-21616966 - TSS,S ENST00000436918.2/ENST00000526194.1 ECE1 endothelin converting

enzyme 1

chr1_-_225609805 1.19 0.81 4.37E-02 chr1:225609805-225609973 - TSSregion500,S ENST00000488632.1 LBR lamin B receptor

chr1_-_226820555 -1.93 0.00 9.14E-02 chr1:226820555-226820652 - 3UTR_last_exon,S ENST00000272117.3/ENST00000429204.1 ITPKB inositol-trisphosphate 3-

kinase B




chr1_-_243418501 0.75 3.41 4.29E-03 chr1:243418501-243418586 - TSS,S ENST00000522522.1/ENST00000523581.1 CEP170 centrosomal protein

170kDa

chr1_-_245027309 0.81 3.65 3.40E-02 chr1:245027309-245027470 - TSSregion500,S ENST00000483966.1/ENST00000476241.1 HNRNPU

heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)


ENST00000373857.3/ENST00000539896.1/ENST00000305392.3

PTAFR platelet-activating factor receptor


ENST00000294507.3/ENST00000424259.2/ENST00000464569.1

LAPTM5 lysosomal protein transmembrane 5


ENST00000373416.1/ENST00000373418.3 PHC2 polyhomeotic homolog 2

(Drosophila)

chr1_-_36941018 0.75 4.00 9.06E-02 chr1:36941018-36941126 - TSSregion500,S ENST00000464365.2 CSF3R colony stimulating factor 3 receptor (granulocyte)

8585

Persson et al.

chr1_-_36948439 0.38 9.18 4.15E-02 chr1:36948439-36948567 - TSS,S ENST00000526980.1/ENST00000489551.1 CSF3R colony stimulating factor

3 receptor (granulocyte)

chr1_-_45987517 -0.39 5.94 8.82E-02 chr1:45987517-45987710 - TSS,S


PRDX1 peroxiredoxin 1

chr1_-_98386462 0.40 8.08 2.97E-02 chr1:98386462-98386637 - TSS,S



chr20_+_15497339 -0.85 2.33 4.44E-02 chr20:15497339-15497349 + 5UTR_inner_intron,S ENST00000402914.1 MACROD2 MACRO domain

containing 2

chr20_+_24911243 1.78 1.08 9.20E-04 chr20:24911243-24911352 + CDS_or_noncoding_last_exon,AS ENST00000508332.1 AL035661.1 NA

chr20_+_390518 1.44 -0.41 5.56E-02 chr20:390518-390631 + TSS,S ENST00000414880.1 RBCK1RanBP-type and C3HC4-type zinc finger containing 1

chr20_+_39657421 0.35 7.39 9.33E-02 chr20:39657421-39657533 + TSS,S ENST00000361337.2 TOP1 topoisomerase (DNA) I

chr20_+_48429216 0.76 3.28 4.66E-02 chr20:48429216-48429302 + TSS,S ENST00000417961.1 SLC9A8


chr20_+_54987221 0.42 5.70 6.25E-02 chr20:54987221-54987332 + TSS,S ENST00000371336.3/ENST00000434344.1 CASS4 Cas scaffolding protein

family member 4



CASS4 Cas scaffolding protein family member 4



C20ORF43 NA


8686

Persson et al.



GNAS GNAS complex locus

chr20_+_60126569 -0.83 2.21 6.47E-02 chr20:60126569-60126580 + CDS_or_noncoding_inner_intron,S ENST00000360469.4 CDH4 cadherin 4, type 1, R-

cadherin (retinal)



TPD52L2 tumor protein D52-like 2

chr20_+_641294 0.67 3.37 9.38E-02 chr20:641294-641469 + CDS_or_noncoding_first_intron,AS ENST00000488788.1 SRXN1

CDNA FLJ25552 fis, clone JTH02127; HBV preS1-transactivated protein 5; Sulfiredoxin 1 homolog (S. cerevisiae), isoform CRA_a; Uncharacterized protein

chr20_-_1350022 -1.94 -0.30 3.04E-02 chr20:1350022-1350071 - 3UTR_last_exon,S ENST00000400137.4 FKBP1A FK506 binding protein 1A, 12kDa


ENST00000429387.1/ENST00000381621.1/ENST00000381623.3

SIRPD signal-regulatory protein delta



chr20_-_35519412 -1.40 -0.16 6.10E-02 chr20:35519412-35519538 - 3UTR_last_exon,S ENST00000262878.4 SAMHD1 SAM domain and HD domain 1

chr20_-_3996108 0.47 6.77 1.72E-02 chr20:3996108-3996301 - TSS,S ENST00000358395.6/ENST00000545616.1 RNF24 ring finger protein 24

chr20_-_46365548 1.11 2.32 3.86E-02 chr20:46365548-46365698 - TSS,S ENST00000478766.1 SULF2 sulfatase 2chr20_-_46414166 0.67 4.73 1.90E-02 chr20:46414166-46414260 - TSS,S ENST00000437955.1 SULF2 sulfatase 2


ENST00000371941.3/ENST00000396220.1 PREX1


8787

Persson et al.


ENST00000371941.3/ENST00000396220.1 PREX1


chr20_-_48330352 0.58 5.06 1.04E-02 chr20:48330352-48330483 - TSS,S ENST00000371711.4 B4GALT5

UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5



chr21_+_30671121 0.39 6.82 6.76E-02 chr21:30671121-30671276 + TSS,S ENST00000286800.3 BACH1BTB and CNC homology 1, basic leucine zipper transcription factor 1


ENST00000547341.1/ENST00000547595.1/ENST00000548700.1



ENST00000547341.1/ENST00000547595.1/ENST00000548700.1



ENST00000547341.1/ENST00000547595.1/ENST00000548700.1


chr21_+_39668828 1.65 -0.39 5.83E-02 chr21:39668828-39668898 + TSS,S ENST00000419868.1 KCNJ15potassium inwardly-rectifying channel, subfamily J, member 15




8888

Persson et al.




chr21_+_45719910 -0.28 5.55 6.10E-02 chr21:45719910-45720042 + TSS,S


PFKL phosphofructokinase, liver

chr21_+_46937836 0.84 2.01 6.49E-02 chr21:46937836-46938013 + CDS_or_noncoding_inner_intron,AS

ENST00000417954.1/ENST00000380014.2 SLC19A1

solute carrier family 19 (folate transporter), member 1

chr22_+_17565815 0.43 7.93 3.57E-02 chr22:17565815-17565966 + TSS,S


IL17RA interleukin 17 receptor A



chr22_+_23260269 -1.27 -0.22 8.35E-02 chr22:23260269-23260341 + CDS_or_noncoding_first_exon,S ENST00000390328.2 IGLJ6 immunoglobulin lambda

joining 6

chr22_+_31608191 0.46 6.93 3.92E-02 chr22:31608191-31608381 + TSS,S


LIMK2 LIM domain kinase 2


NCF4 neutrophil cytosolic factor 4, 40kDa


ENST00000248899.6/ENST00000397147.4/ENST00000415063.1

NCF4 neutrophil cytosolic factor 4, 40kDa


CSF2RB

colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)

8989

Persson et al.

chr22_+_37319274 0.92 2.79 8.79E-02 chr22:37319274-37319334 + TSSregion500,S ENST00000536485.1 CSF2RB




CSF2RB


chr22_+_37688657 1.70 -0.22 2.50E-02 chr22:37688657-37688753 + TSSregion500,S ENST00000467664.1 CYTH4 cytohesin 4

chr22_+_38071589 -0.57 7.06 3.50E-02 chr22:38071589-38071690 + TSS,S


LGALS1 lectin, galactoside-binding, soluble, 1

chr22_+_39348673 0.34 7.13 6.96E-02 chr22:39348673-39348788 + TSS,S ENST00000402255.1/ENST00000495988.1 APOBEC3A

apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A

chr22_+_40367790 -1.30 0.20 6.41E-02 chr22:40367790-40367865 + 3UTR_last_exon,S ENST00000344138.4/ENST00000544006.1 GRAP2 GRB2-related adaptor

protein 2

chr22_+_41488564 0.63 4.96 1.13E-02 chr22:41488564-41488632 + 5UTR_first_exon,S ENST00000263253.7 EP300 E1A binding protein

p300


ENST00000381031.3/ENST00000445282.2/ENST00000451998.1

TTC38 tetratricopeptide repeat domain 38


MAPK1 mitogen-activated protein kinase 1


PPM1Fprotein phosphatase, Mg2+/Mn2+ dependent, 1F

chr22_-_30742329 0.89 2.13 5.14E-02 chr22:30742329-30742519 - TSS,S ENST00000471342.1 SF3A1 splicing factor 3a, subunit 1, 120kDa

9090

Persson et al.




chr22_-_37532297 1.72 0.11 6.41E-02 chr22:37532297-37532440 - TSSregion500,S ENST00000483573.1 IL2RB interleukin 2 receptor, beta

chr22_-_42828270 0.42 8.17 2.28E-02 chr22:42828270-42828460 - TSS,S ENST00000329021.5/ENST00000355469.4 NFAM1 NFAT activating protein

with ITAM motif 1

chr22_-_43411034 0.38 6.42 5.38E-02 chr22:43411034-43411208 - TSS,S


PACSIN2protein kinase C and casein kinase substrate in neurons 2

chr2_+_102314123 0.58 6.65 1.63E-03 chr2:102314123-102314207 + TSS,S ENST00000425019.1 MAP4K4mitogen-activated protein kinase kinase kinase kinase 4

chr2_+_102314454 1.81 -0.13 1.25E-02 chr2:102314454-102314482 + TSS,SENST00000302217.5/ENST00000324219.4/ENST00000350198.4

MAP4K4mitogen-activated protein kinase kinase kinase kinase 4

chr2_+_102578487 0.74 2.94 5.92E-02 chr2:102578487-102578594 + TSS,S ENST00000508786.1 AC005035.2 NA




chr2_+_170684269 2.14 -0.86 3.71E-02 chr2:170684269-170684432 + CDS_or_noncoding_first_exon,S

ENST00000272793.5/ENST00000442603.1/ENST00000418381.1

UBR3ubiquitin protein ligase E3 component n-recognin 3 (putative)

chr2_+_192543694 0.60 3.16 7.36E-02 chr2:192543694-192543736 + TSS,S ENST00000435931.1 OBFC2A NAchr2_+_199716837 -0.60 4.93 8.82E-02 chr2:199716837-199716853 + intergenic intergenic NA NA

chr2_+_201980869 0.35 7.81 4.02E-02 chr2:201980869-201981060 + TSS,S


CFLAR CASP8 and FADD-like apoptosis regulator

9191

Persson et al.

chr2_+_209130906 0.46 6.37 3.79E-02 chr2:209130906-209131086 + TSS,S


PIKFYVE phosphoinositide kinase, FYVE finger containing

chr2_+_216981374 1.01 2.07 2.88E-02 chr2:216981374-216981567 + TSSregion500,S ENST00000460284.1 XRCC5

X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)

chr2_+_217363518 -0.41 10.32 6.46E-02 chr2:217363518-217363623 + TSS,S



chr2_+_219082177 1.35 1.39 4.02E-02 chr2:219082177-219082213 + TSS,S ENST00000465395.1 ARPC2actin related protein 2/3 complex, subunit 2, 34kDa

chr2_+_219100132 -0.94 1.66 9.00E-02 chr2:219100132-219100261 + TSSregion500,S ENST00000477992.1 ARPC2actin related protein 2/3 complex, subunit 2, 34kDa

chr2_+_219246723 1.03 0.94 9.70E-02 chr2:219246723-219246756 + TSS,S ENST00000233202.6/ENST00000468221.1 SLC11A1

solute carrier family 11 (proton-coupled divalent metal ion transporters), member 1

chr2_+_219246887 0.62 7.86 9.20E-04 chr2:219246887-219247077 + TSS,S


SLC11A1


chr2_+_219249876 1.19 1.61 1.15E-02 chr2:219249876-219249970 + TSS,S ENST00000460592.1 SLC11A1


9292

Persson et al.

chr2_+_219610206 0.72 3.42 2.90E-02 chr2:219610206-219610350 + TSS,S ENST00000494428.1 TTLL4 tubulin tyrosine ligase-like family, member 4

chr2_+_232326246 -1.18 1.29 7.85E-02 chr2:232326246-232326433 + CDS_or_noncoding_inner_exon,AS


NCL nucleolin

chr2_+_238536151 1.04 1.53 5.36E-02 chr2:238536151-238536288 + TSS,S ENST00000308482.9/ENST00000465870.1 LRRFIP1 leucine rich repeat (in

FLII) interacting protein 1



LRRFIP1 leucine rich repeat (in FLII) interacting protein 1







chr2_+_24714107 0.39 5.84 6.41E-02 chr2:24714107-24714155 + upstream1000,S


NCOA1 nuclear receptor coactivator 1

chr2_+_28618534 0.39 4.61 9.46E-02 chr2:28618534-28618609 + TSS,S ENST00000545753.1 FOSL2 FOS-like antigen 2


PPP1CBprotein phosphatase 1, catalytic subunit, beta isozyme

chr2_+_37571768 0.46 6.98 3.64E-02 chr2:37571768-37571897 + TSS,S ENST00000537448.1/ENST00000470075.1 QPCT glutaminyl-peptide

cyclotransferase

9393

Persson et al.


ENST00000338415.3/ENST00000470075.1 QPCT glutaminyl-peptide

cyclotransferase



QPCT glutaminyl-peptide cyclotransferase

chr2_+_37844443 1.21 0.97 3.95E-02 chr2:37844443-37844534 + CDS_or_noncoding_inner_intron,S ENST00000419425.1 AC006369.2


ENST00000356805.4/ENST00000467371.1 SPTBN1 spectrin, beta, non-

erythrocytic 1


chr2_+_68607452 0.97 2.48 4.23E-02 chr2:68607452-68607579 + CDS_or_noncoding_inner_exon,S ENST00000234313.7 PLEK pleckstrin


ENST00000234313.7/ENST00000474788.1 PLEK pleckstrin

chr2_+_68623050 0.76 1.84 8.73E-02 chr2:68623050-68623206 + 3UTR_last_exon,S ENST00000234313.7 PLEK pleckstrin



DYSFdysferlin, limb girdle muscular dystrophy 2B (autosomal recessive)







9494

Persson et al.

chr2_+_71804280 1.47 0.67 1.26E-02 chr2:71804280-71804359 + CDS_or_noncoding_first_intron,S ENST00000475076.1 DYSF

dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive)



CCT7 chaperonin containing TCP1, subunit 7 (eta)

chr2_+_74212020 0.62 3.65 2.35E-02 chr2:74212020-74212167 + TSSregion500,S ENST00000441217.1 AC073046.25chr2_+_7865810 -0.74 4.90 1.68E-02 chr2:7865810-7865995 + TSS,S ENST00000417930.1 AC092580.4chr2_+_85132767 -0.40 10.64 1.63E-02 chr2:85132767-85132811 + TSSregion500,S ENST00000233143.4 TMSB10 thymosin beta 10


ENST00000424632.1/ENST00000295317.3 RNF149 ring finger protein 149

chr2_-_101925032 0.30 9.22 6.68E-02 chr2:101925032-101925202 - TSS,S ENST00000424632.1/ENST00000295317.3 RNF149 ring finger protein 149

chr2_-_127453574 -2.41 -0.18 6.61E-02 chr2:127453574-127453653 - CDS_or_noncoding_last_exon,AS


GYPC glycophorin C (Gerbich blood group)

chr2_-_128145482 0.36 6.42 3.36E-02 chr2:128145482-128145644 - TSS,S ENST00000409179.2 MAP3K2mitogen-activated protein kinase kinase kinase 2

chr2_-_133012865 -1.14 5.90 4.06E-02 chr2:133012865-133012913 - CDS_or_noncoding_first_intron,S ENST00000470729.1 ANKRD30BL ankyrin repeat domain

30B-likechr2_-_133038162 -0.71 3.20 8.15E-02 chr2:133038162-133038243 - intergenic intergenic NA NA


ENST00000540637.1/ENST00000264192.3/ENST00000418920.1

CYTIP cytohesin 1 interacting protein

chr2_-_160472897 0.53 5.85 2.89E-02 chr2:160472897-160473078 - TSS,S


BAZ2B bromodomain adjacent to zinc finger domain, 2B

9595

Persson et al.










chr2_-_198175391 0.45 6.99 2.87E-02 chr2:198175391-198175567 - TSS,S



chr2_-_202245651 -1.41 0.50 6.21E-02 chr2:202245651-202245660 - CDS_or_noncoding_inner_exon,S ENST00000542292.1 TRAK2 trafficking protein,

kinesin binding 2

chr2_-_231077512 1.00 2.55 4.23E-02 chr2:231077512-231077673 - TSS,S ENST00000486146.1 SP110 SP110 nuclear body protein

chr2_-_235403494 -2.04 -0.36 4.21E-02 chr2:235403494-235403598 - 3UTR_first_exon,S ENST00000390645.2 ARL4C ADP-ribosylation factor-

like 4C

chr2_-_235403833 -1.51 0.07 2.54E-02 chr2:235403833-235403954 - 3UTR_first_exon,S ENST00000390645.2 ARL4C ADP-ribosylation factor-

like 4C

chr2_-_235405663 -0.96 2.25 5.19E-02 chr2:235405663-235405664 - TSSregion500,S ENST00000390645.2/ENST00000339728.3 ARL4C ADP-ribosylation factor-

like 4C

9696

Persson et al.

chr2_-_24583288 0.41 6.18 4.46E-02 chr2:24583288-24583431 - TSS,S


ITSN2 intersectin 2

chr2_-_27294239 0.80 1.56 6.97E-02 chr2:27294239-27294240 - TSSregion500,S ENST00000429985.1 OST4oligosaccharyltransferase 4 homolog (S. cerevisiae)

chr2_-_27294243 0.75 3.80 1.40E-02 chr2:27294243-27294261 - TSSregion500,S ENST00000429985.1 OST4oligosaccharyltransferase 4 homolog (S. cerevisiae)

chr2_-_37898705 0.50 7.03 2.02E-02 chr2:37898705-37898841 - TSSregion500,S ENST00000295324.3 CDC42EP3 CDC42 effector protein (Rho GTPase binding) 3



chr2_-_61698201 0.68 3.90 2.34E-02 chr2:61698201-61698395 - TSSregion500,S ENST00000398571.2/ENST00000453133.1 USP34 ubiquitin specific

peptidase 34

chr2_-_64502577 0.66 3.05 4.15E-02 chr2:64502577-64502686 - intergenic intergenic NA NAchr2_-_74381768 -1.29 1.34 8.18E-02 chr2:74381768-74381872 - intergenic intergenic NA NA


ENST00000258439.2/ENST00000432959.1/ENST00000435268.1



chr3_+_122513657 0.79 3.53 3.92E-02 chr3:122513657-122513757 + TSSregion500,S ENST00000261038.5/ENST00000477647.1 DIRC2 disrupted in renal

carcinoma 2

chr3_+_122513900 0.64 4.34 5.75E-03 chr3:122513900-122513988 + TSS,S ENST00000477647.1 DIRC2 disrupted in renal carcinoma 2

chr3_+_129295962 -2.03 -0.66 7.43E-02 chr3:129295962-129296081 + CDS_or_noncoding_first_intron,AS ENST00000505505.1 PLXND1 plexin D1

chr3_+_134204894 0.45 5.63 7.80E-02 chr3:134204894-134205087 + TSS,S


CEP63 centrosomal protein 63kDa


9797

Persson et al.


EPHB1 EPH receptor B1

chr3_+_134334086 0.73 2.88 2.23E-02 chr3:134334086-134334242 + TSS,S ENST00000460895.1 EPHB1 EPH receptor B1




chr3_+_14444052 0.39 8.36 4.19E-02 chr3:14444052-14444251 + TSS,S


SLC6A6

solute carrier family 6 (neurotransmitter transporter, taurine), member 6

chr3_+_152132711 0.87 2.79 4.15E-02 chr3:152132711-152132878 + TSS,S ENST00000478535.1/ENST00000460166.1 MBNL1 muscleblind-like splicing

regulator 1

chr3_+_152173823 -2.07 -0.61 2.66E-02 chr3:152173823-152173858 + CDS_or_noncoding_inner_intron,S



chr3_+_152180436 -1.30 0.52 3.56E-02 chr3:152180436-152180459 + CDS_or_noncoding_last_exon,S ENST00000497971.1 MBNL1 muscleblind-like splicing

regulator 1

chr3_+_152881837 -1.21 2.56 8.21E-02 chr3:152881837-152881954 + 3UTR_first_exon,S ENST00000323534.2 RAP2B RAP2B, member of RAS

oncogene family

chr3_+_154797641 0.45 5.41 6.58E-02 chr3:154797641-154797694 + TSS,S ENST00000481828.1 MME membrane metallo-endopeptidase

9898

Persson et al.



MME membrane metallo-endopeptidase


MME membrane metallo-endopeptidase



chr3_+_182511253 0.37 6.74 6.84E-02 chr3:182511253-182511417 + TSS,S ENST00000323116.5/ENST00000493826.1 ATP11B ATPase, class VI, type

11B





chr3_+_196509483 1.41 0.48 3.64E-02 chr3:196509483-196509678 + 5UTR_inner_exon,S ENST00000327134.3 PAK2

p21 protein (Cdc42/Rac)-activated kinase 2


ENST00000327134.3/ENST00000488224.2 PAK2

p21 protein (Cdc42/Rac)-activated kinase 2

chr3_+_24215269 1.86 -0.22 4.06E-02 chr3:24215269-24215356 + CDS_or_noncoding_inner_intron,AS



9999

Persson et al.





TGFBR2transforming growth factor, beta receptor II (70/80kDa)


ENST00000383765.3/ENST00000439925.2 TGFBR2

transforming growth factor, beta receptor II (70/80kDa)

chr3_+_32071636 -0.85 0.92 6.41E-02 chr3:32071636-32071652 + TSSregion500,S ENST00000428586.1 RPL21P40 ribosomal protein L21 pseudogene 40


ABHD5 abhydrolase domain containing 5


ENST00000456453.1/ENST00000454293.1 ABHD5 abhydrolase domain

containing 5

chr3_+_47029431 0.41 6.53 2.50E-02 chr3:47029431-47029533 + TSS,S ENST00000296147.3 NBEAL2 neurobeachin-like 2



RBM5 RNA binding motif protein 5

chr3_+_50289821 0.84 2.37 5.42E-02 chr3:50289821-50289947 + 5UTR_inner_exon, ENST00000536647.1 GNAI2 guanine nucleotide

100100

Persson et al.

Sbinding protein (G protein), alpha inhibiting activity polypeptide 2

chr3_+_50290446 0.72 4.60 8.17E-02 chr3:50290446-50290591 + TSS,S ENST00000468422.1 GNAI2

guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2



GNAI2

guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2

chr3_+_53195520 0.51 3.90 3.34E-02 chr3:53195520-53195563 + TSS,S ENST00000487897.1 PRKCD protein kinase C, delta



CACNA2D3calcium channel, voltage-dependent, alpha 2/delta subunit 3


ENST00000539129.1/ENST00000538065.1 ATXN7 ataxin 7



SLC25A26solute carrier family 25 (S-adenosylmethionine carrier), member 26



SLC25A26solute carrier family 25 (S-adenosylmethionine carrier), member 26

chr3_+_71803493 0.53 4.41 7.82E-02 chr3:71803493-71803677 + CDS_or_noncoding_first_exon,S ENST00000304411.2 GPR27 G protein-coupled

receptor 27chr3_+_71900002 1.43 1.48 2.38E-02 chr3:71900002-71900172 + intergenic intergenic NA NA

101101

Persson et al.

chr3_+_72128314 -1.71 0.07 8.17E-03 chr3:72128314-72128352 + CDS_or_noncoding_first_intron,AS ENST00000470712.1 RP11-398A8.3



HCLS1 hematopoietic cell-specific Lyn substrate 1



HCLS1 hematopoietic cell-specific Lyn substrate 1

chr3_-_122233636 0.36 6.50 4.36E-02 chr3:122233636-122233829 - TSS,S


KPNA1 karyopherin alpha 1 (importin alpha 5)



PARP9poly (ADP-ribose) polymerase family, member 9

chr3_-_122512503 0.59 4.62 1.72E-02 chr3:122512503-122512701 - TSS,S


HSPBAP1HSPB (heat shock 27kDa) associated protein 1



CNBPCCHC-type zinc finger, nucleic acid binding protein

102102

Persson et al.


ENST00000312960.3/ENST00000482706.1 SIAH2 siah E3 ubiquitin protein

ligase 2


chr3_-_167441788 1.32 -0.07 6.33E-02 chr3:167441788-167441886 - 5UTR_first_intron,S


PDCD10 programmed cell death 10


ENST00000406870.2/ENST00000232014.4/ENST00000450123.2

BCL6 B-cell CLL/lymphoma 6

chr3_-_187461786 0.94 0.91 9.44E-02 chr3:187461786-187461894 - 5UTR_first_intron,S ENST00000406870.2 BCL6 B-cell CLL/lymphoma 6


BCL6 B-cell CLL/lymphoma 6


ACAP2ArfGAP with coiled-coil, ankyrin repeat and PH domains 2


CCDC13 coiled-coil domain containing 13

chr3_-_44463096 1.54 0.13 7.09E-02 chr3:44463096-44463294 - CDS_or_noncoding_last_exon,S ENST00000416124.1 RP11-

101C21.1


ENST00000418115.1/ENST00000422781.1/ENST00000445425.1

RHOA ras homolog family member A

chr3_-_71834165 0.51 6.21 3.41E-02 chr3:71834165-71834351 - TSS,S ENST00000295619.3 PROK2 prokineticin 2

chr3_-_71834513 0.76 3.64 1.72E-02 chr3:71834513-71834599 - TSSregion500,S ENST00000353065.3/ENST00000295619.3 PROK2 prokineticin 2

chr3_-_81810672 0.69 3.32 1.05E-02 chr3:81810672-81810857 - TSS,S ENST00000264326.4/ENST00000536832.1 GBE1 glucan (1,4-alpha-),

branching enzyme 1



DAPP1dual adaptor of phosphotyrosine and 3-phosphoinositides

103103

Persson et al.



TET2 tet methylcytosine dioxygenase 2






chr4_+_113218425 0.56 6.82 5.47E-03 chr4:113218425-113218601 + TSS,S



chr4_+_11370217 -0.64 3.79 7.43E-02 chr4:11370217-11370254 + upstream1000,S ENST00000384983.1 MIR572 microRNA 572chr4_+_123073450 0.46 6.00 7.43E-02 chr4:123073450-123073647 + TSS,S ENST00000264501.4 KIAA1109 KIAA1109

chr4_+_144257306 0.77 2.34 4.55E-02 chr4:144257306-144257366 + CDS_or_noncoding_last_exon,AS ENST00000317872.3 AC097658.1

chr4_+_144257546 0.80 2.69 1.24E-02 chr4:144257546-144257682 + TSSregion500,S ENST00000262995.4/ENST00000262994.4 GAB1 GRB2-associated

binding protein 1

104104

Persson et al.




chr4_+_15964123 -1.84 0.59 3.05E-02 chr4:15964123-15964302 + CDS_or_noncoding_first_exon,AS ENST00000259989.6 FGFBP2 fibroblast growth factor

binding protein 2

chr4_+_166128707 0.52 5.17 3.53E-02 chr4:166128707-166128835 + TSS,S ENST00000226725.6 KLHL2 kelch-like 2, Mayven (Drosophila)



TACC3transforming, acidic coiled-coil containing protein 3


LAP3 leucine aminopeptidase 3

chr4_+_17633521 -1.97 -0.39 2.49E-02 chr4:17633521-17633713 + 3UTR_last_exon,AS ENST00000265018.3 FAM184B family with sequence


chr4_+_177252331 -1.23 1.46 5.93E-02 chr4:177252331-177252348 + 3UTR_last_exon,S ENST00000503362.1 SPCS3signal peptidase complex subunit 3 homolog (S. cerevisiae)

chr4_+_185606080 0.82 1.65 8.21E-02 chr4:185606080-185606277 + CDS_or_noncoding_first_intron,S ENST00000508001.1 CCDC111 coiled-coil domain

containing 111


ENST00000261438.5/ENST00000514033.1 KLF3 Kruppel-like factor 3

(basic)

chr4_+_38701349 -2.02 -1.03 5.67E-02 chr4:38701349-38701423 + 3UTR_last_exon,S ENST00000261438.5 KLF3 Kruppel-like factor 3 (basic)

chr4_+_56814940 0.49 3.83 8.59E-02 chr4:56814940-56815130 + TSS,S ENST00000422247.2/ENST00000506809.1 CEP135 centrosomal protein

135kDa


ENST00000285599.3/ENST00000504248.1/ENST00000505907.1

MAN2B2 mannosidase, alpha, class 2B, member 2


KIAA0232 KIAA0232

105105

Persson et al.

chr4_+_6911497 0.43 6.54 1.76E-02 chr4:6911497-6911604 + TSS,S ENST00000409757.4 TBC1D14 TBC1 domain family, member 14

chr4_+_6911938 1.24 0.27 5.97E-02 chr4:6911938-6912022 + TSS,S ENST00000427736.1 TBC1D14 TBC1 domain family, member 14

chr4_+_7339673 -1.79 -0.21 1.62E-02 chr4:7339673-7339685 + CDS_or_noncoding_first_intron,S ENST00000507866.2 SORCS2

sortilin-related VPS10 domain containing receptor 2



CCNG2 cyclin G2

chr4_+_79697462 0.49 5.42 7.31E-02 chr4:79697462-79697578 + TSS,S


BMP2K BMP2 inducible kinase




chr4_+_87927709 1.18 0.16 8.66E-02 chr4:87927709-87927758 + TSSregion500,S ENST00000307808.6 AFF1 AF4/FMR2 family, member 1

chr4_+_87928307 0.49 5.60 5.41E-02 chr4:87928307-87928432 + TSS,S ENST00000511722.1/ENST00000544085.1 AFF1 AF4/FMR2 family,

member 1

chr4_+_89513537 0.38 5.52 3.97E-02 chr4:89513537-89513710 + TSS,S


HERC3HECT and RLD domain containing E3 ubiquitin protein ligase 3

chr4_-_130014582 0.43 6.22 9.41E-02 chr4:130014582-130014775 - TSS,S


SCLT1 sodium channel and clathrin linker 1

chr4_-_13629219 0.40 6.39 8.21E-02 chr4:13629219-13629413 - TSS,S ENST00000040738.5/ENST00000482713.1 BOD1L NA



106106

Persson et al.

chr4_-_140374834 1.13 1.29 3.78E-02 chr4:140374834-140374940 - TSSregion500,AS ENST00000305626.5/ENST00000507271.1 RAB33B RAB33B, member RAS

oncogene family

chr4_-_153601041 0.33 7.97 7.76E-02 chr4:153601041-153601228 - TSS,S ENST00000504064.1 TMEM154 transmembrane protein 154

chr4_-_15661430 0.50 7.22 2.60E-02 chr4:15661430-15661568 - TSS,S ENST00000503196.1/ENST00000509314.1 FBXL5 F-box and leucine-rich

repeat protein 5

chr4_-_169401522 0.49 6.80 4.95E-02 chr4:169401522-169401697 - TSS,S


DDX60LDEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like


ENST00000454703.2/ENST00000437665.3 ACSL1

acyl-CoA synthetase long-chain family member 1


ACSL1acyl-CoA synthetase long-chain family member 1

chr4_-_38858350 0.66 5.19 1.55E-02 chr4:38858350-38858530 - TSS,S



chr4_-_70626248 0.47 6.26 1.32E-02 chr4:70626248-70626448 - TSS,S ENST00000310613.2/ENST00000510821.1 SULT1B1 sulfotransferase family,

cytosolic, 1B, member 1

chr4_-_74702691 1.08 0.85 8.01E-02 chr4:74702691-74702888 - TSSregion500,AS ENST00000503446.1 CXCL6 chemokine (C-X-C motif) ligand 6

chr4_-_74740149 1.16 1.10 8.83E-02 chr4:74740149-74740260 - intergenic intergenic NA NAchr4_-_78742997 -1.43 0.35 1.86E-02 chr4:78742997-78743113 - intergenic intergenic NA NAchr4_-_84010497 -1.15 1.88 4.99E-02 chr4:84010497-84010598 - intergenic intergenic NA NA




chr5_+_115898212 -0.38 6.10 7.31E-02 chr5:115898212-115898282 + TSS,S ENST00000478778.1 CTB-118N6.1

chr5_+_118728528 1.03 2.56 6.10E-02 chr5:118728528-118728687 + 5UTR_last_exon,S ENST00000388882.5 TNFAIP8 tumor necrosis factor, alpha-induced protein 8

107107

Persson et al.


ENST00000542191.1/ENST00000510658.1/ENST00000261368.8/ENST00000512385.1/ENST00000379533.2/ENST00000379536.2/ENST00000379538.3/ENST00000261367.7/ENST00000509023.1/ENST00000414317.2/ENST00000508017.1/ENST00000447854.1/ENST00000514467.1/ENST00000506272.1/ENST00000508681.1

SNCAIP synuclein, alpha interacting protein

chr5_+_133474633 1.53 0.61 4.02E-02 chr5:133474633-133474707 + TSSregion500,S ENST00000522561.1 TCF7 transcription factor 7 (T-cell specific, HMG-box)

chr5_+_133562013 -0.96 0.65 8.17E-02 chr5:133562013-133562139 + TSSregion500,ASENST00000519718.1/ENST00000481195.1/ENST00000231504.5

SKP1 S-phase kinase-associated protein 1

chr5_+_133889496 -1.78 -0.45 5.36E-02 chr5:133889496-133889505 + CDS_or_noncoding_inner_intron,S


PHF15 PHD finger protein 15

chr5_+_135382538 1.05 1.54 4.84E-02 chr5:135382538-135382650 + TSSregion500,S ENST00000508767.1/ENST00000509749.1 TGFBI

transforming growth factor, beta-induced, 68kDa

chr5_+_137676863 0.84 1.72 5.83E-02 chr5:137676863-137677048 + TSS,S ENST00000505136.1 FAM53C family with sequence similarity 53, member C


ENST00000434981.2/ENST00000239906.5 FAM53C family with sequence




ENST00000432126.2/ENST00000194118.4/ENST00000508751.1

KIAA0141 KIAA0141

108108

Persson et al.


protein 26

chr5_+_142548033 1.30 1.13 9.65E-03 chr5:142548033-142548044 + CDS_or_noncoding_first_intron,S ENST00000486650.1 ARHGAP26 Rho GTPase activating

protein 26

chr5_+_151186143 -2.34 -0.77 6.06E-03 chr5:151186143-151186332 + 3UTR_last_exon,S ENST00000394123.3 G3BP1GTPase activating protein (SH3 domain) binding protein 1

chr5_+_156712333 1.32 0.73 6.11E-02 chr5:156712333-156712461 + TSS,S ENST00000517753.1/ENST00000541131.1 CYFIP2 cytoplasmic FMR1

interacting protein 2

chr5_+_169064213 0.37 7.69 7.43E-02 chr5:169064213-169064346 + TSS,S



chr5_+_17217686 0.59 9.02 2.80E-03 chr5:17217686-17217882 + TSS,S ENST00000447228.2 BASP1brain abundant, membrane attached signal protein 1

chr5_+_172378236 1.75 0.46 4.29E-03 chr5:172378236-172378322 + CDS_or_noncoding_last_exon,S ENST00000523215.1 ERGIC1

endoplasmic reticulum-golgi intermediate compartment (ERGIC) 1


ENST00000519374.1/ENST00000519911.1/ENST00000517669.1

ATP6V0E1ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e1


ENST00000322611.3/ENST00000447228.2 BASP1

brain abundant, membrane attached signal protein 1

chr5_+_173315944 0.97 2.11 6.73E-02 chr5:173315944-173316023 + TSSregion500,S ENST00000520867.1/ENST00000334035.5 CPEB4

cytoplasmic polyadenylation element binding protein 4

chr5_+_17444094 0.53 4.25 6.99E-02 chr5:17444094-17444198 + TSS,S ENST00000503267.1/ENST00000504998.1 RP11-321E2.4

chr5_+_179155766 -1.26 1.45 6.41E-02 chr5:179155766-179155922 + CDS_or_noncoding_last_exon,S ENST00000376953.4 CANX calnexin

chr5_+_179157241 -1.39 0.64 7.25E-02 chr5:179157241-179157294 + 3UTR_last_exon,S ENST00000247461.4/ENST00000452673.2 CANX calnexin

chr5_+_180336524 0.48 5.00 4.23E-02 chr5:180336524-180336631 + TSS,S


BTNL8 butyrophilin-like 8

109109

Persson et al.

chr5_+_25909587 1.16 1.60 8.56E-02 chr5:25909587-25909698 + TSS,S ENST00000511640.1 MSNP1 moesin pseudogene 1

chr5_+_60659450 1.26 0.39 8.56E-02 chr5:60659450-60659626 + CDS_or_noncoding_first_intron,S ENST00000252744.5 ZSWIM6 zinc finger, SWIM-type

containing 6



KIF2A kinesin heavy chain member 2A



PIK3R1phosphoinositide-3-kinase, regulatory subunit 1 (alpha)

chr5_+_75698844 0.64 4.83 2.34E-02 chr5:75698844-75698883 + TSSregion500,S ENST00000274364.6/ENST00000379730.3 IQGAP2

IQ motif containing GTPase activating protein 2

chr5_+_77080624 -1.01 4.48 8.31E-02 chr5:77080624-77080630 + TSSregion500,S ENST00000515712.1 CTD-2309M13.1 NA

chr5_+_79703805 0.38 5.08 6.24E-02 chr5:79703805-79703925 + TSS,S





VCAN versican

110110

Persson et al.

chr5_-_131132613 0.44 4.96 7.80E-02 chr5:131132613-131132787 - TSS,S


FNIP1 folliculin interacting protein 1

chr5_-_131762256 0.49 5.48 5.52E-02 chr5:131762256-131762442 - TSS,S ENST00000454380.1 AC116366.5

chr5_-_139971628 0.44 5.09 9.50E-02 chr5:139971628-139971762 - TSS,S ENST00000507279.1 APBB3

amyloid beta (A4) precursor protein-binding, family B, member 3

chr5_-_141061717 0.47 5.25 4.30E-02 chr5:141061717-141061832 - TSS,S ENST00000508305.1/ENST00000239440.4 ARAP3

ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3


ENST00000353334.6/ENST00000518797.1/ENST00000009530.7

CD74

CD74 molecule, major histocompatibility complex, class II invariant chain



CD74




CD74




RBM22 RNA binding motif protein 22

chr5_-_171583622 0.82 2.43 4.94E-02 chr5:171583622-171583805 - TSS,S ENST00000519710.1 STK10 serine/threonine kinase 10

111111

Persson et al.




chr5_-_180668523 0.98 3.03 2.75E-02 chr5:180668523-180668647 - TSS,S ENST00000504128.1 GNB2L1

guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1

chr5_-_39202933 0.90 3.03 2.34E-02 chr5:39202933-39202960 - CDS_or_noncoding_first_exon,S ENST00000515010.1 FYB FYN binding protein



FYB FYN binding protein

chr5_-_39219629 0.42 7.59 6.81E-02 chr5:39219629-39219767 - TSS,S


FYB FYN binding protein

chr5_-_90610188 0.42 5.84 8.93E-02 chr5:90610188-90610335 - TSS,S ENST00000511918.1/ENST00000513626.1

RP11-213H15.3


KIAA0825 KIAA0825

chr5_-_94417257 0.38 6.54 3.58E-02 chr5:94417257-94417377 - TSS,S




chr6_+_114178493 0.33 8.63 8.33E-02 chr6:114178493-114178688 + TSS,S ENST00000368635.4 MARCKSmyristoylated alanine-rich protein kinase C substrate

chr6_+_114178781 0.59 3.46 7.82E-02 chr6:114178781-114178932 + TSSregion500,S ENST00000368635.4 MARCKSmyristoylated alanine-rich protein kinase C substrate

112112

Persson et al.

chr6_+_116691961 0.55 5.69 2.45E-02 chr6:116691961-116692148 + TSS,S ENST00000359564.2 DSE dermatan sulfate epimerase

chr6_+_12012162 0.55 3.53 7.80E-02 chr6:12012162-12012261 + TSS,S ENST00000487103.1 HIVEP1

human immunodeficiency virus type I enhancer binding protein 1


HIVEP1

human immunodeficiency virus type I enhancer binding protein 1

chr6_+_139456460 1.23 1.16 4.78E-02 chr6:139456460-139456510 + TSSregion500,S ENST00000367658.2 HECA headcase homolog (Drosophila)

chr6_+_139694684 -1.26 0.75 5.19E-02 chr6:139694684-139694833 + CDS_or_noncoding_first_exon,AS ENST00000392312.1 CITED2

Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2

chr6_+_144606710 0.70 3.91 1.04E-02 chr6:144606710-144606829 + TSSregion500,S ENST00000433557.1 UTRN utrophin


STXBP5 syntaxin binding protein 5 (tomosyn)


ENST00000367469.1/ENST00000367467.3/ENST00000392284.5

SASH1 SAM and SH3 domain containing 1

chr6_+_15246181 0.45 7.40 2.75E-02 chr6:15246181-15246332 + TSSregion500,S ENST00000341776.2 JARID2 jumonji, AT rich interactive domain 2

chr6_+_155542345 1.09 1.21 6.63E-02 chr6:155542345-155542540 + 5UTR_first_intron,S ENST00000275246.7 TIAM2

T-cell lymphoma invasion and metastasis 2

chr6_+_159074990 -1.38 0.84 9.74E-02 chr6:159074990-159075106 + 5UTR_inner_intron,S

ENST00000360448.3/ENST00000543689.1 SYTL3 synaptotagmin-like 3

chr6_+_160390062 0.47 8.09 1.02E-02 chr6:160390062-160390200 + TSS,S ENST00000356956.1 IGF2R insulin-like growth factor 2 receptor

chr6_+_160461588 0.80 1.62 7.35E-02 chr6:160461588-160461759 + CDS_or_noncoding_inner_exon,S ENST00000356956.1 IGF2R insulin-like growth factor

2 receptor

chr6_+_17609219 -1.42 -0.20 6.10E-02 chr6:17609219-17609288 + 3UTR_last_exon,S ENST00000259963.3 FAM8A1 family with sequence similarity 8, member A1

chr6_+_18399703 1.85 -0.47 3.33E-02 chr6:18399703-18399883 + 5UTR_inner_exon,S ENST00000259939.3 RNF144B ring finger protein 144B

chr6_+_26020670 -0.63 5.83 5.64E-02 chr6:26020670-26020734 + TSS,S ENST00000357647.3 HIST1H3A histone cluster 1, H3achr6_+_26044171 -0.66 2.36 8.84E-02 chr6:26044171-26044191 + TSSregion500,S ENST00000454320.1 U91328.2chr6_+_26204717 -0.35 9.24 6.58E-02 chr6:26204717-26204861 + TSS,S ENST00000360441.4 HIST1H4E histone cluster 1, H4echr6_+_26271788 -1.66 -0.51 8.73E-02 chr6:26271788-26271880 + TSSregion500,AS ENST00000305910.3 HIST1H3G histone cluster 1, H3gchr6_+_27805220 -0.72 2.74 6.19E-02 chr6:27805220-27805336 + upstream1000,S ENST00000449538.2 HIST1H2BN histone cluster 1, H2bn

113113

Persson et al.


chr6_+_3000060 0.66 5.62 3.57E-02 chr6:3000060-3000182 + TSS,S ENST00000397717.2 NQO2NAD(P)H dehydrogenase, quinone 2

chr6_+_3000222 1.54 -0.24 1.68E-02 chr6:3000222-3000274 + TSS,SENST00000380441.1/ENST00000380455.4/ENST00000380454.4

NQO2NAD(P)H dehydrogenase, quinone 2



PSMB9

proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2)


UBR2ubiquitin protein ligase E3 component n-recognin 2


UBR2ubiquitin protein ligase E3 component n-recognin 2

chr6_+_42906582 1.07 1.30 2.30E-02 chr6:42906582-42906615 + 3UTR_last_exon,S ENST00000372836.4/ENST00000394142.3 CNPY3 canopy 3 homolog

(zebrafish)

chr6_+_80410434 -1.77 -0.35 1.95E-02 chr6:80410434-80410532 + 3UTR_last_exon,S ENST00000369838.4 SH3BGRL2SH3 domain binding glutamic acid-rich protein like 2

chr6_+_84569325 0.38 7.44 1.94E-02 chr6:84569325-84569466 + TSS,S ENST00000369681.3/ENST00000369679.4 CYB5R4 cytochrome b5

reductase 4

chr6_+_89790868 2.14 1.33 1.49E-02 chr6:89790868-89790877 + 5UTR_last_intron,S ENST00000369472.1 PNRC1 proline-rich nuclear

receptor coactivator 1

chr6_+_89793470 0.78 2.57 6.40E-02 chr6:89793470-89793580 + 5UTR_last_exon,S ENST00000369472.1/ENST00000354922.2 PNRC1 proline-rich nuclear

receptor coactivator 1


ENST00000463016.1/ENST00000460913.1 CDK19 cyclin-dependent kinase

19



CDK19 cyclin-dependent kinase 19

114114

Persson et al.

chr6_-_11382405 0.39 7.91 2.18E-02 chr6:11382405-11382593 - TSS,S


NEDD9

neural precursor cell expressed, developmentally down-regulated 9

chr6_-_133055790 0.75 5.57 2.50E-03 chr6:133055790-133055913 - TSS,S


VNN3 vanin 3


ENST00000326499.6/ENST00000525270.1 VNN2 vanin 2

chr6_-_137113491 0.54 5.33 2.02E-02 chr6:137113491-137113690 - TSS,S ENST00000359015.4/ENST00000367768.3 MAP3K5

mitogen-activated protein kinase kinase kinase 5

chr6_-_160113764 1.06 4.48 1.40E-03 chr6:160113764-160113904 - TSSregion500,S ENST00000540491.1 SOD2 superoxide dismutase 2, mitochondrial

chr6_-_167369951 0.53 8.47 4.15E-02 chr6:167369951-167370100 - TSS,S


RNASET2 ribonuclease T2

chr6_-_167383112 2.26 -0.15 4.89E-02 chr6:167383112-167383308 - CDS_or_noncoding_last_exon,S ENST00000444102.1 RP1-167A14.2

115115

Persson et al.

chr6_-_16761542 0.46 5.99 2.51E-02 chr6:16761542-16761737 - TSS,S


ATXN1Ataxin 1, isoform CRA_a; Uncharacterized protein

chr6_-_17987804 0.67 4.61 1.40E-02 chr6:17987804-17987919 - TSS,S ENST00000502704.1 KIF13A kinesin family member 13A


KIAA0319 KIAA0319

chr6_-_26235187 -0.47 4.78 7.87E-02 chr6:26235187-26235254 - TSS,S ENST00000244534.5 HIST1H1D histone cluster 1, H1dchr6_-_27805997 -0.52 5.71 7.43E-02 chr6:27805997-27806196 - TSS,S ENST00000330180.2 HIST1H2AK histone cluster 1, H2ak

chr6_-_2889093 -1.18 1.97 2.99E-02 chr6:2889093-2889290 - 3UTR_last_exon,S ENST00000380698.4 SERPINB9serpin peptidase inhibitor, clade B (ovalbumin), member 9



ATF6B activating transcription factor 6 beta

chr6_-_33271952 -1.48 -0.17 9.23E-02 chr6:33271952-33272002 - CDS_or_noncoding_inner_exon,S


TAPBP TAP binding protein (tapasin)





ENST00000467025.1/ENST00000476333.1 TAPBP TAP binding protein

(tapasin)

116116

Persson et al.

chr6_-_35888789 0.51 6.38 7.24E-03 chr6:35888789-35888948 - TSS,S


SRPK1 SRSF protein kinase 1

chr6_-_35992307 1.19 1.47 8.31E-03 chr6:35992307-35992479 - TSS,S ENST00000355574.2 SLC26A8 solute carrier family 26, member 8

chr7_+_112063143 0.51 5.40 6.66E-02 chr7:112063143-112063275 + TSS,S ENST00000005558.4 IFRD1interferon-related developmental regulator 1


TES testis derived transcript (3 LIM domains)

chr7_+_116558729 -1.45 0.72 7.48E-02 chr7:116558729-116558929 + 3UTR_last_exon,S ENST00000361183.2 CAPZA2capping protein (actin filament) muscle Z-line, alpha 2

chr7_+_130794778 0.74 2.21 5.09E-02 chr7:130794778-130794894 + TSS,S ENST00000421797.2 MKLN1muskelin 1, intracellular mediator containing kelch motifs

chr7_+_131012587 0.36 6.70 4.11E-02 chr7:131012587-131012732 + TSS,S




ENST00000344924.3/ENST00000418040.1/ENST00000393132.2

BPGM 2,3-bisphosphoglycerate mutase

chr7_+_139649693 1.58 -0.52 6.27E-02 chr7:139649693-139649866 + CDS_or_noncoding_inner_intron,S


TBXAS1 thromboxane A synthase 1 (platelet)

117117

Persson et al.

chr7_+_141688603 0.70 7.09 5.98E-03 chr7:141688603-141688776 + 5UTR_inner_intron,S ENST00000465654.1 MGAM maltase-glucoamylase

(alpha-glucosidase)

chr7_+_141718992 1.82 0.99 5.23E-03 chr7:141718992-141719100 + TSS,S ENST00000548812.1 MGAM maltase-glucoamylase (alpha-glucosidase)

chr7_+_143079400 0.84 3.62 2.60E-02 chr7:143079400-143079515 + TSSregion500,S ENST00000436448.1 ZYX zyxinchr7_+_143079964 0.88 3.81 6.06E-03 chr7:143079964-143080096 + TSS,S ENST00000446634.1 ZYX zyxinchr7_+_143080180 2.43 -0.49 4.06E-02 chr7:143080180-143080182 + TSSregion500,S ENST00000446634.1 ZYX zyxinchr7_+_143080281 1.52 1.03 5.99E-02 chr7:143080281-143080312 + TSSregion500,S ENST00000446634.1 ZYX zyxin



ZYX zyxin


chr7_+_15276749 1.42 4.69 2.26E-04 chr7:15276749-15276943 + CDS_or_noncoding_last_intron,AS ENST00000342526.3 AGMO alkylglycerol

monooxygenase


HOTAIRM1HOXA transcript antisense RNA, myeloid-specific 1

chr7_+_28725711 0.50 7.72 3.47E-02 chr7:28725711-28725788 + TSS,S ENST00000468391.1/ENST00000484383.1 CREB5

cAMP responsive element binding protein 5



CREB5cAMP responsive element binding protein 5



OGDH

oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)

118118

Persson et al.



IKZF1 IKAROS family zinc finger 1 (Ikaros)

chr7_+_56019485 -0.52 3.30 6.10E-02 chr7:56019485-56019643 + TSS,S ENST00000446692.1/ENST00000285298.4 GBAS glioblastoma amplified

sequence




ADAM22 ADAM metallopeptidase domain 22


chr7_+_97736149 0.48 5.13 6.39E-02 chr7:97736149-97736291 + TSS,S ENST00000297293.5 LMTK2 lemur tyrosine kinase 2

chr7_+_98984295 1.31 1.25 4.31E-02 chr7:98984295-98984379 + TSS,S ENST00000461486.1 ARPC1Bactin related protein 2/3 complex, subunit 1B, 41kDa

chr7_+_99528236 -1.62 -0.68 9.37E-02 chr7:99528236-99528242 + CDS_or_noncoding_first_intron,S ENST00000456499.1 RP4-604G5.1


SRPK2 SRSF protein kinase 2



NAMPTnicotinamide phosphoribosyltransferase

119119

Persson et al.




chr7_-_105925364 0.50 8.96 2.02E-02 chr7:105925364-105925459 - TSS,S





chr7_-_130792748 0.49 5.83 5.92E-02 chr7:130792748-130792910 - TSS,S ENST00000423414.1/ENST00000429901.1 AC058791.2

chr7_-_130794642 0.67 2.92 6.02E-02 chr7:130794642-130794706 - TSSregion500,S ENST00000451786.1 AC058791.2

chr7_-_137563911 -1.38 0.76 3.93E-02 chr7:137563911-137564040 - CDS_or_noncoding_last_exon,S ENST00000417785.2 CREB3L2

cAMP responsive element binding protein 3-like 2

chr7_-_150930288 -1.67 -0.63 7.81E-02 chr7:150930288-150930381 - 5UTR_first_exon,AS

ENST00000377851.2/ENST00000035307.2 CHPF2 chondroitin polymerizing

factor 2


MLL3myeloid/lymphoid or mixed-lineage leukemia 3

120120

Persson et al.

chr7_-_17980042 0.37 5.87 4.15E-02 chr7:17980042-17980146 - TSS,S


SNX13 sorting nexin 13



SKAP2 src kinase associated phosphoprotein 2

chr7_-_26904058 0.51 7.29 6.73E-03 chr7:26904058-26904257 - TSS,S ENST00000497511.1/ENST00000487720.1 SKAP2 src kinase associated

phosphoprotein 2

chr7_-_36639590 1.10 1.44 5.75E-02 chr7:36639590-36639753 - TSS,S ENST00000449672.1 AOAH-IT1 AOAH intronic transcript 1 (non-protein coding)

chr7_-_38339823 -0.51 5.19 6.39E-02 chr7:38339823-38339996 - TSS,S ENST00000390341.2 TRGV10T cell receptor gamma variable 10 (non-functional)

chr7_-_5463173 1.03 0.38 9.74E-02 chr7:5463173-5463221 - TSS,S


TNRC18 trinucleotide repeat containing 18

chr7_-_5567118 -0.91 3.02 4.89E-02 chr7:5567118-5567188 - CDS_or_noncoding_last_exon,S

ENST00000464611.1/ENST00000462494.1 ACTB actin, beta

chr7_-_64467002 0.38 6.40 4.89E-02 chr7:64467002-64467123 - TSS,S


ERV3-1 endogenous retrovirus group 3, member 1

chr7_-_76828893 0.82 2.64 6.17E-02 chr7:76828893-76828955 - CDS_or_noncoding_first_exon,S ENST00000248598.5 FGL2 fibrinogen-like 2

121121

Persson et al.











FAM91A1 family with sequence similarity 91, member A1

chr8_+_131218744 0.63 3.13 7.80E-02 chr8:131218744-131218916 + 5UTR_inner_intron,AS ENST00000520342.1 ASAP1

ArfGAP with SH3 domain, ankyrin repeat and PH domain 1

chr8_+_133787556 0.50 5.98 4.65E-02 chr8:133787556-133787752 + TSS,S


PHF20L1 PHD finger protein 20-like 1

122122

Persson et al.



PHF20L1 PHD finger protein 20-like 1




ATP6V1B2ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2

chr8_+_22974139 1.39 0.69 5.34E-02 chr8:22974139-22974242 + CDS_or_noncoding_inner_exon,S ENST00000544885.1 TNFRSF10C

tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain

chr8_+_22974440 0.90 3.11 2.50E-02 chr8:22974440-22974628 + CDS_or_noncoding_inner_exon,S ENST00000544885.1 TNFRSF10C

tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain

chr8_+_23399094 0.57 3.94 8.56E-02 chr8:23399094-23399233 + TSS,S ENST00000520949.1 SLC25A37solute carrier family 25 (mitochondrial iron transporter), member 37



chr8_+_23432452 -1.27 3.15 6.25E-02 chr8:23432452-23432621 + 3UTR_first_exon,S ENST00000399967.3 AC051642.1

chr8_+_25042178 0.57 6.66 2.84E-03 chr8:25042178-25042326 + TSS,S ENST00000410074.1/ENST00000481100.1 DOCK5 dedicator of cytokinesis

5

chr8_+_26268733 -0.87 3.91 8.61E-02 chr8:26268733-26268833 + 3UTR_last_exon,S ENST00000380629.2 BNIP3LBCL2/adenovirus E1B 19kDa interacting protein 3-like

chr8_+_26513318 -0.76 3.11 5.83E-02 chr8:26513318-26513328 + 3UTR_inner_exon,S ENST00000522745.1 DPYSL2 dihydropyrimidinase-like

2

chr8_+_38662940 0.42 5.06 7.81E-02 chr8:38662940-38663123 + TSS,S ENST00000524193.1/ENST00000522955.1 TACC1

transforming, acidic coiled-coil containing protein 1

123123

Persson et al.

chr8_+_52593946 -0.73 3.11 9.23E-02 chr8:52593946-52593959 + CDS_or_noncoding_first_intron,AS

ENST00000356297.4/ENST00000543296.1 PXDNL peroxidasin homolog

(Drosophila)-like

chr8_+_56792355 0.37 8.34 9.43E-02 chr8:56792355-56792466 + TSS,S ENST00000519728.1/ENST00000520220.1 LYN

v-yes-1 Yamaguchi sarcoma viral related oncogene homolog


UBXN2B UBX domain protein 2B



PGCP NA



PABPC1 poly(A) binding protein, cytoplasmic 1

chr8_-_131028646 0.41 8.20 3.19E-02 chr8:131028646-131028826 - TSS,S


FAM49B family with sequence similarity 49, member B


ENST00000357668.1/ENST00000343135.6 ASAP1

ArfGAP with SH3 domain, ankyrin repeat and PH domain 1

chr8_-_133772746 0.47 7.37 1.04E-02 chr8:133772746-133772920 - TSS,S



124124

Persson et al.



SLA Src-like-adaptor

chr8_-_134087128 0.40 7.55 3.62E-02 chr8:134087128-134087311 - TSS,S


SLA Src-like-adaptor


ZFAT zinc finger and AT hook domain containing

chr8_-_144618450 2.22 -1.00 1.45E-02 chr8:144618450-144618600 - CDS_or_noncoding_inner_exon,S ENST00000262577.5 ZC3H3 zinc finger CCCH-type

containing 3

chr8_-_145115552 1.06 0.93 6.41E-02 chr8:145115552-145115657 - TSS,S ENST00000534424.1/ENST00000426825.1 OPLAH 5-oxoprolinase (ATP-

hydrolysing)

chr8_-_146012666 -1.18 -0.03 4.89E-02 chr8:146012666-146012744 - TSS,S


ZNF34 zinc finger protein 34


C8ORF80 NA

chr8_-_48775161 0.70 4.41 3.36E-02 chr8:48775161-48775358 - CDS_or_noncoding_inner_intron,S


PRKDCprotein kinase, DNA-activated, catalytic polypeptide

chr8_-_62627045 0.91 4.21 7.16E-04 chr8:62627045-62627200 - TSS,S


ASPH aspartate beta-hydroxylase

125125

Persson et al.

chr8_-_9008120 0.41 5.36 8.19E-02 chr8:9008120-9008249 - TSS,S ENST00000310455.3 PPP1R3B protein phosphatase 1, regulatory subunit 3B

chr8_-_92052955 0.42 7.56 1.62E-02 chr8:92052955-92053127 - TSS,S


TMEM55A transmembrane protein 55A

chr8_-_99057735 -0.70 9.79 4.02E-02 chr8:99057735-99057818 - TSS,S





chr9_+_120470833 1.05 0.93 6.65E-02 chr9:120470833-120470959 + 5UTR_inner_exon,S ENST00000394487.4 TLR4 toll-like receptor 4


NEK6 NIMA-related kinase 6

chr9_+_127023630 0.77 3.38 5.49E-02 chr9:127023630-127023768 + TSS,S ENST00000373596.1/ENST00000425237.1 NEK6 NIMA-related kinase 6

chr9_+_132649842 -1.96 -0.54 8.41E-02 chr9:132649842-132649946 + CDS_or_noncoding_last_exon,AS ENST00000479142.1 FNBP1 formin binding protein 1


ENST00000372124.1/ENST00000339463.3 GFI1B

growth factor independent 1B transcription repressor

chr9_+_214829 0.38 7.50 6.12E-02 chr9:214829-214905 + TSS,S



126126

Persson et al.




chr9_+_95737509 1.65 0.71 6.33E-02 chr9:95737509-95737647 + TSS,S ENST00000467786.1 FGD3 FYVE, RhoGEF and PH domain containing 3



FGD3 FYVE, RhoGEF and PH domain containing 3




chr9_-_117160213 0.63 2.36 9.67E-02 chr9:117160213-117160265 - CDS_or_noncoding_first_intron,S ENST00000448674.1 RP11-9M16.2


ENST00000426959.1/ENST00000373930.3 MEGF9 multiple EGF-like-

domains 9

chr9_-_123476661 0.48 6.70 6.70E-03 chr9:123476661-123476826 - TSS,S ENST00000373930.3 MEGF9 multiple EGF-like-domains 9

chr9_-_139258134 -0.80 3.01 3.58E-02 chr9:139258134-139258255 - TSS,S ENST00000371739.3/ENST00000371738.3 DNLZ DNL-type zinc finger

chr9_-_34088310 -1.04 2.99 3.50E-02 chr9:34088310-34088405 - CDS_or_noncoding_last_exon,S ENST00000361264.3 DCAF12 DDB1 and CUL4

associated factor 12

chr9_-_34126465 1.38 3.18 8.35E-02 chr9:34126465-34126514 - TSSregion500,S ENST00000361264.3 DCAF12 DDB1 and CUL4 associated factor 12

chr9_-_74979780 1.22 2.73 3.04E-02 chr9:74979780-74979938 - TSS,S ENST00000487330.1 ZFAND5 zinc finger, AN1-type domain 5



AGTPBP1 ATP/GTP binding protein 1

127127

Persson et al.

chr9_-_88969256 0.40 6.94 4.02E-02 chr9:88969256-88969454 - TSS,S


ZCCHC6 zinc finger, CCHC domain containing 6

chr9_-_94186065 0.53 5.78 5.48E-02 chr9:94186065-94186172 - TSS,S ENST00000375724.1/ENST00000297689.2 NFIL3 nuclear factor,

interleukin 3 regulated

chrM_+_10055 -0.66 5.94 5.36E-02 chrM:10055-10087 + intergenic intergenic NA NAchrM_+_10855 -1.11 2.68 9.74E-02 chrM:10855-10856 + intergenic intergenic NA NAchrM_+_11848 -0.60 6.21 6.11E-02 chrM:11848-11913 + intergenic intergenic NA NAchrM_+_13053 -0.86 3.83 4.04E-02 chrM:13053-13056 + intergenic intergenic NA NAchrM_+_13100 -0.82 3.65 8.60E-02 chrM:13100-13107 + intergenic intergenic NA NAchrM_+_13179 -0.89 2.64 8.31E-02 chrM:13179-13182 + intergenic intergenic NA NAchrM_+_13632 -0.70 5.05 8.21E-02 chrM:13632-13644 + intergenic intergenic NA NAchrM_+_13709 -0.92 6.63 5.42E-02 chrM:13709-13738 + intergenic intergenic NA NAchrM_+_13828 -0.93 3.34 4.00E-02 chrM:13828-13833 + intergenic intergenic NA NAchrM_+_13838 -0.97 2.58 4.94E-02 chrM:13838-13840 + intergenic intergenic NA NAchrM_+_15042 -0.88 4.12 5.38E-02 chrM:15042-15052 + intergenic intergenic NA NAchrM_+_5462 -2.07 -0.30 5.14E-02 chrM:5462-5463 + intergenic intergenic NA NA

chrX_+_100667002 1.13 1.72 1.51E-02 chrX:100667002-100667030 + CDS_or_noncoding_inner_exon,S ENST00000457902.1 HNRNPH2 heterogeneous nuclear

ribonucleoprotein H2 (H')

chrX_+_117629770 0.52 4.44 6.46E-02 chrX:117629770-117629835 + TSSregion500,S ENST00000276204.6/ENST00000276202.7 DOCK11 dedicator of cytokinesis

11

chrX_+_128926304 0.81 2.40 6.65E-02 chrX:128926304-128926425 + CDS_or_noncoding_inner_exon,S

ENST00000443760.2/ENST00000356892.3 SASH3 SAM and SH3 domain

containing 3

chrX_+_12924650 0.37 7.86 5.48E-02 chrX:12924650-12924803 + TSS,S ENST00000218032.6/ENST00000311912.5 TLR8 toll-like receptor 8

chrX_+_14891459 0.43 5.88 4.15E-02 chrX:14891459-14891655 + TSS,S


MOSPD2 motile sperm domain containing 2

chrX_+_153668294 1.55 0.67 2.06E-02 chrX:153668294-153668383 + TSS,S ENST00000489589.1 GDI1 GDP dissociation inhibitor 1

chrX_+_17024264 0.65 5.67 7.54E-03 chrX:17024264-17024436 + 5UTR_inner_exon,S ENST00000380064.4 REPS2 RALBP1 associated Eps

domain containing 2chrX_+_17546479 1.05 2.34 6.49E-03 chrX:17546479-17546575 + TSS,S ENST00000433228.1 RP1-60N8.1

128128

Persson et al.

chrX_+_23801430 1.87 0.27 2.99E-02 chrX:23801430-23801433 + TSSregion500,S


SAT1 spermidine/spermine N1-acetyltransferase 1

chrX_+_37672187 -1.16 0.59 6.65E-02 chrX:37672187-37672196 + 3UTR_last_exon,S ENST00000378588.4 CYBB cytochrome b-245, beta polypeptide

chrX_+_48542669 0.94 2.69 7.80E-02 chrX:48542669-48542780 + CDS_or_noncoding_inner_exon,S


WAS Wiskott-Aldrich syndrome

chrX_+_54590685 -1.61 0.20 2.50E-02 chrX:54590685-54590858 + intergenic intergenic NA NA

chrX_+_64947678 1.70 0.76 1.12E-02 chrX:64947678-64947746 + CDS_or_noncoding_inner_exon,S ENST00000360270.5 MSN moesin

chrX_+_70520082 -0.68 3.82 4.15E-02 chrX:70520082-70520265 + TSSregion500,S ENST00000536900.1 AL590762.1

chrX_+_70782720 -1.26 0.68 9.46E-02 chrX:70782720-70782820 + CDS_or_noncoding_inner_exon,S

ENST00000373719.3/ENST00000373701.3/ENST00000488174.1

OGTO-linked N-acetylglucosamine (GlcNAc) transferase

chrX_+_70787821 -1.46 -0.35 6.10E-02 chrX:70787821-70787915 + CDS_or_noncoding_inner_exon,S

ENST00000373719.3/ENST00000373701.3/ENST00000488174.1

OGTO-linked N-acetylglucosamine (GlcNAc) transferase

chrX_+_9431316 0.68 2.39 8.39E-02 chrX:9431316-9431381 + TSS,S


TBL1X transducin (beta)-like 1X-linked

chrX_-_108975973 2.06 -0.53 1.58E-02 chrX:108975973-108976076 - 5UTR_first_intron,S


ACSL4acyl-CoA synthetase long-chain family member 4

chrX_-_119694781 0.49 3.36 7.33E-02 chrX:119694781-119694785 - TSSregion500,S ENST00000371322.5 CUL4B cullin 4B

chrX_-_13397356 -0.50 4.57 9.02E-02 chrX:13397356-13397518 - TSS,S ENST00000388829.3 GPX1P1 glutathione peroxidase pseudogene 1

129129

Persson et al.

chrX_-_19905539 0.37 6.74 7.41E-02 chrX:19905539-19905722 - TSS,SENST00000379702.2/ENST00000397821.3/ENST00000379697.3

SH3KBP1 SH3-domain kinase binding protein 1

chrX_-_30907364 0.48 3.35 6.41E-02 chrX:30907364-30907558 - 5UTR_inner_intron,S

ENST00000288422.2/ENST00000378932.2 TAB3

TGF-beta activated kinase 1/MAP3K7 binding protein 3

chrY_-_21903194 1.76 -0.20 6.25E-02 chrY:21903194-21903364 - CDS_or_noncoding_inner_exon,S


KDM5D lysine (K)-specific demethylase 5D

130130

236

Persson et al.

Table E6. Differentially expressed tag clusters for CA vs CTRL (glm analysis adjusted for neutrophil, eosinophil and lymphocyte counts as fractions of total leukocyte counts).


chr10_+_17271431 -2.20 0.89 2.02E-02 chr10:17271431-17271436 + TSSregion500,S ENST00000485947.1 VIM vimentin


CREM cAMP responsive element modulator



chr10_+_89623808 -1.24 1.54 6.26E-02 chr10:89623808-89623866 + TSSregion500,S ENST00000462694.1/ENST00000487939.1 PTEN phosphatase and tensin

homolog



chr10_-_64576013 -1.41 2.27 8.42E-02 chr10:64576013-64576175 - TSS,S ENST00000242480.3/ENST00000411732.1 EGR2 early growth response 2

chr11_-_85522024 0.68 4.68 9.92E-02 chr11:85522024-85522224 - TSS,S



chr14_-_35872416 -1.43 3.05 7.77E-02 chr14:35872416-35872424 - TSSregion500,S ENST00000555371.1/ENST00000556664.1 NFKBIA


chr14_-_35873848 -1.11 7.13 3.60E-02 chr14:35873848-35873985 - TSS,S


NFKBIAnuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha

chr15_+_81616636 -1.28 1.03 7.15E-02 chr15:81616636-81616832 + TSS,S ENST00000559781.1/ENST00000560973.1 RP11-761I4.3

131131

237238239

Persson et al.

chr16_+_3096707 -1.32 2.24 7.15E-02 chr16:3096707-3096711 + TSSregion500,S ENST00000336577.3 MMP25 matrix metallopeptidase 25

chr17_+_56408834 1.99 0.64 8.42E-02 chr17:56408834-56408982 + upstream1000,AS ENST00000384835.1 MIR142 microRNA 142





GIT1 G protein-coupled receptor kinase interacting ArfGAP 1

chr17_-_68165434 -1.45 0.88 9.38E-02 chr17:68165434-68165544 - TSSregion500,AS ENST00000243457.2 KCNJ2

potassium inwardly-rectifying channel, subfamily J, member 2

chr19_+_39897475 -0.59 10.52 8.42E-02 chr19:39897475-39897519 + TSS,S ENST00000248673.3 ZFP36 zinc finger protein 36, C3H type, homolog (mouse)

chr19_+_39898819 -1.40 2.43 4.47E-02 chr19:39898819-39898828 + CDS_or_noncoding_last_exon,S ENST00000248673.3 ZFP36 zinc finger protein 36, C3H

type, homolog (mouse)chr19_+_7437754 -1.62 0.83 7.94E-02 chr19:7437754-7437912 + intergenic intergenic NA NA




elongation factor 2



ENST00000418674.1/ENST00000427110.2/ENST00000391970.3

PTPRCprotein tyrosine phosphatase, receptor type, C

chr1_+_24829354 -0.57 5.85 4.47E-02 chr1:24829354-24829538 + TSS,S ENST00000436717.2/ENST00000374395.3 RCAN3 RCAN family member 3

chr1_+_40854389 -1.09 2.58 2.91E-02 chr1:40854389-40854414 + CDS_or_noncoding_first_intron,S

ENST00000372718.3/ENST00000372708.1 SMAP2 small ArfGAP2



132132

Persson et al.


ENST00000362089.5/ENST00000392122.3/ENST00000483825.1






FAM207A family with sequence similarity 207, member A

chr21_-_40720929 -0.56 5.02 6.09E-02 chr21:40720929-40721049 - TSS,S


HMGN1high mobility group nucleosome binding domain 1

chr22_-_38539356 1.11 1.91 8.42E-02 chr22:38539356-38539520 - TSS,S ENST00000498338.1 PLA2G6phospholipase A2, group VI (cytosolic, calcium-independent)


ENST00000264170.4/ENST00000375773.2/ENST00000409512.1

KYNU kynureninase

chr2_+_7865810 0.84 4.80 2.18E-02 chr2:7865810-7865995 + TSS,S ENST00000417930.1 AC092580.4

chr2_+_98329970 2.06 0.64 9.22E-02 chr2:98329970-98329976 + TSSregion500,S ENST00000264972.5/ENST00000483781.1 ZAP70



ENST00000390645.2/ENST00000339728.3 ARL4C ADP-ribosylation factor-like

4C

chr2_-_47387476 2.46 0.80 3.85E-02 chr2:47387476-47387641 - CDS_or_noncoding_last_exon,S ENST00000460218.1 CALM2



133133

Persson et al.






ENST00000411801.2/ENST00000535792.1 EGR1 early growth response 1



chr6_-_170893668 -0.40 5.94 9.56E-02 chr6:170893668-170893767 - TSS,S


PDCD2 programmed cell death 2

chr6_-_31560676 0.79 5.20 9.38E-02 chr6:31560676-31560808 - TSS,S


NCR3 natural cytotoxicity triggering receptor 3


C6ORF108 NA

chr7_+_50343639 -0.44 5.76 9.38E-02 chr7:50343639-50343696 + TSSregion500,S ENST00000484847.1 IKZF1 IKAROS family zinc finger 1 (Ikaros)

chr9_+_4662265 -0.99 2.74 2.27E-02 chr9:4662265-4662424 + TSS,S ENST00000381883.2/ENST00000537542.1 PPAPDC2

phosphatidic acid phosphatase type 2 domain containing 2

chr9_-_37027589 -1.06 1.98 6.26E-02 chr9:37027589-37027706 - 5UTR_first_intron,S

ENST00000377849.3/ENST00000522003.1/ENST00000523145.1

PAX5 paired box 5

chrM_+_650 -1.81 5.25 7.15E-02 chrM:650-653 + intergenic intergenic NA NAchrM_+_811 -1.41 4.58 4.47E-02 chrM:811-814 + intergenic intergenic NA NA

134134

Persson et al.

chrX_+_1387667 6.79 4.26 9.22E-02 chrX:1387667-1387812 + TSS,S


CSF2RAcolony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)

chrX_+_155110927 7.01 4.40 7.15E-02 chrX:155110927-155111078 + TSS,S


VAMP7 vesicle-associated membrane protein 7

chrX_+_2609209 8.88 6.65 2.02E-02 chrX:2609209-2609401 + TSS,SENST00000381192.3/ENST00000381187.3/ENST00000381184.1

CD99 CD99 molecule

chrX_-_1510944 8.95 7.01 2.02E-02 chrX:1510944-1511062 - TSS,S ENST00000475167.1/ENST00000484026.1 SLC25A6

solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6

chrX_-_1655991 7.49 5.19 3.60E-02 chrX:1655991-1656187 - TSS,S ENST00000381297.4 P2RY8 purinergic receptor P2Y, G-protein coupled, 8

135135

240

Persson et al.

Table E7. Differentially expressed tag clusters for SA vs CTRL (glm analysis adjusted for neutrophil, eosinophil and lymphocyte counts as fractions of total leukocyte counts).




chr10_+_114206949 0.51 5.86 1.97E-02 chr10:114206949-114207088 + TSS,S


VTI1Avesicle transport through interaction with t-SNAREs homolog 1A (yeast)


ENST00000378847.3/ENST00000378845.1 CAMK1D


chr10_+_135044125 -1.36 1.17 2.99E-02 chr10:135044125-135044239 + CDS_or_noncoding_first_exon,S ENST00000304477.2 UTF1

undifferentiated embryonic cell transcription factor 1

chr10_+_17727413 -1.25 0.91 7.26E-02 chr10:17727413-17727587 + 5UTR_inner_intron,S ENST00000540523.1 STAM

signal transducing adaptor molecule (SH3 domain and ITAM motif) 1

chr10_+_20105327 0.45 5.33 5.55E-02 chr10:20105327-20105379 + TSS,S ENST00000536022.1 PLXDC2 plexin domain containing 2




chr10_+_23727931 -0.52 4.77 5.56E-02 chr10:23727931-23728090 + TSSregion500,S ENST00000376495.3 OTUD1 OTU domain containing 1



chr10_+_89636687 0.91 4.03 9.04E-02 chr10:89636687-89636701 + CDS_or_noncoding_first_intron,S ENST00000371953.3 PTEN phosphatase and tensin

homolog

chr10_+_90639943 0.54 3.67 9.18E-02 chr10:90639943-90640043 + TSS,S ENST00000461650.1 STAMBPL1 STAM binding protein-like 1

chr10_-_15902420 0.62 4.63 1.16E-02 chr10:15902420-15902532 - TSS,S ENST00000277632.3/ENST00000477891.1 FAM188A family with sequence

similarity 188, member A

chr10_-_22292557 0.55 4.86 2.78E-02 chr10:22292557-22292701 - TSS,S ENST00000376980.3/ENST00000376946.1 DNAJC1 DnaJ (Hsp40) homolog,

subfamily C, member 1

136136

241242243

Persson et al.

chr10_-_27112108 1.01 1.69 7.57E-02 chr10:27112108-27112244 - TSS,S ENST00000473481.1 ABI1 abl-interactor 1


ENST00000375400.3/ENST00000375398.2 SVIL supervillin

chr10_-_30024715 0.43 4.94 7.79E-02 chr10:30024715-30024904 - TSS,S ENST00000375400.3/ENST00000375398.2 SVIL supervillin


ENST00000432689.1/ENST00000305623.8

RP11-445P17.4

chr10_-_64576013 -1.28 2.27 4.66E-02 chr10:64576013-64576175 - TSS,S ENST00000242480.3/ENST00000411732.1 EGR2 early growth response 2


ENST00000397167.1/ENST00000379713.3/ENST00000397160.3

SFMBT2 Scm-like with four mbt domains 2

chr11_+_101785734 1.17 1.21 7.00E-02 chr11:101785734-101785762 + TSS,S ENST00000263468.8 KIAA1377 KIAA1377

chr11_+_105052451 -1.93 0.53 3.12E-02 chr11:105052451-105052609 +CDS_or_noncoding_inner_intron,AS

ENST00000528811.1 RP11-94P11.4

chr11_+_108094041 0.60 4.72 2.03E-02 chr11:108094041-108094204 + TSSregion500,S ENST00000530958.1/ENST00000526567.1 ATM ataxia telangiectasia

mutated

chr11_+_112832057 0.98 3.86 8.17E-02 chr11:112832057-112832246 + TSS,S


NCAM1 neural cell adhesion molecule 1


ENST00000260197.6/ENST00000532451.1 SORL1





METTL15 methyltransferase like 15



ALKBH3 alkB, alkylation repair homolog 3 (E. coli)

137137

Persson et al.

chr11_+_44939434 1.08 3.14 1.64E-02 chr11:44939434-44939570 + TSSregion500,S ENST00000520245.1 TSPAN18 tetraspanin 18






















ENST00000544868.1/ENST00000534336.1 MALAT1


chr11_+_65272872 1.89 0.52 6.33E-02 chr11:65272872-65272878 + CDS_or_noncoding_first_exon,S ENST00000534336.1 MALAT1


chr11_+_75526208 0.53 5.66 1.40E-02 chr11:75526208-75526325 + TSS,S ENST00000356136.3 UVRAG UV radiation resistance associated

138138

Persson et al.

chr11_+_76156033 0.41 5.60 6.09E-02 chr11:76156033-76156137 + TSS,S


C11ORF30 NA


RPLP2 ribosomal protein, large, P2

chr11_+_8704273 -0.43 7.54 6.32E-02 chr11:8704273-8704391 + TSS,S




chr11_-_107328431 0.54 5.93 1.18E-02 chr11:107328431-107328604 - TSS,S ENST00000282251.5/ENST00000433523.1 CWF19L2 CWF19-like 2, cell cycle

control (S. pombe)

chr11_-_17229430 0.46 5.30 7.17E-02 chr11:17229430-17229557 - TSS,S


PIK3C2A

phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha


OSBPL5 oxysterol binding protein-like 5

chr11_-_46142520 0.57 4.65 1.67E-02 chr11:46142520-46142695 - TSS,S



chr11_-_6767576 0.38 6.23 7.94E-02 chr11:6767576-6767772 - TSS,S ENST00000526769.1 GVINP1GTPase, very large interferon inducible pseudogene 1

chr11_-_85522024 0.78 4.68 9.58E-03 chr11:85522024-85522224 - TSS,S



139139

Persson et al.

chr11_-_85779972 0.48 8.47 1.18E-02 chr11:85779972-85780172 - TSS,S



chr11_-_8985914 -0.40 5.98 8.17E-02 chr11:8985914-8986044 - TSS,S ENST00000309134.5/ENST00000528117.1 TMEM9B TMEM9 domain family,

member B

chr11_-_96076282 0.43 5.83 7.94E-02 chr11:96076282-96076481 - TSS,S ENST00000524717.1/ENST00000440572.2 MAML2 mastermind-like 2

(Drosophila)

chr12_+_102513893 0.99 1.49 6.89E-02 chr12:102513893-102514065 + TSS,S


C12ORF48 NA


ENST00000549260.1/ENST00000303694.5 CHST11 carbohydrate (chondroitin

4) sulfotransferase 11


ENST00000549260.1/ENST00000303694.5 CHST11 carbohydrate (chondroitin

4) sulfotransferase 11

chr12_+_119442508 -1.23 1.64 5.56E-02 chr12:119442508-119442521 + CDS_or_noncoding_first_intron,S ENST00000267260.4 SRRM4 serine/arginine repetitive

matrix 4








ENST00000552933.1/ENST00000547866.1

RP11-386G11.5

140140

Persson et al.


ENST00000548553.1/ENST00000332160.4 METTL7A methyltransferase like 7A

chr12_+_56320945 -1.21 1.83 3.92E-02 chr12:56320945-56321130 + TSS,S ENST00000546878.1 DGKA diacylglycerol kinase, alpha 80kDa


chr12_+_62749547 1.29 0.97 7.17E-02 chr12:62749547-62749627 + CDS_or_noncoding_first_intron,S ENST00000549268.1 USP15 ubiquitin specific

peptidase 15

chr12_+_62860543 0.44 5.93 7.91E-02 chr12:62860543-62860657 + TSS,S


MON2 MON2 homolog (S. cerevisiae)



PTMS parathymosin

141141

Persson et al.


ENST00000250559.9/ENST00000393436.5/ENST00000425247.2/ENST00000489473.2/ENST00000422358.2/ENST00000541167.1/ENST00000538283.1/ENST00000341355.5/ENST00000537460.1/ENST00000450214.2/ENST00000545270.1/ENST00000538980.1/ENST00000542018.1/ENST00000543393.1/ENST00000534899.1/ENST00000453560.2/ENST00000378985.3/ENST00000540209.1/ENST00000540781.1/ENST00000535492.1/ENST00000539091.1/ENST00000542145.1/ENST00000485252.2/ENST00000456697.2/ENST00000541386.1/ENST00000538877.1/ENST00000543697.1/ENST00000545720.1/ENST00000541216.1

RAP1B RAP1B, member of RAS oncogene family


chr12_+_82752262 0.49 3.89 6.84E-02 chr12:82752262-82752351 + TSS,S


C12ORF26 NA



chr12_+_9979978 1.18 6.46 3.43E-02 chr12:9979978-9980163 + TSS,S


KLRF1killer cell lectin-like receptor subfamily F, member 1

142142

Persson et al.

chr12_-_11324071 0.82 5.05 1.70E-03 chr12:11324071-11324256 - TSS,S


PRR4 proline rich 4 (lacrimal)

chr12_-_26986078 0.66 5.08 6.67E-03 chr12:26986078-26986222 - TSS,S ENST00000381340.3 ITPR2inositol 1,4,5-trisphosphate receptor, type 2

chr12_-_49582757 -0.65 2.35 5.55E-02 chr12:49582757-49582759 - TSSregion500,S ENST00000295766.5/ENST00000552924.1 TUBA1A tubulin, alpha 1a



ATF7 activating transcription factor 7

chr12_-_57039668 -0.37 8.09 1.19E-02 chr12:57039668-57039866 - TSS,S


ATP5B

ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide


chr12_-_80328804 0.44 6.06 8.34E-02 chr12:80328804-80328979 - TSS,S ENST00000450142.2/ENST00000547330.1 PPP1R12A protein phosphatase 1,

regulatory subunit 12Achr12_-_8605602 0.98 2.47 4.02E-02 chr12:8605602-8605787 - intergenic intergenic NA NA

chr12_-_89746177 -0.59 6.30 5.52E-02 chr12:89746177-89746298 - TSS,S ENST00000308385.6/ENST00000548755.1 DUSP6 dual specificity

phosphatase 6



FGD6 FYVE, RhoGEF and PH domain containing 6

chr13_+_100741266 0.65 3.05 7.32E-02 chr13:100741266-100741435 + TSS,S


PCCApropionyl CoA carboxylase, alpha polypeptide



ENST00000382292.3 SACSspastic ataxia of Charlevoix-Saguenay (sacsin)

143143

Persson et al.





chr13_+_28819357 1.81 0.99 2.67E-02 chr13:28819357-28819541 + CDS_or_noncoding_first_intron,S ENST00000282391.5 PAN3








chr13_+_35516400 1.22 1.64 4.38E-02 chr13:35516400-35516504 + TSS,S


NBEA neurobeachin


ENST00000379498.3/ENST00000239882.3/ENST00000405737.2



chr13_+_49550030 0.44 4.92 2.52E-02 chr13:49550030-49550222 + TSS,S ENST00000492622.1/ENST00000378383.1 FNDC3A fibronectin type III domain

containing 3A

chr13_-_111364724 -1.30 0.73 7.10E-02 chr13:111364724-111364837 - TSS,S ENST00000540629.1 CARS2cysteinyl-tRNA synthetase 2, mitochondrial (putative)

chr13_-_111567337 0.48 5.62 8.06E-02 chr13:111567337-111567441 - TSS,S




ENST00000323076.2/ENST00000398576.1/ENST00000416500.1

LCP1 lymphocyte cytosolic protein 1 (L-plastin)

144144

Persson et al.

chr14_+_102276127 0.41 6.35 6.23E-02 chr14:102276127-102276227 + TSS,S


PPP2R5Cprotein phosphatase 2, regulatory subunit B', gamma


ENST00000392715.2/ENST00000216554.3/ENST00000558506.1

EIF5 eukaryotic translation initiation factor 5




chr14_+_20905818 1.11 1.89 7.28E-02 chr14:20905818-20905985 + TSSregion500,S ENST00000553568.1 RP11-203M5.6

chr14_+_39736548 0.40 5.57 4.95E-02 chr14:39736548-39736636 + TSS,S ENST00000556148.1/ENST00000348007.3 CTAGE5 CTAGE family, member 5

chr14_+_64319669 0.64 5.42 1.73E-02 chr14:64319669-64319734 + TSS,S


SYNE2spectrin repeat containing, nuclear envelope 2

chr14_+_65879691 0.74 2.56 4.28E-02 chr14:65879691-65879845 + TSS,S


FUT8fucosyltransferase 8 (alpha (1,6) fucosyltransferase)

chr14_+_66974827 0.79 3.02 7.19E-02 chr14:66974827-66974881 + TSS,S ENST00000459628.1 GPHN gephyrin

chr14_+_68286453 0.62 2.78 7.28E-02 chr14:68286453-68286561 + TSS,S


RAD51B RAD51 homolog B (S. cerevisiae)



ENST00000381232.3/ENST00000555818.1/ENST00000358550.2


chr14_+_75748467 -1.79 0.71 2.06E-02 chr14:75748467-75748500 + 3UTR_last_exon,S ENST00000303562.4 FOS

FBJ murine osteosarcoma viral oncogene homolog

chr14_+_86400942 0.64 4.16 6.33E-02 chr14:86400942-86401126 + TSS,S ENST00000557195.1 CTD-2341M24.1

145145

Persson et al.

chr14_-_23771335 -1.69 0.70 2.52E-02 chr14:23771335-23771340 - 5UTR_inner_intron,AS ENST00000553824.1 BCL2L2 BCL2-like 2



GZMB

granzyme B (granzyme 2, cytotoxic T-lymphocyte-associated serine esterase 1)


ENST00000555855.1/ENST00000555034.1/ENST00000553904.1

FOXN3 forkhead box N3


chr15_+_55611346 0.85 2.16 7.99E-02 chr15:55611346-55611380 + TSSregion500,S ENST00000164305.4/ENST00000539642.1 PIGB

phosphatidylinositol glycan anchor biosynthesis, class B

chr15_+_69111448 -0.79 2.19 6.83E-02 chr15:69111448-69111534 + CDS_or_noncoding_last_intron,S ENST00000560188.1 RP11-

696L21.1 NA

chr15_+_78462578 -1.16 2.44 5.08E-03 chr15:78462578-78462718 + CDS_or_noncoding_last_exon,S ENST00000558535.1 IDH3A isocitrate dehydrogenase

3 (NAD+) alpha


protein 13



AKAP13 A kinase (PRKA) anchor protein 13



chr15_+_98503887 -0.75 4.28 5.60E-02 chr15:98503887-98504027 + TSS,S ENST00000268042.6 ARRDC4 arrestin domain containing 4


ENST00000268035.6/ENST00000558762.1/ENST00000559925.1

IGF1R insulin-like growth factor 1 receptor


MTMR10 myotubularin related protein 10

146146

Persson et al.

chr15_-_34729924 0.97 4.74 3.85E-03 chr15:34729924-34730078 - 5UTR_inner_intron,S ENST00000543376.1 GOLGA8A golgin A8 family, member

A

chr15_-_34875771 0.59 5.75 8.81E-02 chr15:34875771-34875955 - TSSregion500,S ENST00000267731.7/ENST00000268079.6 GOLGA8B golgin A8 family, member

B


UBR1 ubiquitin protein ligase E3 component n-recognin 1

chr15_-_44955746 0.43 5.96 2.99E-02 chr15:44955746-44955936 - TSS,S


SPG11 spastic paraplegia 11 (autosomal recessive)


chr15_-_52971505 0.47 4.39 7.03E-02 chr15:52971505-52971615 - upstream1000,S ENST00000261844.6 KIAA1370 NA



RORA RAR-related orphan receptor A

chr15_-_77197646 0.61 3.71 3.42E-02 chr15:77197646-77197811 - TSS,S ENST00000303521.5 SCAPERS-phase cyclin A-associated protein in the ER

chr16_+_2014895 -0.72 4.02 7.17E-02 chr16:2014895-2015093 + TSS,S ENST00000531523.1 SNHG9small nucleolar RNA host gene 9 (non-protein coding)







ENST00000382301.2/ENST00000544933.1/ENST00000301740.7


147147

Persson et al.

chr16_+_29817622 -0.46 4.90 3.82E-02 chr16:29817622-29817713 + TSSregion500,S ENST00000219782.5/ENST00000322945.5 MAZ


chr16_+_3070329 -0.87 3.46 3.10E-02 chr16:3070329-3070402 + TSS,S ENST00000341627.4 TNFRSF12Atumor necrosis factor receptor superfamily, member 12A


ENST00000302312.4 AHSP alpha hemoglobin stabilizing protein

chr16_+_3546158 -0.45 4.08 9.16E-02 chr16:3546158-3546174 + TSSregion500,S ENST00000459875.1 LA16C-306E5.1 NA


ENST00000544297.1/ENST00000456916.1/ENST00000388812.4


chr16_+_57685422 2.85 0.43 5.56E-02 chr16:57685422-57685484 + 5UTR_inner_exon,S ENST00000544297.1 GPR56 G protein-coupled

receptor 56

chr16_+_67876183 -0.43 4.82 4.26E-02 chr16:67876183-67876240 + TSS,S ENST00000303596.1 THAP11 THAP domain containing 11

chr16_+_69599832 0.56 5.53 1.29E-02 chr16:69599832-69599959 + TSS,S ENST00000354436.2 NFAT5nuclear factor of activated T-cells 5, tonicity-responsive


ENST00000539778.1/ENST00000537098.1 CMIP c-Maf inducing protein

chr16_+_85833176 -0.39 8.26 2.58E-02 chr16:85833176-85833356 + TSS,S ENST00000253452.2 COX4I1 cytochrome c oxidase subunit IV isoform 1

chr16_-_2059758 -0.92 1.61 8.81E-02 chr16:2059758-2059845 - TSS,S ENST00000431526.1 ZNF598 zinc finger protein 598

chr16_-_2205324 -0.73 2.30 9.41E-02 chr16:2205324-2205430 - TSSregion500,AS ENST00000326181.6 TRAF7

TNF receptor-associated factor 7, E3 ubiquitin protein ligase



chr16_-_405193 1.08 3.60 6.92E-03 chr16:405193-405380 - intergenic intergenic NA NAchr16_-_4465808 1.07 1.46 8.17E-02 chr16:4465808-4465939 - TSS,S ENST00000539968.1 CORO7 coronin 7

chr16_-_68056996 -0.73 3.69 2.69E-02 chr16:68056996-68057147 - 5UTR_first_exon,S ENST00000332395.5 DDX28 DEAD (Asp-Glu-Ala-Asp)

box polypeptide 28



MPRIP myosin phosphatase Rho interacting protein


148148

Persson et al.

chr17_+_37865774 1.10 3.49 6.83E-02 chr17:37865774-37865959 + CDS_or_noncoding_first_intron,S ENST00000445658.2 ERBB2

v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)


ENST00000225941.1/ENST00000419580.2 ABI3 ABI family, member 3

chr17_+_53046052 0.79 3.24 9.63E-02 chr17:53046052-53046205 + TSS,S


STXBP4 syntaxin binding protein 4






LLGL2 lethal giant larvae homolog 2 (Drosophila)

chr17_+_7789501 1.69 0.96 1.16E-02 chr17:7789501-7789570 + CDS_or_noncoding_first_intron,S ENST00000380358.4 CHD3 chromodomain helicase

DNA binding protein 3

chr17_+_78261987 1.20 2.33 2.04E-02 chr17:78261987-78262127 + TSSregion500,S ENST00000559070.1 RNF213 ring finger protein 213


chr17_-_33864635 0.59 5.93 2.42E-02 chr17:33864635-33864792 - TSSregion500,S ENST00000361112.4 SLFN12L schlafen family member 12-like

chr17_-_3749374 1.53 0.51 7.91E-02 chr17:3749374-3749439 - TSSregion500,S ENST00000158149.3 C17ORF85 NA


ENST00000316878.6/ENST00000501501.2/ENST00000513579.1

PPP1R9B protein phosphatase 1, regulatory subunit 9B

chr17_-_49198086 0.43 5.75 6.33E-02 chr17:49198086-49198263 - TSS,S



chr17_-_5342333 -0.33 6.53 7.17E-02 chr17:5342333-5342501 - TSS,S ENST00000225698.3 C1QBPcomplement component 1, q subcomponent binding protein


149149

Persson et al.


ENST00000448097.1/ENST00000254846.4 KDM6B lysine (K)-specific

demethylase 6B




ENST00000261598.8/ENST00000320876.5 SMCHD1



ENST00000261598.8/ENST00000320876.5 SMCHD1


chr18_+_32650149 2.06 0.46 2.84E-02 chr18:32650149-32650248 + 5UTR_inner_exon,S ENST00000413393.1 MAPRE2

microtubule-associated protein, RP/EB family, member 2

chr18_+_39535136 0.35 6.23 8.71E-02 chr18:39535136-39535324 + TSS,S ENST00000262039.2/ENST00000398870.2 PIK3C3

phosphatidylinositol 3-kinase, catalytic subunit type 3


WDR7 WD repeat domain 7

chr18_+_59854480 0.48 6.42 1.80E-02 chr18:59854480-59854597 + TSS,S ENST00000398130.2/ENST00000256858.5 KIAA1468 KIAA1468


ENST00000398130.2/ENST00000256858.5 KIAA1468 KIAA1468

chr18_+_72265072 0.51 4.29 7.10E-02 chr18:72265072-72265154 + TSSregion500,AS ENST00000382649.2 AC116904.1 NA

chr18_+_76829382 0.57 4.84 6.60E-02 chr18:76829382-76829482 + TSS,S


ATP9B ATPase, class II, type 9B

chr19_+_1274437 -2.25 0.36 8.81E-02 chr19:1274437-1274441 + 3UTR_inner_exon,S ENST00000444172.2 CIRBP cold inducible RNA

binding protein

chr19_+_12848278 -0.50 5.65 5.26E-03 chr19:12848278-12848408 + TSS,S ENST00000357332.3 ASNA1arsA arsenite transporter, ATP-binding, homolog 1 (bacterial)


ENST00000397661.1/ENST00000360105.3/ENST00000358552.3

NFIXnuclear factor I/X (CCAAT-binding transcription factor)

150150

Persson et al.

chr19_+_16254473 0.43 7.11 4.26E-02 chr19:16254473-16254655 + TSS,S ENST00000535834.1 HSH2D hematopoietic SH2 domain containing


ENST00000253680.6/ENST00000397372.4/ENST00000535834.1

HSH2D hematopoietic SH2 domain containing

chr19_+_17295404 0.94 2.24 5.44E-02 chr19:17295404-17295548 + 5UTR_inner_intron,S ENST00000319396.5 MYO9B myosin IXB

chr19_+_1905326 -0.40 4.83 8.80E-02 chr19:1905326-1905429 + TSS,S



chr19_+_3094285 -0.96 1.79 8.94E-02 chr19:3094285-3094411 + TSS,S ENST00000078429.3 GNA11

guanine nucleotide binding protein (G protein), alpha 11 (Gq class)




chr19_+_39897475 -0.56 10.52 5.24E-02 chr19:39897475-39897519 + TSS,S ENST00000248673.3 ZFP36zinc finger protein 36, C3H type, homolog (mouse)




ENST00000352456.2/ENST00000392006.2/ENST00000378215.3

HNRNPUL1 heterogeneous nuclear ribonucleoprotein U-like 1


chr19_+_45971244 -1.62 5.40 5.26E-03 chr19:45971244-45971289 + TSS,S



chr19_+_48824690 0.70 2.35 6.72E-02 chr19:48824690-48824806 +CDS_or_noncoding_first_intron,AS

ENST00000504608.1/ENST00000497803.1 CTC-241F20.2

chr19_+_49617600 0.98 1.82 7.26E-02 chr19:49617600-49617652 + TSS,S ENST00000221459.2 LIN7B lin-7 homolog B (C. elegans)

chr19_+_49999627 -0.39 9.52 8.15E-02 chr19:49999627-49999702 + TSS,S ENST00000270625.1 RPS11 ribosomal protein S11

151151

Persson et al.



MYADM myeloid-associated differentiation marker

chr19_+_6361522 -0.38 4.68 8.15E-02 chr19:6361522-6361673 + TSSregion500,S ENST00000245816.3 CLPP

ClpP caseinolytic peptidase, ATP-dependent, proteolytic subunit homolog (E. coli)


ENST00000458235.1/ENST00000527670.1 JAK3 Janus kinase 3



MKNK2 MAP kinase interacting serine/threonine kinase 2



ENST00000316763.2/ENST00000377011.1/ENST00000424804.2

VRK3 vaccinia related kinase 3

chr19_-_50512488 1.64 0.49 7.91E-02 chr19:50512488-50512639 - 5UTR_inner_intron,S ENST00000443401.2 VRK3 vaccinia related kinase 3


CDC14ACDC14 cell division cycle 14 homolog A (S. cerevisiae)

chr1_+_110193969 -1.67 0.60 3.50E-02 chr1:110193969-110193982 + TSSregion500,S ENST00000411964.1 RP5-1160K1.1

chr1_+_113217056 1.14 2.17 1.59E-03 chr1:113217056-113217109 + TSS,S ENST00000369645.1 MOV10Mov10, Moloney leukemia virus 10, homolog (mouse)

chr1_+_113711575 -0.66 3.51 5.17E-02 chr1:113711575-113711613 + TSSregion500,S ENST00000457967.1 RP11-389O22.4

chr1_+_116519121 0.78 2.38 8.81E-02 chr1:116519121-116519164 + TSSregion500,S ENST00000369503.4/ENST00000369502.1 SLC22A15 solute carrier family 22,

member 15

chr1_+_118168067 -1.73 0.61 8.32E-02 chr1:118168067-118168082 + 3UTR_last_exon,S ENST00000369448.3 FAM46C family with sequence



ENST00000362074.6/ENST00000344859.3 NOTCH2NL


HIST2H4A histone cluster 2, H4a

152152

Persson et al.

chr1_+_151227171 -0.39 5.54 9.88E-02 chr1:151227171-151227268 + TSS,S


PSMD4proteasome (prosome, macropain) 26S subunit, non-ATPase, 4


chr1_+_158901305 0.70 6.62 2.82E-02 chr1:158901305-158901446 + TSS,S


PYHIN1 pyrin and HIN domain family, member 1

chr1_+_158979798 0.74 3.98 7.67E-02 chr1:158979798-158979808 + TSS,S ENST00000430894.2 IFI16 interferon, gamma-inducible protein 16


ENST00000367853.3/ENST00000474729.1 MPZL1 myelin protein zero-like 1




chr1_+_174128592 0.58 5.70 2.53E-02 chr1:174128592-174128765 + TSS,S ENST00000251507.4/ENST00000457696.1 RABGAP1L RAB GTPase activating

protein 1-like

chr1_+_174188243 1.23 2.71 9.72E-03 chr1:174188243-174188403 + TSS,S ENST00000367692.3 RABGAP1L RAB GTPase activating protein 1-like


ENST00000251507.4/ENST00000367692.3 RABGAP1L RAB GTPase activating

protein 1-like


RGS13 regulator of G-protein signaling 13

chr1_+_193091121 0.37 5.93 9.36E-02 chr1:193091121-193091296 + TSS,S ENST00000367435.3/ENST00000445394.2 CDC73



CDC73



ENST00000391959.3/ENST00000367270.4 PPP1R12B protein phosphatase 1,

regulatory subunit 12B

chr1_+_221052669 -0.60 4.51 8.61E-02 chr1:221052669-221052863 + 5UTR_first_exon,S ENST00000366903.5 HLX H2.0-like homeobox

chr1_+_228675040 -0.53 6.62 4.14E-02 chr1:228675040-228675163 + TSSregion500,S ENST00000305943.7 RNF187 ring finger protein 187

153153

Persson et al.

chr1_+_231762403 0.65 3.55 2.67E-02 chr1:231762403-231762591 + TSS,S





ENST00000389794.3/ENST00000389793.2/ENST00000468626.1



chr1_+_243419304 0.48 4.60 8.80E-02 chr1:243419304-243419465 + TSS,S


SDCCAG8 serologically defined colon cancer antigen 8

chr1_+_246690894 2.35 0.42 8.08E-02 chr1:246690894-246690947 + CDS_or_noncoding_last_intron,S ENST00000412354.1 RP11-

690C23.5

chr1_+_29424310 -0.76 2.88 7.95E-02 chr1:29424310-29424422 + TSSregion500,S ENST00000462032.1 EPB41


chr1_+_36396682 0.46 4.53 6.13E-02 chr1:36396682-36396870 + TSS,S ENST00000397828.2/ENST00000246314.6 EIF2C3 eukaryotic translation

initiation factor 2C, 3chr1_+_47845938 1.98 0.83 1.72E-02 chr1:47845938-47845953 + intergenic intergenic NA NA

chr1_+_53289085 -1.32 0.86 9.54E-02 chr1:53289085-53289215 + 3UTR_last_exon,S ENST00000294353.6 ZYG11B zyg-11 homolog B (C.

elegans)


ENST00000358193.3/ENST00000371273.3 C1ORF177 NA

chr1_+_67390620 0.38 4.86 9.30E-02 chr1:67390620-67390724 + TSS,S


MIER1mesoderm induction early response 1 homolog (Xenopus laevis)

chr1_+_67773024 1.62 1.28 3.70E-02 chr1:67773024-67773089 + TSS,S ENST00000371000.1/ENST00000262345.1 IL12RB2 interleukin 12 receptor,

beta 2

154154

Persson et al.

chr1_+_67773521 1.13 2.28 6.60E-02 chr1:67773521-67773591 + TSS,S ENST00000541374.1 IL12RB2 interleukin 12 receptor, beta 2

chr1_+_84609941 0.31 7.58 9.89E-02 chr1:84609941-84610054 + TSS,S ENST00000370685.3/ENST00000470673.1 PRKACB protein kinase, cAMP-

dependent, catalytic, beta

chr1_+_97187205 0.73 4.74 2.78E-03 chr1:97187205-97187402 + TSS,S


PTBP2 polypyrimidine tract binding protein 2

chr1_-_109506011 0.49 4.13 7.06E-02 chr1:109506011-109506152 - TSS,S


AKNAD1 AKNA domain containing 1

chr1_-_115053701 0.46 6.17 9.72E-03 chr1:115053701-115053873 - TSS,S ENST00000358465.2/ENST00000369543.2 TRIM33 tripartite motif containing

33

chr1_-_153918391 1.65 0.59 5.00E-02 chr1:153918391-153918513 - 5UTR_first_intron,S ENST00000361217.4 DENND4B DENN/MADD domain

containing 4B




SH2D1B SH2 domain containing 1B


ENST00000362089.5/ENST00000392122.3/ENST00000483825.1





chr1_-_170043623 0.54 4.12 7.99E-02 chr1:170043623-170043806 - TSS,S ENST00000367767.1 KIFAP3 kinesin-associated protein 3

chr1_-_173446127 0.75 2.79 3.47E-02 chr1:173446127-173446327 - TSS,S ENST00000421168.2 AL645568.1 NA



RFWD2ring finger and WD repeat domain 2, E3 ubiquitin protein ligase

155155

Persson et al.



chr1_-_206306021 0.70 3.70 6.33E-02 chr1:206306021-206306190 - TSS,S ENST00000436158.1/ENST00000455672.1 RP11-38J22.6

chr1_-_235292089 -0.52 6.62 1.54E-02 chr1:235292089-235292278 - TSS,S ENST00000366607.4 TOMM20translocase of outer mitochondrial membrane 20 homolog (yeast)


ENST00000430629.2/ENST00000536657.1 WASF2 WAS protein family,

member 2chr1_-_28437760 -1.68 0.56 9.44E-02 chr1:28437760-28437836 - intergenic intergenic NA NA



PTP4A2protein tyrosine phosphatase type IVA, member 2

chr1_-_51425737 0.46 4.70 5.18E-02 chr1:51425737-51425916 - TSS,S ENST00000371778.4/ENST00000543607.1 FAF1 Fas (TNFRSF6)

associated factor 1


LRP8low density lipoprotein receptor-related protein 8, apolipoprotein e receptor

chr1_-_89488399 0.61 4.14 7.99E-02 chr1:89488399-89488591 - TSS,S


GBP3 guanylate binding protein 3

chr1_-_93250595 0.65 3.75 6.75E-02 chr1:93250595-93250734 - TSS,S ENST00000474806.1 EVI5 ecotropic viral integration site 5

chr1_-_98386462 0.68 7.99 2.09E-06 chr1:98386462-98386637 - TSS,S



chr20_+_10415814 0.65 4.05 3.28E-02 chr20:10415814-10416011 + TSS,S ENST00000334534.5 C20ORF94 NA

chr20_+_15497339 -0.93 2.61 9.36E-02 chr20:15497339-15497349 + 5UTR_inner_intron,S ENST00000402914.1 MACROD2 MACRO domain

containing 2



156156

Persson et al.



RALGAPBRal GTPase activating protein, beta subunit (non-catalytic)




RBCK1RanBP-type and C3HC4-type zinc finger containing 1


ENST00000217086.3/ENST00000371539.3/ENST00000395997.3

SALL4 sal-like 4 (Drosophila)



PLCB1phospholipase C, beta 1 (phosphoinositide-specific)

chr20_-_1350022 -1.96 0.78 1.48E-02 chr20:1350022-1350071 - 3UTR_last_exon,S ENST00000400137.4 FKBP1A FK506 binding protein

1A, 12kDa






TRPM2transient receptor potential cation channel, subfamily M, member 2

chr21_-_36421080 1.48 0.73 8.06E-02 chr21:36421080-36421110 - 5UTR_inner_intron,S

ENST00000431176.1/ENST00000399245.2/ENST00000486278.2

RUNX1 runt-related transcription factor 1


ENST00000338785.3/ENST00000455097.1/ENST00000426672.1

DYRK1Adual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A



157157

Persson et al.

chr22_+_44584298 -0.79 3.42 7.91E-02 chr22:44584298-44584310 + CDS_or_noncoding_first_exon,S ENST00000468564.1 PARVG parvin, gamma




chr22_-_38539356 1.00 1.91 6.13E-02 chr22:38539356-38539520 - TSS,S ENST00000498338.1 PLA2G6phospholipase A2, group VI (cytosolic, calcium-independent)

chr22_-_39715561 -0.48 7.57 9.36E-02 chr22:39715561-39715684 - TSS,S




MLC1megalencephalic leukoencephalopathy with subcortical cysts 1

chr2_+_102353931 1.92 1.49 9.72E-03 chr2:102353931-102353966 + CDS_or_noncoding_first_intron,S ENST00000417294.1 MAP4K4

mitogen-activated protein kinase kinase kinase kinase 4

chr2_+_103034997 0.92 5.47 6.38E-03 chr2:103034997-103035149 + TSS,S ENST00000264260.2 IL18RAP interleukin 18 receptor accessory protein

chr2_+_120687240 0.61 6.12 8.98E-02 chr2:120687240-120687438 + TSS,S ENST00000544261.1 PTPN4

protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)

chr2_+_130939729 -0.54 5.91 3.15E-02 chr2:130939729-130939893 + TSS,S ENST00000409255.1/ENST00000455239.1 MZT2B mitotic spindle organizing

protein 2Bchr2_+_143828458 0.77 7.46 6.27E-02 chr2:143828458-143828623 + intergenic intergenic NA NA


protein 15


ENST00000295095.6/ENST00000552641.1/ENST00000469117.1



ENST00000295095.6/ENST00000552641.1/ENST00000469117.1


158158

Persson et al.


ENST00000295095.6/ENST00000552641.1/ENST00000469117.1



ENST00000295095.6/ENST00000552641.1/ENST00000469117.1



ENST00000295095.6/ENST00000552641.1/ENST00000469117.1



ENST00000295095.6/ENST00000552641.1/ENST00000469117.1




HNRNPA3 heterogeneous nuclear ribonucleoprotein A3

chr2_+_197076186 -1.63 1.21 6.33E-02 chr2:197076186-197076333 +CDS_or_noncoding_last_intron,AS

ENST00000409111.1/ENST00000260983.2 HECW2

HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2


chr2_+_202047797 0.44 5.62 9.33E-02 chr2:202047797-202047887 + TSS,S


CASP10caspase 10, apoptosis-related cysteine peptidase

chr2_+_203043983 -0.70 2.86 8.98E-02 chr2:203043983-203044092 + TSS,S ENST00000429685.1 AC079354.2


ENST00000303116.6/ENST00000392238.2 FAM117B family with sequence


chr2_+_209130906 0.47 6.33 2.80E-02 chr2:209130906-209131086 + TSS,S



chr2_+_223725685 0.42 5.62 3.43E-02 chr2:223725685-223725816 + TSS,S ENST00000535678.1 ACSL3acyl-CoA synthetase long-chain family member 3



SP140 SP140 nuclear body protein

159159

Persson et al.

chr2_+_232826324 0.55 4.38 9.72E-03 chr2:232826324-232826474 + TSS,S


DIS3L2DIS3 mitotic control homolog (S. cerevisiae)-like 2


ENST00000338315.4/ENST00000406420.3/ENST00000495018.1

MFSD2Bmajor facilitator superfamily domain containing 2B

chr2_+_29237233 1.01 2.21 6.33E-02 chr2:29237233-29237376 + TSS,S ENST00000465300.1 FAM179A family with sequence similarity 179, member A


CLIP4CAP-GLY domain containing linker protein family, member 4

chr2_+_30457125 -0.54 4.67 9.33E-02 chr2:30457125-30457217 + TSS,S ENST00000484150.1 LBHlimb bud and heart development homolog (mouse)

chr2_+_43453937 -0.91 1.86 7.48E-02 chr2:43453937-43454014 + TSSregion500,AS ENST00000282388.3 ZFP36L2 zinc finger protein 36,

C3H type-like 2

chr2_+_61404537 0.61 5.28 3.37E-03 chr2:61404537-61404667 + TSS,S


AHSA2

AHA1, activator of heat shock 90kDa protein ATPase homolog 2 (yeast)

chr2_+_65495021 2.04 0.84 7.79E-02 chr2:65495021-65495028 + CDS_or_noncoding_last_intron,S

ENST00000260641.5/ENST00000377982.4/ENST00000535303.1

ACTR2 ARP2 actin-related protein 2 homolog (yeast)




160160

Persson et al.

chr2_+_71558805 0.43 6.53 4.30E-02 chr2:71558805-71558997 + TSS,S


ZNF638 zinc finger protein 638


chr2_+_98329970 2.48 0.64 3.72E-03 chr2:98329970-98329976 + TSSregion500,S ENST00000264972.5/ENST00000483781.1 ZAP70


chr2_+_99061292 0.41 6.47 7.94E-02 chr2:99061292-99061491 + TSS,S


INPP4Ainositol polyphosphate-4-phosphatase, type I, 107kDa

chr2_-_114514074 0.40 5.12 3.61E-02 chr2:114514074-114514261 - TSS,S ENST00000409342.1/ENST00000498768.1 SLC35F5 solute carrier family 35,

member F5

chr2_-_136875661 -0.70 9.95 6.83E-02 chr2:136875661-136875767 - TSS,S ENST00000241393.3/ENST00000537957.1 CXCR4 chemokine (C-X-C motif)

receptor 4

chr2_-_15701338 0.46 5.09 6.28E-02 chr2:15701338-15701511 - TSS,S ENST00000441750.1/ENST00000281513.5 NBAS neuroblastoma amplified

sequence


GALNT3

UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)

chr2_-_169103949 0.69 3.98 8.80E-02 chr2:169103949-169104145 - 5UTR_first_exon,S ENST00000355999.4 STK39 serine threonine kinase

39


STAT4 signal transducer and activator of transcription 4

chr2_-_192700462 1.74 0.53 5.27E-02 chr2:192700462-192700500 - 3UTR_last_exon,S ENST00000304141.4 SDPR serum deprivation

response

chr2_-_198175391 0.41 6.94 6.71E-02 chr2:198175391-198175567 - TSS,S



161161

Persson et al.


PUM2 pumilio homolog 2 (Drosophila)


ATAD2B ATPase family, AAA domain containing 2B


MAP4K3mitogen-activated protein kinase kinase kinase kinase 3


chr2_-_8464701 1.67 2.34 1.76E-02 chr2:8464701-8464864 - TSS,S ENST00000430192.1 LINC00299 long intergenic non-protein coding RNA 299

chr2_-_85829443 1.75 0.65 7.17E-02 chr2:85829443-85829549 - TSS,S ENST00000409668.1 TMEM150A transmembrane protein 150A


CHMP3 charged multivesicular body protein 3


ENST00000296161.4/ENST00000383661.3 DTX3L deltex 3-like (Drosophila)

chr3_+_134514064 1.56 1.90 3.35E-02 chr3:134514064-134514224 + TSS,S ENST00000482618.1/ENST00000398015.3 EPHB1 EPH receptor B1


ENST00000398015.3/ENST00000493838.1 EPHB1 EPH receptor B1




chr3_+_142842343 1.36 0.77 6.09E-02 chr3:142842343-142842375 + TSSregion500,S ENST00000483262.1 RP11-80H8.4


ENST00000477171.1 MBNL1 muscleblind-like splicing regulator 1







162162

Persson et al.



chr3_+_187871671 0.79 3.50 2.82E-02 chr3:187871671-187871727 + TSS,S ENST00000414139.1 LPPLIM domain containing preferred translocation partner in lipoma




chr3_+_197677027 -0.42 7.78 3.23E-02 chr3:197677027-197677103 + TSS,S




ENST00000431569.1 FAM157A family with sequence similarity 157, member A




chr3_+_42632316 -0.44 5.33 6.27E-02 chr3:42632316-42632406 + TSSregion500,S ENST00000011691.4/ENST00000474941.1 SS18L2

synovial sarcoma translocation gene on chromosome 18-like 2




163163

Persson et al.

chr3_+_42642112 0.45 5.64 8.31E-02 chr3:42642112-42642235 + TSS,S



chr3_+_51428637 -0.53 4.46 7.95E-02 chr3:51428637-51428755 + TSS,S ENST00000323686.4 RBM15B RNA binding motif protein 15B

chr3_+_63850179 1.16 1.57 1.16E-02 chr3:63850179-63850271 + TSS,S


ATXN7 ataxin 7

chr3_+_97540792 0.58 3.71 4.02E-02 chr3:97540792-97540948 + TSS,S ENST00000419587.1 AC110491.1 NA


CBLB Cbl proto-oncogene, E3 ubiquitin protein ligase B

chr3_-_114866047 0.62 3.97 6.32E-02 chr3:114866047-114866194 - TSS,S ENST00000357258.3/ENST00000488663.1 ZBTB20 zinc finger and BTB

domain containing 20

chr3_-_119813135 0.49 6.14 1.16E-02 chr3:119813135-119813335 - TSS,S ENST00000264235.8 GSK3B glycogen synthase kinase 3 beta

chr3_-_13009094 -0.84 4.58 2.41E-02 chr3:13009094-13009256 - TSS,S ENST00000273221.4 IQSEC1 IQ motif and Sec7 domain 1

chr3_-_141944296 0.69 4.13 3.07E-02 chr3:141944296-141944478 - TSS,S


GK5 glycerol kinase 5 (putative)


ATR ataxia telangiectasia and Rad3 related


SLC9A9



chr3_-_169482780 -0.60 3.79 8.17E-02 chr3:169482780-169482971 - TSS,S ENST00000363312.1 TERC telomerase RNA component

chr3_-_171178062 0.49 5.70 7.28E-02 chr3:171178062-171178262 - TSS,S


TNIK TRAF2 and NCK interacting kinase

164164

Persson et al.

chr3_-_42003514 0.73 3.75 2.58E-02 chr3:42003514-42003686 - TSS,S


ULK4 unc-51-like kinase 4 (C. elegans)

chr4_+_106394618 -1.58 0.72 6.72E-02 chr4:106394618-106394814 + TSSregion500,AS ENST00000502596.1 PPA2 pyrophosphatase

(inorganic) 2

chr4_+_113218425 0.45 6.74 5.70E-02 chr4:113218425-113218601 + TSS,S



chr4_+_117265139 1.19 1.04 6.16E-02 chr4:117265139-117265257 + intergenic intergenic NA NAchr4_+_119199844 -0.88 6.14 8.08E-02 chr4:119199844-119199924 + TSS,S ENST00000500560.1 SNHG8 NAchr4_+_123012762 -1.97 0.54 2.69E-02 chr4:123012762-123012763 + intergenic intergenic NA NAchr4_+_123073450 0.42 5.97 8.80E-02 chr4:123073450-123073647 + TSS,S ENST00000264501.4 KIAA1109 KIAA1109

chr4_+_1243038 -1.14 1.23 9.18E-02 chr4:1243038-1243077 + TSSregion500,S ENST00000507044.1 C4ORF42 NA

chr4_+_146677162 -0.89 2.71 5.00E-02 chr4:146677162-146677176 + CDS_or_noncoding_last_intron,S ENST00000510096.1 C4ORF51 NA



chr4_+_152833938 1.21 1.67 4.58E-02 chr4:152833938-152834099 +CDS_or_noncoding_first_intron,AS

ENST00000510416.1 RP11-73G16.3




WWC2 WW and C2 domain containing 2


ENST00000508235.1 RNF4 ring finger protein 4

165165

Persson et al.

chr4_+_2813932 0.51 5.55 6.33E-02 chr4:2813932-2814108 + TSS,S


SH3BP2 SH3-domain binding protein 2

chr4_+_2965289 1.05 1.20 7.10E-02 chr4:2965289-2965398 + TSS,S ENST00000398051.4/ENST00000503518.1 GRK4 G protein-coupled

receptor kinase 4chr4_+_35068262 -1.75 0.69 2.04E-02 chr4:35068262-35068268 + intergenic intergenic NA NA

chr4_+_37912620 2.06 0.86 2.52E-02 chr4:37912620-37912799 + 5UTR_first_intron,S ENST00000454732.2 TBC1D1

TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1


SLC4A4solute carrier family 4, sodium bicarbonate cotransporter, member 4

chr4_+_89300166 0.64 2.95 8.65E-02 chr4:89300166-89300220 + TSS,S ENST00000502870.1 HERC6

HECT and RLD domain containing E3 ubiquitin protein ligase family member 6

chr4_-_107237292 0.62 3.56 9.23E-02 chr4:107237292-107237440 - TSS,S


TBCK TBC1 domain containing kinase

chr4_-_111119637 1.00 2.39 3.50E-02 chr4:111119637-111119821 - TSS,S ENST00000394607.3/ENST00000506461.1 ELOVL6 ELOVL fatty acid

elongase 6

chr4_-_130014582 0.47 6.17 8.43E-02 chr4:130014582-130014775 - TSS,S


SCLT1 sodium channel and clathrin linker 1



chr4_-_147442994 0.48 4.44 8.80E-02 chr4:147442994-147443132 - TSS,S


SLC10A7

solute carrier family 10 (sodium/bile acid cotransporter family), member 7


LRBALPS-responsive vesicle trafficking, beach and anchor containing

chr4_-_154605156 -1.46 1.45 5.56E-02 chr4:154605156-154605348 - intergenic intergenic NA NAchr4_-_48116463 1.46 3.90 9.50E-03 chr4:48116463-48116595 - TSS,S ENST00000506073.1 TXK TXK tyrosine kinase

166166

Persson et al.

chr4_-_48782181 0.41 4.93 8.17E-02 chr4:48782181-48782341 - TSS,S


FRYL FRY-like

chr4_-_48908707 -0.47 4.31 7.17E-02 chr4:48908707-48908834 - TSS,S


OCIAD2 OCIA domain containing 2

chr4_-_68566794 0.41 5.37 7.67E-02 chr4:68566794-68566955 - TSS,S


UBA6 ubiquitin-like modifier activating enzyme 6

chr4_-_74864383 1.71 0.59 8.15E-02 chr4:74864383-74864384 - TSSregion500,S ENST00000296027.4 CXCL5 chemokine (C-X-C motif) ligand 5




chr5_+_109025071 0.48 3.94 9.54E-02 chr5:109025071-109025143 + TSSregion500,S ENST00000261483.4 MAN2A1 mannosidase, alpha, class 2A, member 1

chr5_+_109257711 -1.96 0.53 9.72E-03 chr5:109257711-109257856 + intergenic intergenic NA NAchr5_+_115898212 -0.79 6.28 2.97E-03 chr5:115898212-115898282 + TSS,S ENST00000478778.1 CTB-118N6.1

chr5_+_139487359 0.89 2.77 2.41E-02 chr5:139487359-139487434 + TSS,S ENST00000505703.1 PURA purine-rich element binding protein A


protein 26


ENST00000378004.3/ENST00000274498.4/ENST00000378013.2








chr5_+_145838658 1.18 1.84 5.00E-02 chr5:145838658-145838847 + TSS,S ENST00000513298.1 TCERG1 transcription elongation regulator 1

167167

Persson et al.



TNIP1 TNFAIP3 interacting protein 1

chr5_+_151176790 1.51 0.66 7.91E-02 chr5:151176790-151176956 + 5UTR_inner_exon,S ENST00000543466.1 G3BP1

GTPase activating protein (SH3 domain) binding protein 1


ENST00000231238.4/ENST00000522793.1 TTC1 tetratricopeptide repeat

domain 1

chr5_+_175665368 0.82 2.05 7.99E-02 chr5:175665368-175665494 + TSS,S


C5ORF25 NA

chr5_+_177027101 -0.77 3.74 2.52E-02 chr5:177027101-177027237 + TSS,S




ENST00000381286.3/ENST00000523039.1 IL6ST

interleukin 6 signal transducer (gp130, oncostatin M receptor)

chr5_+_60628054 0.66 5.47 2.62E-03 chr5:60628054-60628105 + TSS,S ENST00000252744.5 ZSWIM6 zinc finger, SWIM-type containing 6


ENST00000341845.6/ENST00000430046.2/ENST00000512348.1

FCHO2 FCH domain only 2

chr5_+_74348454 -1.47 1.04 5.18E-02 chr5:74348454-74348582 + TSS,AS ENST00000503568.1 RP11-229C3.2

chr5_+_75699065 0.65 5.27 3.23E-02 chr5:75699065-75699177 + TSS,S ENST00000274364.6/ENST00000379730.3 IQGAP2

IQ motif containing GTPase activating protein 2




168168

Persson et al.

chr5_+_79703805 0.53 5.02 2.04E-02 chr5:79703805-79703925 + TSS,S





VCAN versican

chr5_+_85913712 -0.46 8.26 8.89E-02 chr5:85913712-85913905 + TSS,S


COX7C cytochrome c oxidase subunit VIIc


ENST00000502934.1/ENST00000507217.1

RP11-348J24.2

chr5_+_96271737 0.38 6.58 9.36E-02 chr5:96271737-96271841 + 5UTR_first_exon,S ENST00000231368.5 LNPEP leucyl/cystinyl

aminopeptidase

chr5_-_130970776 0.48 5.69 5.00E-02 chr5:130970776-130970953 - TSS,S


RAPGEF6 Rap guanine nucleotide exchange factor (GEF) 6

chr5_-_18746175 1.08 2.80 9.72E-03 chr5:18746175-18746329 - TSS,S ENST00000512978.1 CTD-2023M8.1

chr5_-_36151923 0.45 4.10 8.99E-02 chr5:36151923-36152096 - TSS,S ENST00000296603.4/ENST00000546130.1 LMBRD2 LMBR1 domain

containing 2

chr5_-_53606233 0.45 6.21 5.55E-02 chr5:53606233-53606431 - TSS,S


ARL15 ADP-ribosylation factor-like 15

169169

Persson et al.



TAF9

TAF9 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 32kDa


AP3B1 adaptor-related protein complex 3, beta 1 subunit



chr5_-_94417257 0.45 6.48 4.26E-02 chr5:94417257-94417377 - TSS,S




QRSL1glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1

chr6_+_108880957 -0.59 5.98 4.48E-02 chr6:108880957-108881031 + TSSregion500,S ENST00000343882.6 FOXO3 forkhead box O3

chr6_+_110012444 0.41 5.44 3.43E-02 chr6:110012444-110012546 + TSS,S ENST00000441478.2/ENST00000230124.3 FIG4

FIG4 homolog, SAC1 lipid phosphatase domain containing (S. cerevisiae)


chr6_+_138188328 -1.19 6.72 8.15E-02 chr6:138188328-138188507 + TSS,S ENST00000421450.1/ENST00000420009.1 TNFAIP3 tumor necrosis factor,

alpha-induced protein 3

chr6_+_144606062 0.69 3.30 4.80E-02 chr6:144606062-144606170 + upstream1000,S ENST00000433557.1 UTRN utrophin


chr6_+_144665236 0.65 7.40 2.78E-03 chr6:144665236-144665413 + TSS,S ENST00000421035.1 UTRN utrophin

chr6_+_15249094 0.54 3.72 8.80E-02 chr6:15249094-15249175 + TSS,S ENST00000397311.3 JARID2 jumonji, AT rich interactive domain 2


170170

Persson et al.

chr6_+_16238702 -0.76 6.67 7.99E-02 chr6:16238702-16238902 + TSS,S ENST00000259727.4 GMPRguanosine monophosphate reductase

chr6_+_16295576 -1.75 1.00 7.99E-02 chr6:16295576-16295702 + CDS_or_noncoding_last_exon,S ENST00000544145.1 GMPR

guanosine monophosphate reductase

chr6_+_167370155 -0.66 4.00 8.98E-02 chr6:167370155-167370352 + TSS,AS ENST00000508775.1 RNASET2 ribonuclease T2

chr6_+_20534662 0.56 5.59 1.39E-02 chr6:20534662-20534813 + TSS,S ENST00000378624.4/ENST00000274695.4 CDKAL1

CDK5 regulatory subunit associated protein 1-like 1

chr6_+_26204717 -0.44 9.31 4.75E-02 chr6:26204717-26204861 + TSS,S ENST00000360441.4 HIST1H4E histone cluster 1, H4e

chr6_+_31601762 -1.14 1.96 1.50E-03 chr6:31601762-31601777 + TSSregion500,S ENST00000460302.1/ENST00000484787.1 PRRC2A proline-rich coiled-coil 2A

chr6_+_37897727 1.40 1.21 2.03E-02 chr6:37897727-37897896 + TSS,S ENST00000373389.5 ZFAND3 zinc finger, AN1-type domain 3


ENST00000450671.1 RP3-475N16.1

chr6_+_43603551 -0.53 3.48 7.99E-02 chr6:43603551-43603610 + TSS,S ENST00000372171.4/ENST00000508232.1 MAD2L1BP MAD2L1 binding protein


PRIM2 primase, DNA, polypeptide 2 (58kDa)


ENST00000463016.1/ENST00000460913.1 CDK19 cyclin-dependent kinase

19

chr6_-_116600964 -0.39 5.95 3.82E-02 chr6:116600964-116601122 - TSS,S ENST00000368608.3/ENST00000545830.1 TSPYL1 TSPY-like 1

chr6_-_118972658 0.49 4.29 6.72E-02 chr6:118972658-118972805 - TSSregion500,S ENST00000368491.3/ENST00000419517.2 C6ORF204 NA

chr6_-_130536675 0.72 6.29 1.18E-02 chr6:130536675-130536860 - TSS,S ENST00000532763.1 SAMD3 sterile alpha motif domain containing 3

chr6_-_137113491 0.44 5.30 7.17E-02 chr6:137113491-137113690 - TSS,S ENST00000359015.4/ENST00000367768.3 MAP3K5 mitogen-activated protein

kinase kinase kinase 5


chr6_-_152957914 0.74 4.49 1.69E-02 chr6:152957914-152958087 - TSS,S ENST00000423061.1/ENST00000367248.3 SYNE1

spectrin repeat containing, nuclear envelope 1

chr6_-_25452370 0.71 2.84 7.94E-02 chr6:25452370-25452519 -CDS_or_noncoding_last_exon,AS

ENST00000461945.1 LRRC16A leucine rich repeat containing 16A

171171

Persson et al.




chr6_-_35026708 2.07 0.47 6.33E-02 chr6:35026708-35026834 -CDS_or_noncoding_first_intron,AS

ENST00000470698.1 ANKS1Aankyrin repeat and sterile alpha motif domain containing 1A

chr6_-_38607589 0.59 3.49 7.94E-02 chr6:38607589-38607760 - TSS,S ENST00000481247.1/ENST00000498633.1 BTBD9 BTB (POZ) domain

containing 9

chr6_-_84937306 0.85 2.66 6.27E-02 chr6:84937306-84937410 - TSS,S


KIAA1009 KIAA1009

chr6_-_89673243 0.48 4.93 1.54E-02 chr6:89673243-89673367 - TSS,S


RNGTT RNA guanylyltransferase and 5'-phosphatase

chr7_+_105172607 0.40 4.77 8.15E-02 chr7:105172607-105172776 + TSS,S


RINT1 RAD50 interactor 1

chr7_+_131012587 0.45 6.65 1.84E-02 chr7:131012587-131012732 + TSS,S



chr7_+_132720264 -1.76 0.63 8.17E-02 chr7:132720264-132720434 + 5UTR_inner_exon,AS ENST00000448615.2 MIR3654 microRNA 3654

chr7_+_132937757 0.46 6.07 2.58E-02 chr7:132937757-132937915 + TSS,S


EXOC4 exocyst complex component 4

chr7_+_139586200 1.34 1.96 4.24E-02 chr7:139586200-139586214 + CDS_or_noncoding_first_intron,S ENST00000462275.1 TBXAS1 thromboxane A synthase

1 (platelet)


172172

Persson et al.



CREB5 cAMP responsive element binding protein 5

chr7_+_3018316 0.98 2.49 5.17E-02 chr7:3018316-3018483 + 5UTR_first_intron,AS ENST00000396946.4 CARD11

caspase recruitment domain family, member 11

chr7_+_37723315 0.71 5.40 1.32E-02 chr7:37723315-37723483 + TSS,S





AC004980.7




chr7_+_91570143 0.52 4.97 6.28E-02 chr7:91570143-91570321 + TSS,S


AKAP9 A kinase (PRKA) anchor protein (yotiao) 9

chr7_+_93551021 1.49 0.95 6.27E-02 chr7:93551021-93551028 + TSSregion500,S ENST00000248564.4 GNG11guanine nucleotide binding protein (G protein), gamma 11


ENST00000359863.4/ENST00000355540.3 TRRAP

transformation/transcription domain-associated protein



chr7_-_127634546 1.99 0.42 7.03E-02 chr7:127634546-127634607 -CDS_or_noncoding_inner_intron,AS


SND1staphylococcal nuclease and tudor domain containing 1

173173

Persson et al.

chr7_-_128049944 -0.42 6.23 6.89E-02 chr7:128049944-128050068 - TSS,S


IMPDH1IMP (inosine 5'-monophosphate) dehydrogenase 1

chr7_-_130792748 0.51 5.78 5.75E-02 chr7:130792748-130792910 - TSS,S ENST00000423414.1/ENST00000429901.1 AC058791.2

chr7_-_17980042 0.36 5.84 7.91E-02 chr7:17980042-17980146 - TSS,S


SNX13 sorting nexin 13

chr7_-_25019697 0.57 4.38 7.99E-02 chr7:25019697-25019884 - TSS,S


OSBPL3 oxysterol binding protein-like 3


JAZF1 JAZF zinc finger 1

chr7_-_2883845 -0.69 4.70 4.26E-02 chr7:2883845-2884045 - TSS,S ENST00000275364.3 GNA12guanine nucleotide binding protein (G protein) alpha 12



AOAH acyloxyacyl hydrolase (neutrophil)


ELMO1 engulfment and cell motility 1

chr7_-_76751580 0.88 2.10 9.91E-02 chr7:76751580-76751665 - TSSregion500,S ENST00000443595.1 FAM185BPfamily with sequence similarity 185, member B pseudogene

174174

Persson et al.

chr7_-_91875170 0.67 3.55 5.00E-02 chr7:91875170-91875265 - TSS,S


KRIT1 KRIT1, ankyrin repeat containing




chr8_+_100025481 0.60 4.82 7.42E-02 chr8:100025481-100025543 + TSS,S






chr8_+_100287325 2.17 0.53 8.80E-02 chr8:100287325-100287470 + TSS,S ENST00000522802.1 VPS13B vacuolar protein sorting 13 homolog B (yeast)

chr8_+_119294354 1.30 1.70 8.81E-02 chr8:119294354-119294548 + TSS,S ENST00000366457.2/ENST00000449065.1 AC023590.1 Uncharacterized protein

175175

Persson et al.

chr8_+_124084855 0.77 3.78 2.58E-02 chr8:124084855-124085018 + TSS,S


WDR67 WD repeat domain 67


PVT1 Pvt1 oncogene (non-protein coding)



LRRC14 leucine rich repeat containing 14




ENST00000518881.1/ENST00000523883.1 SLC25A37


chr8_+_23430115 -1.85 0.49 1.74E-02 chr8:23430115-23430150 + TSSregion500,S ENST00000399967.3 AC051642.1

chr8_+_26149005 0.47 5.52 6.33E-02 chr8:26149005-26149147 + TSS,S


PPP2R2Aprotein phosphatase 2, regulatory subunit B, alpha

chr8_+_28747868 0.59 4.86 1.29E-02 chr8:28747868-28747935 + TSS,S


HMBOX1 homeobox containing 1

176176

Persson et al.

chr8_+_29952895 -0.36 7.21 6.33E-02 chr8:29952895-29953042 + TSS,S


LEPROTL1leptin receptor overlapping transcript-like 1

chr8_+_48651019 -1.71 0.54 4.26E-02 chr8:48651019-48651125 + TSSregion500,AS ENST00000542385.1 CEBPD CCAAT/enhancer binding

protein (C/EBP), delta

chr8_+_60568363 1.54 1.73 7.91E-02 chr8:60568363-60568548 + intergenic intergenic NA NAchr8_+_7380136 -1.26 2.19 3.55E-02 chr8:7380136-7380152 + intergenic intergenic NA NA

chr8_+_86132710 1.01 2.15 1.92E-02 chr8:86132710-86132860 + TSS,S ENST00000517831.1/ENST00000517298.1 CA13 carbonic anhydrase XIII



OTUD6B OTU domain containing 6B


PGCP NA

chr8_-_123683573 0.82 4.76 5.27E-02 chr8:123683573-123683766 - 5UTR_inner_intron,S ENST00000521608.1 RP11-

973F15.1

chr8_-_145016749 -0.77 2.66 9.87E-02 chr8:145016749-145016858 - TSSregion500,S ENST00000357649.2 PLEC plectin


ENST00000265713.2/ENST00000396930.3/ENST00000406337.1

KAT6A K(lysine) acetyltransferase 6A



ERICH1 glutamate-rich 1

chr8_-_67525448 1.01 3.55 1.54E-02 chr8:67525448-67525541 - TSS,S ENST00000522677.2/ENST00000517885.1 MYBL1

v-myb myeloblastosis viral oncogene homolog (avian)-like 1

chr8_-_71316022 0.69 2.84 4.19E-02 chr8:71316022-71316077 - TSS,S ENST00000452400.2 NCOA2 nuclear receptor coactivator 2

chr8_-_99057735 -0.71 9.85 8.80E-02 chr8:99057735-99057818 - TSS,S



177177

Persson et al.


ENST00000435485.1 RP11-308N19.1

chr9_+_111389046 -0.60 6.31 2.34E-02 chr9:111389046-111389163 + TSS,S ENST00000306634.3 RP11-220D10.1



AKNA AT-hook transcription factor

chr9_+_127420623 1.34 2.60 2.58E-02 chr9:127420623-127420808 + TSS,S ENST00000429139.1 MIR181A2HG MIR181A2 host gene (non-protein coding)


SNAPC3small nuclear RNA activating complex, polypeptide 3, 50kDa


CNTLN centlein, centrosomal protein

chr9_+_33993703 -1.14 1.08 8.79E-02 chr9:33993703-33993710 + 5UTR_inner_intron,AS ENST00000379239.4 UBAP2 ubiquitin associated

protein 2


JAK2 Janus kinase 2


ENST00000539801.1/ENST00000381652.3/ENST00000544510.1

JAK2 Janus kinase 2


KDM4C lysine (K)-specific demethylase 4C

chr9_+_82846961 0.88 2.30 6.85E-02 chr9:82846961-82847092 + intergenic intergenic NA NAchr9_+_92142178 1.50 1.18 3.47E-02 chr9:92142178-92142376 + intergenic intergenic NA NA



chr9_-_117135368 -1.66 1.04 6.33E-02 chr9:117135368-117135472 - 5UTR_inner_intron,S ENST00000223791.3 AKNA AT-hook transcription

factor

chr9_-_127624192 -0.36 9.02 7.06E-02 chr9:127624192-127624274 - TSS,S



chr9_-_27573654 1.02 2.36 8.97E-02 chr9:27573654-27573803 - TSS,S ENST00000379995.1 C9ORF72 NA

chr9_-_35103092 -0.51 4.74 7.94E-02 chr9:35103092-35103195 - TSS,S ENST00000356493.5/ENST00000452248.2 STOML2 stomatin (EPB72)-like 2


ENST00000286548.4/ENST00000411677.1 GNAQ

guanine nucleotide binding protein (G protein), q polypeptide

178178

Persson et al.


chr9_-_94173418 -1.28 2.36 3.15E-02 chr9:94173418-94173492 - 5UTR_first_intron,S

ENST00000375724.1/ENST00000297689.2 NFIL3 nuclear factor, interleukin

3 regulatedchr9_-_99616742 0.68 2.92 9.87E-02 chr9:99616742-99616832 - TSS,S ENST00000481138.1 ZNF782 zinc finger protein 782chrM_+_11848 -0.91 6.34 1.67E-02 chrM:11848-11913 + intergenic intergenic NA NAchrM_+_13003 -1.83 0.99 2.52E-02 chrM:13003-13004 + intergenic intergenic NA NAchrM_+_13053 -0.92 4.02 6.33E-02 chrM:13053-13056 + intergenic intergenic NA NAchrM_+_2701 -0.93 5.35 7.06E-02 chrM:2701-2704 + intergenic intergenic NA NAchrM_+_3642 -0.82 3.40 6.71E-02 chrM:3642-3644 + intergenic intergenic NA NAchrM_+_8635 -0.57 5.99 9.36E-02 chrM:8635-8670 + intergenic intergenic NA NAchrX_+_106917504 -1.17 1.76 6.34E-02 chrX:106917504-106917612 + intergenic intergenic NA NA

chrX_+_117629589 0.40 6.18 7.67E-02 chrX:117629589-117629665 + TSSregion500,S ENST00000276204.6/ENST00000276202.7 DOCK11 dedicator of cytokinesis

11

chrX_+_1387667 6.79 4.26 3.16E-02 chrX:1387667-1387812 + TSS,S


CSF2RA

colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)

chrX_+_155110927 6.81 4.40 2.75E-02 chrX:155110927-155111078 + TSS,S


VAMP7 vesicle-associated membrane protein 7


AKAP17A A kinase (PRKA) anchor protein 17A

chrX_+_2527283 5.69 2.68 9.26E-02 chrX:2527283-2527483 + TSS,S


CD99P1 CD99 molecule pseudogene 1

179179

Persson et al.


CD99 CD99 molecule

chrX_+_48814922 -1.04 1.62 9.41E-02 chrX:48814922-48814975 + TSSregion500,AS


OTUD5 OTU domain containing 5

chrX_+_77166100 0.40 5.62 7.42E-02 chrX:77166100-77166283 + TSS,S


ATP7AATPase, Cu++ transporting, alpha polypeptide

chrX_+_95939745 0.62 4.48 6.13E-02 chrX:95939745-95939863 + TSSregion500,S


DIAPH2 diaphanous homolog 2 (Drosophila)


chrX_-_1510944 9.08 7.01 5.08E-03 chrX:1510944-1511062 - TSS,S ENST00000475167.1/ENST00000484026.1 SLC25A6

solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6

chrX_-_153979267 0.52 4.42 5.75E-02 chrX:153979267-153979372 - TSS,SENST00000369575.3/ENST00000369568.4/ENST00000424127.2


chrX_-_1655991 7.44 5.19 1.16E-02 chrX:1655991-1656187 - TSS,S ENST00000381297.4 P2RY8 purinergic receptor P2Y, G-protein coupled, 8

chrX_-_53246951 1.45 1.24 6.72E-02 chrX:53246951-53247141 -CDS_or_noncoding_inner_exon,S


KDM5C lysine (K)-specific demethylase 5C

chrX_-_73511850 0.93 1.96 9.37E-02 chrX:73511850-73511920 - TSS,S ENST00000455395.1 FTXFTX transcript, XIST regulator (non-protein coding)

180180

244

Persson et al.

Table E8. Differentially expressed tag clusters for SA vs CA (glm analysis adjusted for neutrophil, eosinophil and lymphocyte counts as fractions of total leukocyte counts).


chr10_-_22292557 0.53 4.86 9.22E-02 chr10:22292557-22292701 - TSS,S ENST00000376980.3/ENST00000376946.1 DNAJC1 DnaJ (Hsp40) homolog,

subfamily C, member 1

chr10_-_98346682 0.41 5.99 9.60E-02 chr10:98346682-98346826 - TSS,S ENST00000371142.4 TM9SF3 transmembrane 9 superfamily member 3

chr11_+_58385890 -1.60 1.18 9.60E-02 chr11:58385890-58386064 + 3UTR_last_exon,S ENST00000316059.6 ZFP91 zinc finger protein 91

homolog (mouse)



chr11_+_75526208 0.47 5.66 9.60E-02 chr11:75526208-75526325 + TSS,S ENST00000356136.3 UVRAG UV radiation resistance associated


chr11_-_107328431 0.46 5.93 9.60E-02 chr11:107328431-107328604 - TSS,S ENST00000282251.5/

ENST00000433523.1 CWF19L2 CWF19-like 2, cell cycle control (S. pombe)


HBB hemoglobin, beta

chr11_-_77531732 0.70 3.41 4.15E-02 chr11:77531732-77531738 - TSSregion500,S ENST00000467567.1/ENST00000530604.1 RSF1 remodeling and spacing

factor 1

chr11_-_85779796 1.42 1.77 9.22E-02 chr11:85779796-85779902 - TSS,S ENST00000356360.5/ENST00000534412.1 PICALM phosphatidylinositol binding

clathrin assembly protein

chr12_+_119442508 -1.44 1.64 7.71E-02 chr12:119442508-

119442521 +CDS_or_noncoding_first_intron,S

ENST00000267260.4 SRRM4 serine/arginine repetitive matrix 4

181181

245246247

Persson et al.

chr12_+_14518558 0.42 5.99 9.60E-02 chr12:14518558-14518670 + TSS,S


ATF7IP activating transcription factor 7 interacting protein

chr12_+_4410650 -1.16 1.76 4.15E-02 chr12:4410650-4410657 + 3UTR_last_exon,S ENST00000261254.3 CCND2 cyclin D2


ENST00000455310.1/ENST00000301180.5/ENST00000549620.1

DIP2B DIP2 disco-interacting protein 2 homolog B (Drosophila)



LRP1 low density lipoprotein receptor-related protein 1

chr12_+_66582922 0.60 5.50 8.81E-02 chr12:66582922-66583121 + TSS,S ENST00000545837.1/ENST00000457197.2 IRAK3 interleukin-1 receptor-

associated kinase 3

chr12_-_109895984 1.16 1.78 9.60E-02 chr12:109895984-109896117 - TSSregion500,S ENST00000540402.1 KCTD10

potassium channel tetramerisation domain containing 10

chr12_-_57107359 0.98 2.71 8.81E-02 chr12:57107359-57107477 - TSS,S ENST00000548386.1 NACAnascent polypeptide-associated complex alpha subunit


ZFC3H1 zinc finger, C3H1-type containing

chr14_+_56764830 -1.55 1.44 9.60E-02 chr14:56764830-56764842 + 3UTR_last_exon,S ENST00000267460.4 PELI2 pellino E3 ubiquitin protein

ligase family member 2



GPHN gephyrin

182182

Persson et al.

chr14_+_68286453 0.68 2.78 9.60E-02 chr14:68286453-68286561 + TSS,S


RAD51B RAD51 homolog B (S. cerevisiae)


ENST00000381232.3/ENST00000555818.1/ENST00000358550.2

SIPA1L1 signal-induced proliferation-associated 1 like 1

chr14_-_81408018 0.85 2.70 9.60E-02 chr14:81408018-81408145 - TSS,S


CEP128 centrosomal protein 128kDa


chr15_+_31664212 1.68 2.36 7.71E-02 chr15:31664212-31664310 + 5UTR_last_exon,S ENST00000558844.1 KLF13 Kruppel-like factor 13

chr15_+_78462578 -1.05 2.44 7.71E-02 chr15:78462578-78462718 + CDS_or_noncoding_last_exon,S ENST00000558535.1 IDH3A isocitrate dehydrogenase 3

(NAD+) alpha


protein 13


chr16_+_23847533 0.97 3.63 9.60E-02 chr16:23847533-23847598 + TSSregion500,S ENST00000498058.1 PRKCB protein kinase C, beta


ENST00000356798.4/ENST00000358164.4/ENST00000454514.2

ITGAL

integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)

chr16_+_75611235 -1.55 1.68 7.71E-02 chr16:75611235-75611426 + CDS_or_noncoding_last_exon,S ENST00000037243.2 GABARAPL2 GABA(A) receptor-associated

protein-like 2



MYO18A myosin XVIIIA


183183

Persson et al.



RABEP1 rabaptin, RAB GTPase binding effector protein 1

chr17_-_49198086 0.45 5.75 9.60E-02 chr17:49198086-49198263 - TSS,S






chr18_+_2655873 0.44 5.75 9.60E-02 chr18:2655873-2655931 + TSS,S ENST00000261598.8/ENST00000320876.5 SMCHD1





ENST00000261598.8/ENST00000320876.5 SMCHD1



ENST00000217652.3/ENST00000536605.1 MYL12A myosin, light chain 12A,

regulatory, non-sarcomeric

chr18_+_59854480 0.46 6.42 7.71E-02 chr18:59854480-59854597 + TSS,S ENST00000398130.2/ENST00000256858.5 KIAA1468 KIAA1468




184184

Persson et al.


ENST00000352456.2/ENST00000392006.2/ENST00000378215.3

HNRNPUL1 heterogeneous nuclear ribonucleoprotein U-like 1

chr19_+_42411506 -1.83 0.84 7.71E-02 chr19:42411506-42411574 + CDS_or_noncoding_last_exon,S ENST00000378152.3 ARHGEF1 Rho guanine nucleotide

exchange factor (GEF) 1


CDC14A CDC14 cell division cycle 14 homolog A (S. cerevisiae)

chr1_+_110168930 2.24 0.61 8.81E-02 chr1:110168930-110169018 + TSSregion500,S ENST00000534144.1 AMPD2 adenosine monophosphate deaminase 2




chr1_+_231762403 0.81 3.55 2.67E-02 chr1:231762403-231762591 + TSS,S



chr1_+_36396682 0.50 4.53 9.22E-02 chr1:36396682-36396870 + TSS,S ENST00000397828.2/ENST00000246314.6 EIF2C3 eukaryotic translation

initiation factor 2C, 3


chr1_+_40840055 1.49 1.96 4.44E-02 chr1:40840055-40840132 + TSSregion500,S ENST00000372708.1 SMAP2 small ArfGAP2


ENST00000368046.3 CD48 CD48 molecule

chr1_-_98386462 0.41 7.99 7.71E-02 chr1:98386462-98386637 - TSS,S



185185

Persson et al.


ENST00000217086.3/ENST00000371539.3/ENST00000395997.3

SALL4 sal-like 4 (Drosophila)


chr20_-_1350022 -1.87 0.78 9.60E-02 chr20:1350022-1350071 - 3UTR_last_exon,S ENST00000400137.4 FKBP1A FK506 binding protein 1A,

12kDa



chr20_-_35519412 -1.83 0.73 6.16E-02 chr20:35519412-35519538 - 3UTR_last_exon,S ENST00000262878.4 SAMHD1 SAM domain and HD domain

1



chr21_+_38445497 0.46 5.15 9.33E-02 chr21:38445497-38445694 + TSS,S


TTC3 tetratricopeptide repeat domain 3

chr22_+_20100542 -1.55 1.54 9.33E-02 chr22:20100542-20100552 + TSSregion500,AS ENST00000480339.1 TRMT2A tRNA methyltransferase 2

homolog A (S. cerevisiae)

chr22_+_39354384 -1.48 1.51 9.24E-02 chr22:39354384-39354441 +CDS_or_noncoding_first_intron,S

ENST00000249116.2 APOBEC3Aapolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A

chr22_+_41488564 0.59 4.98 7.90E-02 chr22:41488564-41488632 + 5UTR_first_exon,S ENST00000263253.7 EP300 E1A binding protein p300

186186

Persson et al.

chr2_+_102314123 0.56 6.69 4.44E-02 chr2:102314123-102314207 + TSS,S ENST00000425019.1 MAP4K4 mitogen-activated protein kinase kinase kinase kinase 4

chr2_+_109403102 0.77 2.39 9.60E-02 chr2:109403102-109403287 + TSS,S




MGAT5

mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase

chr2_+_192700471 -2.54 0.71 7.71E-02 chr2:192700471-192700611 + 3UTR_last_exon,AS ENST00000304141.4 SDPR serum deprivation response

chr2_+_209130906 0.48 6.33 7.71E-02 chr2:209130906-209131086 + TSS,S



chr2_+_210867290 0.66 4.28 9.60E-02 chr2:210867290-210867367 + TSS,S


RPE ribulose-5-phosphate-3-epimerase

chr2_+_70166930 -1.32 2.70 4.44E-02 chr2:70166930-70167078 + 3UTR_last_exon,S ENST00000264444.2 MXD1 MAX dimerization protein 1

chr2_-_169103949 0.78 3.98 9.22E-02 chr2:169103949-169104145 - 5UTR_first_exon,S ENST00000355999.4 STK39 serine threonine kinase 39

187187

Persson et al.


ENST00000542292.1 TRAK2 trafficking protein, kinesin binding 2

chr2_-_235403494 -2.31 0.63 5.03E-02 chr2:235403494-235403598 - 3UTR_first_exon,S ENST00000390645.2 ARL4C ADP-ribosylation factor-like

4C

chr3_+_134334086 0.74 3.00 9.60E-02 chr3:134334086-134334242 + TSS,S ENST00000460895.1 EPHB1 EPH receptor B1



chr3_+_182511253 0.39 6.73 9.60E-02 chr3:182511253-182511417 + TSS,S ENST00000323116.5/ENST00000493826.1 ATP11B ATPase, class VI, type 11B

chr3_+_9775826 1.96 0.50 9.22E-02 chr3:9775826-9775918 + CDS_or_noncoding_first_exon,S ENST00000457855.1 BRPF1 bromodomain and PHD finger

containing, 1


PIK3CBphosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta



PHC3 polyhomeotic homolog 3 (Drosophila)



chr4_+_123073450 0.49 5.97 9.22E-02 chr4:123073450-123073647 + TSS,S ENST00000264501.4 KIAA1109 KIAA1109

chr4_+_144435057 1.30 1.58 9.22E-02 chr4:144435057-144435163 + TSSregion500,S ENST00000283131.3 SMARCA5

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5



KLF3 Kruppel-like factor 3 (basic)

188188

Persson et al.



CCNG2 cyclin G2






PHF15 PHD finger protein 15

chr5_+_142548033 1.29 1.46 9.60E-02 chr5:142548033-142548044 +CDS_or_noncoding_first_intron,S

ENST00000486650.1 ARHGAP26 Rho GTPase activating protein 26



ENST00000425232.2/ENST00000274258.7/ENST00000388739.3

C5ORF42 NA



PIK3R1 phosphoinositide-3-kinase, regulatory subunit 1 (alpha)

chr5_+_77656326 0.42 4.99 9.60E-02 chr5:77656326-77656523 + TSS,S



189189

Persson et al.

chr5_-_39202933 0.91 3.13 9.31E-02 chr5:39202933-39202960 - CDS_or_noncoding_first_exon,S ENST00000515010.1 FYB FYN binding protein


AP3B1 adaptor-related protein complex 3, beta 1 subunit


QRSL1 glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1

chr6_+_116691961 0.61 5.70 3.70E-02 chr6:116691961-116692148 + TSS,S ENST00000359564.2 DSE dermatan sulfate epimerase




LST1 leukocyte specific transcript 1


ENST00000372836.4/ENST00000394142.3 CNPY3 canopy 3 homolog (zebrafish)

chr7_+_143080180 2.39 0.53 9.60E-02 chr7:143080180-143080182 + TSSregion500,S ENST00000446634.1 ZYX zyxin



AC004980.7


chr7_+_91570143 0.57 4.97 7.90E-02 chr7:91570143-91570321 + TSS,S


AKAP9 A kinase (PRKA) anchor protein (yotiao) 9

chr7_+_99528236 -2.41 0.51 4.44E-02 chr7:99528236-99528242 +CDS_or_noncoding_first_intron,S

ENST00000456499.1 RP4-604G5.1




190190

Persson et al.




ENST00000518881.1/ENST00000523883.1 SLC25A37


chr8_+_28747868 0.51 4.86 9.60E-02 chr8:28747868-28747935 + TSS,S


HMBOX1 homeobox containing 1

chr8_-_62627045 0.70 4.24 8.81E-02 chr8:62627045-62627200 - TSS,S


ASPH aspartate beta-hydroxylase

chr9_-_74979780 1.11 3.10 9.60E-02 chr9:74979780-74979938 - TSS,S ENST00000487330.1 ZFAND5 zinc finger, AN1-type domain 5


FRMD3 FERM domain containing 3


AGTPBP1 ATP/GTP binding protein 1

chrM_+_15303 -1.85 1.76 9.60E-02 chrM:15303-15304 + intergenic intergenic NA NA

chrM_+_5462 -2.63 0.62 7.71E-02 chrM:5462-5463 + intergenic intergenic NA NA

chrX_+_117629770 0.55 4.45 9.24E-02 chrX:117629770-117629835 + TSSregion500,S ENST00000276204.6/ENST00000276202.7 DOCK11 dedicator of cytokinesis 11

191191

248

Persson et al.

Table E9. A differentially expressed tag cluster at chr1:154401669-154401846(+) in IL6R is located within the linkage disequilibrium (LD) block of rs4129267, an SNP associated with asthma by GWAS.

chr position r2 D' rsID ref alt MAF Distance to cluster

Enhancer ENCODE

(cell, enhancer)

Promoter Roadmap

Enhancer Roadmap (cell,

enhancer)

DNAse (production

center, cell/tissue treatment)

ChIP-seq proteins (cell,

protein, production

center, treatment)

Motifs

dbSNP functio

nal annotat

ion

1 154395839 0.83 0.92 rs6684439 C T 0.35 -6007 NHEK,5_Strong_Enhancer;HMEC,5_Strong_Enhancer;NHLF,5_Strong_Enhancer;HSMM,6_Weak_Enhancer;Huvec,5_Strong_Enhancer

PFF.1,6_TssD2

SK.MUS62,13_EnhA;CD34.MBP1480,11_EnhWk1;MUS.SC,13_EnhA;SK.MUS63,13_EnhA;R.SMUS,11_EnhWk1;CD4.NP,11_EnhWk1;PFM.2,13_EnhA;LIV.A,13_EnhA;CD3.P,14_Enh;LV,14_Enh;SPL,14_Enh;CC.TPC,11_EnhWk1;PFK.2,13_EnhA;PFM.3,13_EnhA;BR.H35,13_EnhA;CD34.MBP1536,11_EnhWk1;PFK.3,13_EnhA;ADI.MSC,13_EnhA;CCIP.LSMPTP,13_EnhA;ADI.NUC,13_EnhA;ST.MUC,13_EnhA;PFM.1,13_EnhA;SK.MUS,13_EnhA;R.MUC31,11_EnhWk1;PFF.2,13_EnhA;ESO,13_EnhA;DUO.SMUS,11_EnhWk1;MSC.ADIPC,13_EnhA;CD34.MBP1562,13_EnhA;BN.SN,13_EnhA;CD15.P,13_EnhA;BR.MYO,11_EnhWk

Duke,PanIslets,None

. AP-1_disc8;HDAC2_disc6;NF-kappaB_disc3;Pax-4_5;STAT_known1;STAT_known2

INT

192192

249250251

Persson et al.

1;H1.DMSC,13_EnhA;CD34.C,13_EnhA;IMR90,13_EnhA;HD.CD56MESC,11_EnhWk1;HUES64,11_EnhWk1;R.MUC29,11_EnhWk1;GAS,11_EnhWk1;PANC.I,14_Enh;CD34.MBP1549,11_EnhWk1;CCC.TREGP,9_TxEnhG1;BN.ITL,14_Enh;KID.FE,11_EnhWk1;COL.SMUS,14_Enh;DUO.MUC61,11_EnhWk1;CD4.MP,11_EnhWk1;CCIP.LSTP,14_Enh;BN.HM150,13_EnhA;ST.SMUS28,14_Enh;BN.AG,13_EnhA;CCCRA.NP,13_EnhA;CHON.BMMSC,13_EnhA;BM.MSC,11_EnhWk1;BN.AC,13_EnhA;BN.MFL,13_EnhA;NCC.COR2,11_EnhWk1;BN.CC,13_EnhA;NCC.GED2,11_EnhWk1

1 154405024 0.87 0.94 rs56383622 A G 0.36 3178

HMEC,5_Strong_Enhancer;GM12878,7_Weak_Enhancer;NHLF,5_Strong_Enhancer;H1,7_Weak_Enhancer;NHEK,5_Strong_Enhancer;HSM

.

CCC.TREGP,9_TxEnhG1;LIV.A,9_TxEnhG1;GAS,11_EnhWk1;SK.MUS62,9_TxEnhG1;BN.MFL,14_Enh;PFK.2,13_EnhA;BR.MYO,9_TxEnhG1;HUES48,11_EnhWk1;BR.H35,11_EnhWk1;PFK.3,13_EnhA;H1,12_EnhWk2;HUES6,13_

. . . INT

193193

Persson et al.

M,7_Weak_Enhancer;HepG2,7_Weak_Enhancer

EnhA;PFF.1,11_EnhWk1;IPS.DF19,11_EnhWk1;H1.DMSC,11_EnhWk1;CCIP.LSTP,13_EnhA;IPS.18,12_EnhWk2;SK.MUS63,14_Enh;ES.I3,11_EnhWk1;IPS.DF6,11_EnhWk1;ST.SMUS28,13_EnhA;CC.TPC,13_EnhA;CD8.NP,11_EnhWk1;PFM.3,9_TxEnhG1;CCIP.LSMPTP,13_EnhA;ST.MUC,11_EnhWk1;PFF.2,14_Enh;BN.AC,11_EnhWk1;DUO.SMUS,14_Enh;BN.ITL,14_Enh;CD8.MP,11_EnhWk1;LV,14_Enh;CD34.C,9_TxEnhG1;SPL,9_TxEnhG1;COL.SMUS,13_EnhA;R.MUC31,14_Enh;BN.HM150,11_EnhWk1;BN.SN,14_Enh;CCCRA.NP,11_EnhWk1;DUO.MUC61,14_Enh;PFM.1,14_Enh;CD4.MP,11_EnhWk1;ADI.NUC,14_Enh;ESO,14_Enh;MSC.ADIPC,14_Enh;HRT.FE,14_Enh;ADI.MSC,14_Enh;IPS.20,12_EnhWk2;CD4.NP,11_EnhWk1;CD15.P,9_TxEnhG1;BM.MSC,14_Enh;CHON.BMMSC,11_EnhWk1;P

194194

Persson et al.

FM.2,9_TxEnhG1;CD34.MBP1562,9_TxEnhG1;MUS.SC,14_Enh;CCCRO.MP,14_Enh;R.SMUS,9_TxEnhG1

1 154406656 0.87 0.94 rs4845620 A G 0.36 4810

NHEK,5_Strong_Enhancer;HMEC,7_Weak_Enhancer;NHLF,5_Strong_Enhancer

ST.SMUS28,2_TssF;BM.MSC,6_TssD2;DUO.SMUS,3_TssA;COL.SMUS,3_TssA

PFK.3,13_EnhA;DUO.MUC61,14_Enh;ADI.MSC,13_EnhA;R.MUC29,9_TxEnhG1;BN.SN,14_Enh;SK.MUS63,13_EnhA;BN.AC,14_Enh;MUS.SC,14_Enh;BR.MYO,11_EnhWk1;PFM.2,9_TxEnhG1;CD4.MP,14_Enh;PFF.2,14_Enh;CCCRA.NP,14_Enh;GAS,14_Enh;PFF.1,14_Enh;CCIP.LSMPTP,14_Enh;HUES6,14_Enh;ESO,14_Enh;SK.MUS62,14_Enh;R.SMUS,11_EnhWk1;R.MUC31,13_EnhA;LNG.FE,11_EnhWk1;PFM.3,9_TxEnhG1;CHON.BMMSC,13_EnhA;ADI.NUC,13_EnhA;MSC.ADIPC,13_EnhA;SK.MUS,13_EnhA;PFK.2,13_EnhA;PFM.1,13_EnhA;BN.HM150,13_EnhA;NCC.COR2,11_EnhWk1;HRT.FE,13_EnhA;LV,13_EnhA;ST.MUC,13_EnhA

. .

HMG-IY_2;Mef2_disc1;SIX5_disc4

INT

195195

Persson et al.

1 154407419 0.87 0.94 rs7518199 A C 0.36 5573

K562,7_Weak_Enhancer;NHLF,4_Strong_Enhancer;NHEK,5_Strong_Enhancer

COL.SMUS,3_TssA;ADI.MSC,2_TssF;R.SMUS,6_TssD2;DUO.MUC61,2_TssF;ST.SMUS28,2_TssF;MSC.ADIPC,2_TssF;DUO.SMUS,2_TssF

BN.AC,14_Enh;PFM.2,9_TxEnhG1;ESO,14_Enh;HRT.FE,13_EnhA;LV,13_EnhA;ST.MUC,13_EnhA;CD4.MP,9_TxEnhG1;CCIP.LSMPTP,9_TxEnhG1;LIV.A,9_TxEnhG1;BN.FE2,11_EnhWk1;CCCRA.NP,9_TxEnhG1;PFF.1,9_TxEnhG1;R.MUC29,10_TxEnhG2;BN.MFL,9_TxEnhG1;BR.MYO,9_TxEnhG1;BN.ITL,14_Enh;SK.MUS,10_TxEnhG2;COL.MUC32,9_TxEnhG1;SK.MUS63,9_TxEnhG1;PFK.3,9_TxEnhG1;PFK.2,9_TxEnhG1;PFM.1,9_TxEnhG1;PFM.3,9_TxEnhG1;LNG.FE,11_EnhWk1;PFF.2,9_TxEnhG1;BN.HM150,9_TxEnhG1;ADI.NUC,10_TxEnhG2;BM.MSC,13_EnhA;CHON.BMMSC,13_EnhA;R.MUC31,10_TxEnhG2;SK.MUS62,10_TxEnhG2;GAS,9_TxEnhG1;MUS.SC,11_EnhWk1;BN.SN,14_Enh

UW,HMF,None;UW,NHDF-Ad,None

. NRSF_known3 INT

196196

Persson et al.

1 154407713 0.87 0.94 rs7521458 T C 0.36 5867NHEK,5_Strong_Enhancer

R.SMUS,6_TssD2;ST.SMUS28,2_TssF;MSC.ADIPC,2_TssF;COL.SMUS,2_TssF;DUO.SMUS,3_TssA

BN.AC,14_Enh;PFM.2,9_TxEnhG1;ESO,14_Enh;HRT.FE,13_EnhA;LV,13_EnhA;ST.MUC,13_EnhA;LIV.A,9_TxEnhG1;PFF.1,9_TxEnhG1;R.MUC29,10_TxEnhG2;BN.MFL,9_TxEnhG1;COL.MUC32,9_TxEnhG1;SK.MUS63,9_TxEnhG1;PFK.3,9_TxEnhG1;PFK.2,9_TxEnhG1;PFM.1,9_TxEnhG1;PFM.3,9_TxEnhG1;R.MUC31,10_TxEnhG2;SK.MUS62,10_TxEnhG2;GAS,9_TxEnhG1;MUS.SC,11_EnhWk1;BN.SN,14_Enh;ADI.MSC,13_EnhA;BM.MSC,14_Enh;CHON.BMMSC,11_EnhWk1;ADI.NUC,9_TxEnhG1;DUO.MUC61,9_TxEnhG1;SK.MUS,9_TxEnhG1

. . TCF12_disc6 INT

1 154409730 0.87 0.94 rs4845621 G A 0.36 7884 .

ST.SMUS28,4_TssWk;COL.SMUS,4_TssWk

PFK.3,11_EnhWk1;PFK.2,14_Enh;ST.MUC,11_EnhWk1;H1.DMSC,11_EnhWk1

. .

CACD_1;CACD_2;Klf4;Klf7;NRSF_disc9;SP1_known4

INT

1 154411419 0.87 0.94 rs4845622 A C 0.36 9573

GM12878,7_Weak_Enhancer;HepG2,7_Weak_Enhancer

.

CC.TPC,9_TxEnhG1;LIV.A,9_TxEnhG1;CCIP.LSMPTP,9_TxEnhG1;COL.SMUS,9_TxEnhG1;H1.DMSC,14_Enh;CD4.MP,11_EnhWk1;CCC.TREGP,9_TxEnhG1;PFM.

Duke,GM19238,None . Foxm1 INT

197197

Persson et al.

2,9_TxEnhG1;CCCRA.NP,13_EnhA;CD4.NP,11_EnhWk1;ADI.NUC,14_Enh;DUO.MUC61,14_Enh;CD8.NP,11_EnhWk1;COL.MUC32,11_EnhWk1;CCIP.LSTP,13_EnhA;DUO.SMUS,9_TxEnhG1;CD3.P,13_EnhA;CD8.MP,11_EnhWk1;R.MUC31,11_EnhWk1

1 154414037 0.87 0.94 rs4393147 C T 0.36 12191 GM12878,7_Weak_Enhancer;HMEC,7_Weak_Enhancer;NHLF,7_Weak_Enhancer

CD4.NP,6_TssD2;CD3.P,2_TssF;CCIP.LSMPTP,2_TssF;CD8.MP,6_TssD2

LIV.A,9_TxEnhG1;CCC.TREGP,9_TxEnhG1;CC.TPC,13_EnhA;CCCRA.NP,13_EnhA;IMR90,15_EnhP;CCIP.LSTP,13_EnhA;CCCRO.MP,13_EnhA;PFM.2,9_TxEnhG1;CCC.TMP,14_Enh;H1.DMSC,11_EnhWk1;COL.SMUS,9_TxEnhG1;PFM.1,9_TxEnhG1;PFM.3,9_TxEnhG1;CD34.C,11_EnhWk1;HD.CD56MESC,11_EnhWk1;PFF.1,11_EnhWk1;CD34.MBP1480,11_EnhWk1;PFK.2,11_EnhWk1;BR.MYO,11_EnhWk1;R.SMUS,9_TxEnhG1;SPL,11_EnhWk1;CD34.MBP1562,13_EnhA;CD4.MP,13_EnhA;CD15.P,9_TxEnhG1;CD8.NP,13_EnhA;PFK.3,1

. . Hdx;Myc_disc5;Pou5f1_known2;VDR_2

INT

198198

Persson et al.

1_EnhWk1;ESO,11_EnhWk1;IPS.DF19,11_EnhWk1;CD34.MBP1536,9_TxEnhG1;ES.I3,11_EnhWk1;ST.SMUS28,9_TxEnhG1

1 154414086 0.87 0.94 rs4453032 A G 0.36 12240

GM12878,7_Weak_Enhancer;HMEC,7_Weak_Enhancer;NHLF,7_Weak_Enhancer

CD4.NP,6_TssD2;CD3.P,2_TssF;CCIP.LSMPTP,2_TssF;CD8.MP,6_TssD2

LIV.A,9_TxEnhG1;CCC.TREGP,9_TxEnhG1;CC.TPC,13_EnhA;CCCRA.NP,13_EnhA;IMR90,15_EnhP;CCIP.LSTP,13_EnhA;CCCRO.MP,13_EnhA;PFM.2,9_TxEnhG1;CCC.TMP,14_Enh;H1.DMSC,11_EnhWk1;COL.SMUS,9_TxEnhG1;PFM.1,9_TxEnhG1;PFM.3,9_TxEnhG1;CD34.C,11_EnhWk1;HD.CD56MESC,11_EnhWk1;PFF.1,11_EnhWk1;CD34.MBP1480,11_EnhWk1;PFK.2,11_EnhWk1;BR.MYO,11_EnhWk1;R.SMUS,9_TxEnhG1;SPL,11_EnhWk1;CD34.MBP1562,13_EnhA;CD4.MP,13_EnhA;CD15.P,9_TxEnhG1;CD8.NP,13_EnhA;PFK.3,11_EnhWk1;ESO,11_EnhWk1;IPS.DF19,11_EnhWk1;CD34.MBP1536,9_TxEnhG1;ES.I3,11_EnhWk1;ST.SMUS28,9_TxEnhG1

. .Maf_known2;PPAR_3;PU.1_known2

INT

199199

Persson et al.

1 154414296 0.87 0.94 rs6664201 C T 0.36 12450 GM12878,7_Weak_Enhancer;NHLF,7_Weak_Enhancer;HSMM,7_Weak_Enhancer;Huvec,7_Weak_Enhancer;NHEK,7_Weak_Enhancer;HMEC,6_Weak_Enhancer

CD4.NP,6_TssD2;CD3.P,2_TssF;CCIP.LSMPTP,2_TssF;CCCRA.NP,2_TssF

LIV.A,9_TxEnhG1;CCC.TREGP,9_TxEnhG1;CC.TPC,13_EnhA;IMR90,15_EnhP;CCIP.LSTP,13_EnhA;CCCRO.MP,13_EnhA;PFM.2,9_TxEnhG1;CCC.TMP,14_Enh;H1.DMSC,11_EnhWk1;PFM.1,9_TxEnhG1;PFM.3,9_TxEnhG1;CD34.C,11_EnhWk1;HD.CD56MESC,11_EnhWk1;PFF.1,11_EnhWk1;CD34.MBP1480,11_EnhWk1;PFK.2,11_EnhWk1;BR.MYO,11_EnhWk1;R.SMUS,9_TxEnhG1;SPL,11_EnhWk1;CD34.MBP1562,13_EnhA;CD4.MP,13_EnhA;CD15.P,9_TxEnhG1;CD8.NP,13_EnhA;PFK.3,11_EnhWk1;ESO,11_EnhWk1;IPS.DF19,11_EnhWk1;CD34.MBP1536,9_TxEnhG1;ES.I3,11_EnhWk1;ST.SMUS28,9_TxEnhG1;PANC,11_EnhWk1;MUS.SC,11_EnhWk1;CD34.MBP1549,11_EnhWk1;CD34.P,11_EnhWk1;COL.SMUS,13_EnhA;BR.H35,11_EnhWk1;H1.BMP4DT,12_EnhWk2;PFF.2,11_EnhWk1;H

UW,Adult_CD4_Th0,None;UW,HMVEC-dBl-Ad,None;UW,HMVEC-dBl-Neo,None

. HEN1_1 INT

200200

Persson et al.

UES64,11_EnhWk1;ES.WA7,11_EnhWk1;CD8.MP,11_EnhWk1

1 154415396 0.83 0.94 rs4845372 C A 0.37 13550

NHLF,7_Weak_Enhancer;HSMM,7_Weak_Enhancer;HMEC,7_Weak_Enhancer;K562,7_Weak_Enhancer

.

LIV.A,9_TxEnhG1;CC.TPC,13_EnhA;PFM.2,9_TxEnhG1;CCC.TMP,14_Enh;HD.CD56MESC,11_EnhWk1;ST.SMUS28,9_TxEnhG1;CD8.MP,11_EnhWk1;CD4.NP,11_EnhWk1;CD3.P,13_EnhA;CD4.MP,11_EnhWk1;CCCRA.NP,13_EnhA;COL.SMUS,11_EnhWk1;CCIP.LSMPTP,13_EnhA;CD8.NP,11_EnhWk1;PFF.2,9_TxEnhG1;PFF.1,11_EnhWk1;ESO,14_Enh;H1.DMSC,11_EnhWk1

. . Pax-4_4 INT

1 154415777 0.83 0.94 rs4845623 A G 0.37 13931 HSMM,6_Weak_Enhancer

. LIV.A,9_TxEnhG1;PFM.2,9_TxEnhG1;HD.CD56MESC,11_EnhWk1;ST.SMUS28,9_TxEnhG1;CD8.MP,11_EnhWk1;CD4.NP,11_EnhWk1;CD4.MP,11_EnhWk1;CCCRA.NP,13_EnhA;CD8.NP,11_EnhWk1;PFF.2,9_TxEnhG1;ESO,14_Enh;H1.DMSC,11_EnhWk1;COL.SMUS,9_TxEnhG1;CD3.P,9_TxEnhG1;R.SMUS,9_TxEnhG1;CC.TPC,9_TxEnhG1;A

. . . INT

201201

Persson et al.

DI.MSC,11_EnhWk1;BN.MFL,11_EnhWk1;CCCRO.MP,11_EnhWk1;BN.FE2,11_EnhWk1;PFK.2,9_TxEnhG1;ADI.NUC,9_TxEnhG1;CCIP.LSMPTP,9_TxEnhG1;SK.MUS63,11_EnhWk1;PFF.1,14_Enh

1 154416935 0.87 0.94 rs12753254 G A 0.36 15089 . .

CD4.NP,11_EnhWk1;CD8.NP,11_EnhWk1;H1.DMSC,11_EnhWk1;CC.TPC,9_TxEnhG1;PFF.1,14_Enh;CD4.MP,9_TxEnhG1;CCIP.LSTP,11_EnhWk1;CCCRO.MP,11_EnhWk1;PFM.3,9_TxEnhG1;CD3.P,14_Enh;PFF.2,14_Enh;PFK.2,14_Enh;MSC.ADIPC,14_Enh;CCCRA.NP,14_Enh;CCC.TREGP,9_TxEnhG1

. .NRSF_disc9;SETDB1_disc1;Zfx

INT

1 154416969 0.87 0.94 rs12730036

C T 0.36 15123 . . CD4.NP,11_EnhWk1;CD8.NP,11_EnhWk1;H1.DMSC,11_EnhWk1;CC.TPC,9_TxEnhG1;PFF.1,14_Enh;CD4.MP,9_TxEnhG1;CCIP.LSTP,11_EnhWk1;CCCRO.MP,11_EnhWk1;PFM.3,9_TxEnhG1;CD3.P,14_Enh;PFF.2,14_Enh;PFK.2,14_Enh;MSC.ADIPC,14_Enh;CCCRA.NP,14_Enh;CCC.TREGP,9_

. . AP-1_disc7;Ets_disc7;Hic1_1;Osr

INT

202202

Persson et al.

TxEnhG1

1 154417829 0.87 0.94 rs4845373 C T 0.36 15983

NHLF,5_Strong_Enhancer;GM12878,7_Weak_Enhancer;NHEK,7_Weak_Enhancer

.

CD4.NP,11_EnhWk1;CD8.NP,11_EnhWk1;CC.TPC,9_TxEnhG1;CCIP.LSTP,11_EnhWk1;CCCRO.MP,11_EnhWk1;PFM.3,9_TxEnhG1;MSC.ADIPC,14_Enh;CCC.TREGP,9_TxEnhG1;PFF.1,13_EnhA;CD8.MP,11_EnhWk1;CD34.MBP1536,11_EnhWk1;CD34.MBP1562,9_TxEnhG1;CD34.C,11_EnhWk1;ADI.MSC,11_EnhWk1;IMR90,13_EnhA;PFF.2,13_EnhA;CHON.BMMSC,11_EnhWk1;HD.CD56MESC,11_EnhWk1;CD34.MBP1480,11_EnhWk1;COL.SMUS,9_TxEnhG1;ESO,14_Enh;ST.SMUS28,9_TxEnhG1;PFM.2,9_TxEnhG1;CD34.P,11_EnhWk1;DUO.MUC61,11_EnhWk1;CCIP.LSMPTP,9_TxEnhG1;DUO.SMUS,14_Enh;PFM.1,9_TxEnhG1;MUS.SC,11_EnhWk1;PFK.2,14_Enh;R.MUC29,9_TxEnhG1;CD4.MP,11_EnhWk1;CCCRA.NP,11_EnhWk1;H1.DMSC,14_Enh

AWG,Th1,None;Duke,GM12891,None;Duke,GM12892,None;Duke,GM19238,None;Duke,GM19239,None;Duke,GM19240,None;Duke,Osteobl,None;UW,CMK,None;UW,GM06990,None;UW,GM12864,None;UW,GM12865,None;UW,NB4,None;UW,Th2,None

GM12878,BCL11A,HudsonAlpha,None;GM12878,EBF1,HudsonAlpha,None;GM12878,PAX5N19,HudsonAlpha,None;GM15510,NFKB,Stanford,None

CTCF_disc1;CTCF_known1;RFX5_disc1;Rad21_disc1;SMC3_disc1

INT

203203

Persson et al.

1 154418415 0.88 0.95 rs11265613 T C 0.36 16569

GM12878,7_Weak_Enhancer;NHLF,5_Strong_Enhancer

PFF.1,2_TssF

CC.TPC,9_TxEnhG1;PFM.3,9_TxEnhG1;CD8.MP,11_EnhWk1;IMR90,13_EnhA;PFF.2,13_EnhA;CHON.BMMSC,11_EnhWk1;HD.CD56MESC,11_EnhWk1;COL.SMUS,9_TxEnhG1;ESO,14_Enh;ST.SMUS28,9_TxEnhG1;PFM.2,9_TxEnhG1;DUO.SMUS,14_Enh;PFM.1,9_TxEnhG1;MUS.SC,11_EnhWk1;CD4.MP,11_EnhWk1;CCCRA.NP,11_EnhWk1;H1.DMSC,14_Enh;CCCRO.MP,14_Enh;LNG.FE,11_EnhWk1;ADI.NUC,13_EnhA;MSC.ADIPC,13_EnhA;R.SMUS,9_TxEnhG1;SK.MUS,9_TxEnhG1;BM.MSC,11_EnhWk1;ADI.MSC,13_EnhA

. .

Foxp1;GATA_known8;HDAC2_disc6;Mef2_known3;Zfp105;p300_disc5

INT

1 154418749 0.88 0.96 rs4576655 C T 0.37 16903 GM12878,7_Weak_Enhancer;HSMM,6_Weak_Enhancer;NHLF,4_Strong_Enhancer

PFF.1,2_TssF;COL.SMUS,6_TssD2

CC.TPC,9_TxEnhG1;PFM.3,9_TxEnhG1;CD8.MP,11_EnhWk1;IMR90,13_EnhA;PFF.2,13_EnhA;CHON.BMMSC,11_EnhWk1;HD.CD56MESC,11_EnhWk1;ESO,14_Enh;ST.SMUS28,9_TxEnhG1;PFM.2,9_TxEnhG1;DUO.SMUS,14_Enh;PFM.1,9_TxEnhG1;MUS.SC,11_E

Duke,Medullo,None;Duke,PanIslets,None;UW,HMVEC-LBl,None

. AP-1_disc6;PRDM1_known1;Pax-5_known2;Pax-5_known3

INT

204204

Persson et al.

nhWk1;CCCRA.NP,11_EnhWk1;H1.DMSC,14_Enh;ADI.NUC,13_EnhA;MSC.ADIPC,13_EnhA;R.SMUS,9_TxEnhG1;SK.MUS,9_TxEnhG1;BM.MSC,11_EnhWk1;ADI.MSC,13_EnhA;H1.BMP4DT,15_EnhP;LNG.FE,13_EnhA;IPS.DF19,11_EnhWk1;ES.I3,11_EnhWk1;HUES64,11_EnhWk1

1 154418879 0.87 0.95 rs4537545 C T 0.37 17033 GM12878,7_Weak_Enhancer;HSMM,7_Weak_Enhancer;NHLF,5_Strong_Enhancer

PFF.1,2_TssF;COL.SMUS,6_TssD2

PFM.3,9_TxEnhG1;CD8.MP,11_EnhWk1;PFF.2,13_EnhA;CHON.BMMSC,11_EnhWk1;HD.CD56MESC,11_EnhWk1;ST.SMUS28,9_TxEnhG1;PFM.2,9_TxEnhG1;PFM.1,9_TxEnhG1;MUS.SC,11_EnhWk1;CCCRA.NP,11_EnhWk1;H1.DMSC,14_Enh;R.SMUS,9_TxEnhG1;SK.MUS,9_TxEnhG1;BM.MSC,11_EnhWk1;ADI.MSC,13_EnhA;LNG.FE,13_EnhA;IPS.DF19,11_EnhWk1;ES.I3,11_EnhWk1;HUES64,11_EnhWk1;IMR90,14_Enh;PFK.2,11_EnhWk1;MSC.ADIPC,14_Enh;CCC.TREGP,9_TxEnhG1;ADI.NUC,14_En

AWG,H1-hESC,None;AWG,HMEC,None;AWG,HSMM,None;AWG,HSMMtube,None;Duke,8988T,None;Duke,AoSMC,None;Duke,Chorion,None;Duke,FibroP,None;Duke,Fibrobl,None;Duke,Gliobla,None;Duke,HSMM_emb,None;Duke,Melano,None;Duke,Myometr,None;Duke,Osteobl,None;Duke,PanIsletD,None;Duke,ProgFib,None;Duke,Stellate,None;Duke,Urothelia,None;Duke,Urothelia,UT189;NA,HTR8svn,None;UW,AG04449,None;UW,AG04450,None;UW,AG09309,None;UW,AG09319,None;UW

HepG2,MAFK,Stanford,None

. INT

205205

Persson et al.

h

,AG10803,None;UW,AoAF,None;UW,BJ,None;UW,H7-hESC,None;UW,HA-h,None;UW,HA-sp,None;UW,HAEpiC,None;UW,HAc,None;UW,HBMEC,None;UW,HCF,None;UW,HCFaa,None;UW,HCM,None;UW,HCPEpiC,None;UW,HConF,None;UW,HFF,None;UW,HFF-Myc,None;UW,HGF,None;UW,HIPEpiC,None;UW,HMF,None;UW,HMVEC-LBl,None;UW,HNPCEpiC,None;UW,HPAF,None;UW,HPdLF,None;UW,HRCEpiC,None;UW,HRE,None;UW,HRPEpiC,None;UW,NH-A,None;UW,NHDF-Ad,None;UW,NHDF-neo,None;UW,NHLF,None;UW,NT2-D1,None;UW,SKMC,None;UW,WI-38,4OHTAM_20nM_72hr

1 154419892 0.86 0.96 rs12730935

G A 0.34 18046 NHLF,7_Weak_Enhancer

. ADI.NUC,14_Enh;LNG.FE,14_Enh;IMR90,14_Enh;MSC.ADIPC,14_Enh;ADI.MSC,1

. . . INT

206206

Persson et al.

4_Enh

1 154420028 0.89 0.95 rs201517815

TAC T 0.36 18182 . .

ADI.NUC,14_Enh;LNG.FE,14_Enh;IMR90,14_Enh;MSC.ADIPC,14_Enh;ADI.MSC,14_Enh

. .

Cdx;Foxp1;Irx;Pou2f2_known2;Pou3f2_2;TATA_known1

INT

1 154420087 1 1 rs61812598 G A 0.36 18241 . .

ADI.NUC,14_Enh;LNG.FE,14_Enh;IMR90,14_Enh;MSC.ADIPC,14_Enh;ADI.MSC,14_Enh

. . AP-3;Pou3f3 INT

1 154420402 0.96 1 rs7512646 G C 0.37 18556 . .

LNG.FE,14_Enh;ADI.MSC,14_Enh;COL.SMUS,9_TxEnhG1;ADI.NUC,11_EnhWk1;IPS.DF19,11_EnhWk1;ESO,14_Enh;IMR90,9_TxEnhG1;MSC.ADIPC,9_TxEnhG1

. .

ERalpha-a_known4;YY1_disc1;Zic_2;Zic_3

INT

1 154420778 0.96 1 rs7529229 T C 0.37 18932 . .

COL.SMUS,9_TxEnhG1;IPS.DF19,11_EnhWk1;ESO,14_Enh;IMR90,9_TxEnhG1;MSC.ADIPC,9_TxEnhG1;R.MUC31,9_TxEnhG1;SK.MUS63,9_TxEnhG1;ADI.MSC,13_EnhA;LNG.FE,13_EnhA;HD.CD184EC,15_EnhP;HD.CD56MESC,11_EnhWk1;ADI.NUC,9_TxEnhG1

AWG,HSMMtube,None;Duke,Osteobl,None

. ZEB1_known5 INT

1 154425456 1 1 rs12126142 G A 0.36 23610 . .

CD15.P,9_TxEnhG1;PFF.1,14_Enh;PFK.2,14_Enh;ADI.NUC,14_Enh;MSC.ADIPC,11_EnhWk1;ADI.MSC,11_EnhWk1;BN.SN,14_Enh

. . LXR_2;Myc_disc9;Sp4 INT

207207

Persson et al.

1 154426264 1 1 rs4129267 C T 0.36 24418 NHLF,5_Strong_Enhancer;HMEC,5_Strong_Enhancer;HSMM,6_Weak_Enhancer;Huvec,7_Weak_Enhancer;HepG2,6_Weak_Enhancer;GM12878,7_Weak_Enhancer;NHEK,5_Strong_Enhancer

CD15.P,2_TssF;PFF.1,6_TssD2

IMR90,9_TxEnhG1;CD34.MBP1562,9_TxEnhG1;PFK.2,13_EnhA;CCIP.LSMPTP,9_TxEnhG1;BR.MYO,9_TxEnhG1;BR.H35,11_EnhWk1;CD34.MBP1480,11_EnhWk1;CD34.MBP1536,9_TxEnhG1;PFK.3,11_EnhWk1;PFM.3,9_TxEnhG1;SK.MUS62,9_TxEnhG1;ADI.NUC,13_EnhA;CCCRA.NP,11_EnhWk1;DUO.SMUS,9_TxEnhG1;LV,9_TxEnhG1;ST.MUC,9_TxEnhG1;CD8.NP,11_EnhWk1;ST.SMUS28,9_TxEnhG1;BM.MSC,11_EnhWk1;BN.AG,9_TxEnhG1;CHON.BMMSC,11_EnhWk1;GAS,9_TxEnhG1;MUS.SC,9_TxEnhG1;SK.MUS,9_TxEnhG1;CD3.P,9_TxEnhG1;H1.DMSC,11_EnhWk1;CD4.MP,9_TxEnhG1;BN.CC,11_EnhWk1;BN.ITL,11_EnhWk1;CD34.C,9_TxEnhG1;CC.TPC,9_TxEnhG1;CD8.MP,11_EnhWk1;ESO,14_Enh;NCC.COR2,11_EnhWk1;CCIP.LSTP,9_TxEnhG1;BN.MFL,9_TxEnhG1;DUO.MUC6

AWG,HMEC,None;AWG,HeLa-S3,None;AWG,HepG2,None;AWG,NHEK,None;Duke,AoSMC,None;Duke,FibroP,None;Duke,GM19240,None;Duke,Gliobla,None;Duke,Myometr,None;Duke,ProgFib,None;Duke,RWPE1,None;Duke,Stellate,None;Duke,Urothelia,None;Duke,Urothelia,UT189;Duke,pHTE,None;NA,HTR8svn,None;UW,AG04449,None;UW,AG04450,None;UW,AG09309,None;UW,AG10803,None;UW,Adult_CD4_Th0,None;UW,AoAF,None;UW,BJ,None;UW,H7-hESC,None;UW,HA-h,None;UW,HA-sp,None;UW,HAc,None;UW,HBMEC,None;UW,HCF,None;UW,HCFaa,None;UW,HCM,None;UW,HCPEpiC,None;UW,HConF,None;UW,HEEpiC,None;UW,HFF,None;UW,HFF-Myc,None;UW,HGF,None;UW,HIPEpiC,None;UW,HL-60,None;UW,H

MCF10A-Er-Src,STAT3,Harvard(Weissman),EtOH_0.01pct_4hr;MCF10A-Er-Src,STAT3,Harvard(Weissman),TAM_1uM_36hr;U2OS,KAP1,Stanford,None

EBF_known3;Elf3;Pou1f1_2

INT

208208

Persson et al.

1,9_TxEnhG1;CD34.MBP1508,9_TxEnhG1;SPL,9_TxEnhG1;LNG.FE,11_EnhWk1;BN.FE2,12_EnhWk2;CD4.NP,9_TxEnhG1;COL.MUC32,11_EnhWk1;ES.I3,11_EnhWk1;CD19.P,13_EnhA;CD34.P,11_EnhWk1;PFF.2,11_EnhWk1;NCC.GED2,11_EnhWk1;ADI.MSC,11_EnhWk1;BN.AC,14_Enh;HD.CD56MESC,11_EnhWk1;MSC.ADIPC,11_EnhWk1;BN.SN,11_EnhWk1

MF,None;UW,HMVEC-LBl,None;UW,HMVEC-dBl-Ad,None;UW,HMVEC-dBl-Neo,None;UW,HNPCEpiC,None;UW,HPAF,None;UW,HPF,None;UW,HPdLF,None;UW,HRCEpiC,None;UW,HRE,None;UW,HRPEpiC,None;UW,HVMF,None;UW,Monocytes-CD14+_RO01746,None;UW,NB4,None;UW,NH-A,None;UW,NHDF-Ad,None;UW,NHDF-neo,None;UW,NHLF,None;UW,NT2-D1,None;UW,RPTEC,None;UW,SAEC,None;UW,SK-N-MC,None;UW,SKMC,None;UW,WI-38,4OHTAM_20nM_72hr;UW,WI-38,None

1 154426970 0.99 1 rs2228145 A C.T

0.36 25124 HMEC,7_Weak_Enhancer;GM12878,7_Weak_Enhancer

CD15.P,2_TssF

PFK.2,13_EnhA;CCIP.LSMPTP,9_TxEnhG1;BR.MYO,9_TxEnhG1;NCC.COR2,11_EnhWk1;CCIP.LSTP,9_TxEnhG1;BN.MFL,9_TxEnhG1;DUO.MUC61,9_TxEnhG1;CD34.MBP1508,9_TxEnhG1;SPL,

. . . NSM;INT

209209

Persson et al.

9_TxEnhG1;CD19.P,13_EnhA;CD34.P,11_EnhWk1;BN.SN,11_EnhWk1;CCCRA.NP,11_EnhWk1

1 154428283 0.97 0.99 rs12133641 A G 0.36 26437 . CD15.P,2_Ts

sF SPL,14_Enh . .

Cphx;Mrg1::Hoxa9_2;STAT_known3;TEF

INT

210210

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Table E10. A differentially expressed tag cluster at chr22:37532297-37532440(-) in IL2RB is located within the linkage disequilibrium (LD)

block of rs2284033, an SNP associated with asthma by GWAS.

chr position r2 D' rsID ref alt MAF Distance to cluster

Enhancer ENCODE

Enhancer Roadmap

DNAse (production

center, cell/tissue treatment)

ChIP-seq proteins (cell, protein,

production center, treatment)

MotifsdbSNP

functional annotation

22 37531117 0.88 0.94 rs2543537 C T 0.42 1180 .IPS.DF19,11_EnhWk1;PFF.2,15_EnhP

. .

CTCF_disc5;CTCF_disc9;Rad21_disc7;Roaz_2;ZBTB7A_known1;Zic_4

INT

22 37531436 0.94 0.97 rs228953 G A 0.42 861 . .

Duke,Medullo,None;Duke,Melano,None;Duke,Osteobl,None

.

ERalpha-a_disc4;NF-E2_disc4;NF-E2_known1;PLAG1;Rad21_disc1

SYN

22 37532665 0.95 0.99 rs228954 T C 0.42 -225 . . UW,Caco-2,None . PPAR_2 INT

22 37532699 0.92 0.98 rs228955 C T 0.41 -259 . .Duke,GM19240,None;UW,Caco-2,None

.

AP-1_disc7;CHD2_disc3;ETF;Ets_disc9;Mtf1_1;NRSF_disc4;NRSF_known1;Pax-5_known1;Rad21_disc5;SRF_disc2;VDR_2

INT

22 37533786 0.96 0.99 rs228957 C G 0.43 -1346 .

CCIP.LSMPTP,9_TxEnhG1;CCIP.LSTP,14_Enh;BR.MYO,14_Enh

AWG,Th1,None GM12878,PAX5C20,HudsonAlpha,None

PLAG1;Rad21_disc3;Zfp281;Zfp740

INT

22 37533795 0.98 0.99 rs228958 G C.T 0.42 -1355 .

CCIP.LSMPTP,9_TxEnhG1;CCIP.LSTP,14_Enh;BR.MYO,14_Enh

AWG,Th1,None GM12878,PAX5C20,HudsonAlpha,None . INT

22 37534034 1 1 rs2284033 G A 0.42 -1594 .

CCIP.LSMPTP,9_TxEnhG1;BR.MYO,14_Enh;CCIP.LSTP,14_Enh

Duke,Melano,None .

RORalpha1_1;RORalpha1_2;RORalpha1_3;RXR::LXR

INT

211211

253

254

255

Persson et al.

22 37534947 0.94 1 rs228960 G A 0.4 -2507NHEK,7_Weak_En

hancer

CCIP.LSMPTP,9_TxEnhG1;BR.MYO,14_Enh;SPL,9_TxEnhG1;PFK.2,11_EnhWk1;PFK.3,11_EnhWk1;CCIP.LSTP,13_EnhA;ESO,11_EnhWk1

AWG,GM12878,None;Duke,Fibrobl,None

.

CHD2_disc3;NRSF_disc8;Rad21_disc10;ZNF263_disc1

INT

22 37535948 0.89 0.96 rs228963 A G 0.41 -3508NHEK,7_Weak_En

hancer

CCIP.LSMPTP,9_TxEnhG1;BR.MYO,14_Enh;PFK.2,11_EnhWk1;PFK.3,11_EnhWk1;CCIP.LSTP,13_EnhA

AWG,GM12878,None;AWG,H1-hESC,None;AWG,HepG2,None;AWG,LNCaP,None;Duke,8988T,None;Duke,GM12892,None;Duke,GM18507,None;Duke,GM19239,None;Duke,GM19240,None;Duke,H9ES,None;Duke,Huh-7,None;Duke,Medullo,None;Duke,Osteobl,None;Duke,iPS,None;UW,CD34+_Mobilized,None;UW,Caco-2,None;UW,GM06990,None;UW,GM12865,None;UW,H7-hESC,None;UW,WERI-Rb-1,None

Caco-2,CTCF,UW,None;GM06990,CTCF,UW,None;H1-C,RAD21,HudsonAlpha,None;HepG2,CTCF,Broad,None;HepG2,CTCF,HudsonAlpha,None;HepG2,RAD21,HudsonAlpha,None;WERI-Rb-1,CTCF,UW,None

. INT

22 37537058 0.9 0.96 rs228965 C G 0.41 -4618 .

CCIP.LSMPTP,9_TxEnhG1;BR.MYO,14_Enh;CCC.TREGP,9_TxEnhG1;PFM.1,15_EnhP;CCIP.LSTP,14_Enh

Duke,GM19240,None;Duke,iPS,None

.

BDP1_disc1;CHD2_disc3;LBP-1_3;LBP-9;Rad21_disc6;Sin3Ak-20_disc6;p300_disc9

INT

22 37537514 0.87 0.94 rs228966 T C 0.41 -5074 .

CCIP.LSMPTP,9_TxEnhG1;CCC.TREGP,9_TxEnhG1;CCIP.LSTP,14_Enh;BR.MYO,13_EnhA

Duke,pHTE,None . . INT

212212

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Persson et al.

Table E11. Top ten significant transcription factor motifs from motif activity response

analysis (MARA) for the pairwise comparisons between sample groups for the proximal

promoter region (-300 to +100 bp) of all tag clusters near a known TSS, including our high-

confidence set of novel TSSs. A negative score implies lower motif activity in the first group

and a positive score higher activity.

Motif Score P-valueSA vs CA

STAT2,4,6 -6.45 3.11E-03ZNF148 -5.16 5.91E-03NFY{A,B,C} -5.13 9.45E-03MYFfamily 5.35 3.78E-04TFAP2B 5.59 1.39E-03ESR1 5.03 8.92E-03ZBTB6 5.29 9.25E-03MYB 6.54 9.70E-03MZF1 5.59 1.07E-02PRDM1 5.26 1.49E-02

CA vs CTRLPAX5 -5.46 3.45E-03TFAP2{A,C} -4.73 1.05E-02ELK1,4_GABP{A,B1} -5.71 1.18E-02PATZ1 -6.20 5.62E-02RREB1 -6.91 6.86E-02MTF1 -7.69 7.28E-02NFKB1_REL_RELA -6.51 9.39E-02STAT2,4,6 7.22 5.10E-03KLF4 6.42 1.03E-02SPI1 7.07 1.99E-02

SA vs CTRLPAX5 -9.21 4.73E-03STAT2,4,6 -6.56 8.23E-03ELK1,4_GABP{A,B1} -4.96 1.55E-02PATZ1 -9.15 6.31E-02MTF1 -6.69 7.33E-02RREB1 -8.03 7.48E-02NFKB1_REL_RELA -5.26 8.76E-02KLF4 5.70 1.09E-02TFAP2{A,C} 4.32 1.51E-02SPI1 6.73 2.23E-02

SA, therapy-resistant asthma; CA, controlled asthma; CTRL, healthy control.

213213

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262

263

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Table E12. Comparison between CAGE and microarray expression for genes differentially

expressed in the edgeR classic analysis for the pairwise comparisons SA vs CA, CA vs

CTRL, and SA vs CTRL. CAGE tag clusters and microarray probes were mapped to gene

symbols and the array data was then classified as concordant if the log2 fold change was

positive (>0.1) for significantly upregulated tag clusters or negative (<-0.1) for significantly

downregulated tag clusters. A tag cluster that matched several array probes with both positive

and negative log fold change values was classified as ‘mixed’. Results are shown separately

for genes where the corresponding tag cluster is located near the transcription start site of a

gene (TSS) or in downstream exons (non-TSS).

SA vs CA CA vs CTRL SA vs CTRLTSS non-TSS TSS non-TSS TSS non-TSS

concordant 0.50 0.31 0.59 0.46 0.81 0.54discordant 0.03 0.09 0.03 0.03 0.00 0.08mixed 0.00 0.01 0.00 0.00 0.00 0.00unchanged 0.47 0.59 0.38 0.51 0.19 0.38ratio concordant/discordant 16.50 3.68 17.80 17.00 - 6.50

SA, therapy-resistant asthma; CA, controlled asthma; CTRL, healthy control.

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Figure legends

Figure E1. Overview of the analyses performed in this paper with Table and Figure

references.

Figure E2. Distribution of tag cluster annotation based on comparison with GENCODE

reference transcripts. bp, base pairs; S, sense orientation; AS, antisense orientation; TSS,

transcription start site; UTR, untranslated region; CDS, coding sequence.

Figure E3. Hierarchical clustering based on 680 tag clusters differentially expressed in any of

the three pairwise comparisons CTRL vs CA, CTRL vs SA, or CA vs SA in the glm analysis.

CTRL, healthy control; CA, controlled persistent asthma; SA, therapy-resistant asthma. The

distance measure for clustering of samples and tag clusters (expression in normalized tags per

million, tpm) was Spearman rank correlation.

Figure E4. Venn diagrams illustrating the overlap between differentially expressed tag

clusters in the conventional (“classic”) and cell counts-adjusted (“glm”) analyses of

differential expression for the three pairwise comparisons CA vs CTRL, SA vs CTRL, and SA

vs CA. CTRL, healthy control; CA, controlled persistent asthma; SA, therapy-resistant

asthma.

Figure E5. Estimated statistical power for SA vs CA in a glm analysis without adjustment for

cell composition (A) and with adjustment (B). Estimated power for SA vs CTRL in a glm

analysis without adjustment for cell composition (C) and with adjustment (D). Power was

estimated at an FDR of 0.1 for the sample size used in our manuscript as well as 2 and 3 times

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the sample size. Statistical power could not be estimated for CA vs CTRL since the software

could not produce a valid model based on this particular set of data.

Figure E6. The number of tag clusters significantly differentially expressed between SA and

CA increases with sample number during repeated (20x) subsampling, but remains very low

when group labels are randomized. Boxes are paired for each sample number, the first with

true group labels; the second with randomized labels.

Figure E7. Hierarchical clustering of (A) CD4+ and (B) CD8+ T cells from adults with

severe or nonsevere asthma and healthy controls based on microarray probes for GENCODE

transcripts that were differentially expressed in our CAGE data for the pairwise comparisons

between children with controlled asthma, therapy-resistant asthma, and healthy controls.

Expression data from Tsitsiou E, et al. Transcriptome analysis shows activation of circulating

CD8+ T cells in patients with severe asthma. J Allergy Clin Immunol 2012;129(1):95-103.

Figure E8. Hierarchical clustering of (A) CD4+ and (B) CD8+ T cells from adults with severe

or nonsevere asthma and healthy controls based on microarray probes for GENCODE

transcripts that were differentially expressed in our CAGE data for the pairwise glm

comparisons between children with controlled asthma, therapy-resistant asthma, and healthy

controls. Expression data from Tsitsiou E, et al. Transcriptome analysis shows activation of

circulating CD8+ T cells in patients with severe asthma. J Allergy Clin Immunol

2012;129(1):95-103.

Figure E9. Hierarchical clustering of CD8+ T cells based on microarray probes matching

CAGE tag clusters differentially expressed in the classic (top) or glm (bottom) edgeR

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analyses. Values in red denote the ”average unbiased” (AU) p-values from multiscale

bootstrap resampling in the pvclust R package. Note that an AU p-value > 0.95 is equivalent

to rejecting the hypothesis “the cluster does not exist” with significance level 0.05.

Figure E10. KEGG pathway diagram of natural killer (NK) cell-mediated signaling

illustrating the differences between controlled persistent asthma (CA) and therapy-resistant

asthma (SA). Upregulated genes are highlighted in blue for CA and red for SA.

Figure E11. Validation of novel transcription start sites by RT-PCR in two children from the

healthy control group (cDNA1 and cDNA2). The sequenced product is indicated with an

arrow when gel purification was performed before confirmation by Sanger sequencing.

Abbreviations: alt, alternative; TSS, transcription start site; cDNA, complementary DNA;

NRT, no reverse transcriptase negative control; bp, base pairs.

Figure E12. CAGE expression in tags per million reads (tpm) for (A) the novel alternative

transcription start site (TSS) and (B) the known TSS for ARHGAP15. Both TSSs are

significantly upregulated in therapy-resistant asthma (SA) in the glm analysis, but only the

novel TSS is significant without adjustment for cell counts. CTRL, healthy control; CA,

controlled persistent asthma; WBC, white blood cells.

Figure E13. Expression of novel TSSs in sorted leukocyte populations and airway epithelial

cells from the FANTOM5 CAGE dataset (Forrest ARR, Kawaji H, Rehli M, Baillie JK et al.

A promoter level mammalian expression atlas. Nature 2014; 507(7493):462-470). The

distance measure for clustering of samples and tag clusters (expression in log 2-transformed,

normalized tags per million, tpm) was Spearman rank correlation.

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Figure E14. Group-wise expression of differentially expressed tag clusters overlapping genes

linked to asthma in genome-wide association studies (GWAS). tpm, tags per million reads;

CTRL, healthy controls; CA, controlled persistent asthma; SA, therapy-resistant asthma.

Figure E15. Transcription factor binding site motif activities divided by sample group for the

top ten most significantly differentially active motifs in the pairwise comparison between SA

and CA for the -1000 to +200 bp promoter region. SA, therapy-resistant asthma; CA,

controlled persistent asthma; CTRL, healthy control.


top ten most significantly differentially active motifs in the pairwise comparison between CA

and CTRL for the -1000 to +200 bp promoter region. SA, therapy-resistant asthma; CA,



top ten most significantly differentially active motifs in the pairwise comparison between SA

and CTRL for the -1000 to +200 bp promoter region. SA, therapy-resistant asthma; CA,


Figure E18. Expression of transcription factors corresponding to motifs with significantly

different activity in the pairwise comparisons between sample groups for the -1000 to +200

bp promoter region. Samples are sorted leukocyte populations and airway epithelial cells from

the FANTOM5 CAGE dataset (Forrest ARR, Kawaji H, Rehli M, Baillie JK et al. A promoter

level mammalian expression atlas. Nature 2014; 507(7493):462-470). The distance measure

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for clustering of samples and tag clusters (expression in log 2-transformed, normalized tags

per million, tpm) was Spearman rank correlation.

Figure E19. Regulatory network for transcription factor motifs with significantly different

motif activity between CA and SA (adjusted p < 0.1) for the -300 to +100 bp promoter region.

Node color corresponds to fold change (blue, lower motif activity in SA; red, higher activity)

and node size is inversely proportional to the p-value. Edge color reflects gene-specific motif

activity (darker equals higher activity, i.e. stronger regulatory effect). Target genes are

represented by green circles for TFs and yellow circles for other genes. CA, controlled

persistent asthma; SA, therapy-resistant asthma; bp, base pairs; TSS, transcription start site.


motif activity between CTRL and CA (adjusted p < 0.1) for the -300 to +100 bp promoter

region. Node color corresponds to fold change (blue, lower motif activity in SA; red, higher

activity) and node size is inversely proportional to the p-value. Edge color reflects gene-

specific motif activity (darker equals higher activity, i.e. stronger regulatory effect). Target

genes are represented by green circles for TFs and yellow circles for other genes. CTRL,

healthy control; CA, controlled persistent asthma; bp, base pairs; TSS, transcription start site.


motif activity between CTRL and CA (adjusted p < 0.1) for the -1000 to +200 bp promoter

region. Node color corresponds to fold change (blue, lower motif activity in CA; red, higher



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healthy control; CA, controlled persistent asthma; bp, base pairs; TSS, transcription start site.


motif activity between CTRL and SA (adjusted p < 0.1) for the -300 to +100 bp promoter





healthy control; SA, therapy-resistant asthma; bp, base pairs; TSS, transcription start site.


motif activity between CTRL and SA (adjusted p < 0.1) for the -1000 to +200 bp promoter





healthy control; SA, therapy-resistant asthma; bp, base pairs; TSS, transcription start site.

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· Web viewaDept of Biosciences and Nutrition and Center for Innovative Medicine (CIMED), Karolinska Institutet (KI), Stockholm, Sweden, bOmics Science Center, RIKEN Yokohama Institute,

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