Table 1 Full list of ChIP-Seq TSS-Promoter genes.

Abcc10

ATP-binding cassette, subfamily C (CFTR/MRP), member 10

NM_001108201

protein-coding

Acot13

acyl-CoA thioesterase 13

NM_001106111

protein-coding

Acp1

acid phosphatase 1, soluble

NM_021262

protein-coding

Acpt

acid phosphatase, testicular

NM_001107510

protein-coding

Actc1

actin, alpha, cardiac muscle 1

NM_019183

protein-coding

Adra2b

adrenoceptor alpha 2B

NM_138505

protein-coding

Agrn

agrin

NM_175754

protein-coding

Ahrr

aryl-hydrocarbon receptor repressor

NM_001024285

protein-coding

Aldh3a2

aldehyde dehydrogenase 3 family, member A2

NM_031731

protein-coding

Alg11

ALG11, alpha-1,2-mannosyltransferase

NM_001108401

protein-coding

Alg8

ALG8, alpha-1,3-glucosyltransferase

NM_001034127

protein-coding

Amdhd1

amidohydrolase domain containing 1

NM_001191781

protein-coding

Anxa2

annexin A2

NM_019905

protein-coding

Arfgap2

ADP-ribosylation factor GTPase activating protein 2

NM_001033707

protein-coding

Arhgap4

Rho GTPase activating protein 4

NM_144740

protein-coding

Asl

argininosuccinate lyase

NM_021577

protein-coding

Atp6v0e1

ATPase, H+ transporting, lysosomal, V0 subunit e1

NM_053578

protein-coding

Atraid

all-trans retinoic acid-induced differentiation factor

NM_001127526

protein-coding

B3galt4

UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 4

NM_133553

protein-coding

Bbs2

Bardet-Biedl syndrome 2

NM_053618

protein-coding

Bbs5

Bardet-Biedl syndrome 5

NM_001108583

protein-coding

Bin2

bridging integrator 2

NM_001012223

protein-coding

Bphl

biphenyl hydrolase-like (serine hydrolase)

NM_001037206

protein-coding

Brd9

bromodomain containing 9

NM_001107453

protein-coding

Cacng8

calcium channel, voltage-dependent, gamma subunit 8

NM_080696

protein-coding

Cap1

CAP, adenylate cyclase-associated protein 1 (yeast)

NM_022383

protein-coding

Casp6

caspase 6

NM_031775

protein-coding

Cblc

Cbl proto-oncogene C, E3 ubiquitin protein ligase

NM_001034920

protein-coding

Cct6a

chaperonin containing Tcp1, subunit 6 A (zeta 1)

NM_001033684

protein-coding

Cdc20

cell division cycle 20

NM_171993

protein-coding

Cers1

ceramide synthase 1

NM_001044230

protein-coding

Chad

chondroadherin

NM_019164

protein-coding

Chmp1a

charged multivesicular body protein 1 A

NM_001083313

protein-coding

Chrnb1

cholinergic receptor, nicotinic, beta 1 (muscle)

NM_012528

protein-coding

Ciapin1

cytokine induced apoptosis inhibitor 1

NM_001007689

protein-coding

Cidea

cell death-inducing DFFA-like effector a

NM_001170467

protein-coding

Clpsl2

colipase-like 2

NM_001135002

protein-coding

Cnksr1

connector enhancer of kinase suppressor of Ras 1

NM_001039011

protein-coding

Col4a3

collagen, type IV, alpha 3

NM_001135759

protein-coding

Col7a1

collagen, type VII, alpha 1

NM_001106858

protein-coding

Cpne6

copine VI (neuronal)

NM_001191113

protein-coding

Cpsf3l

cleavage and polyadenylation specific factor 3-like

NM_001033892

protein-coding

Cpsf4

cleavage and polyadenylation specific factor 4

NM_001012351

protein-coding

Crcp

CGRP receptor component

NM_053670

protein-coding

Cth

cystathionine gamma-lyase

NM_017074

protein-coding

Ctr9

CTR9 homolog, Paf1/RNA polymerase II complex component

NM_001100661

protein-coding

Cyb5r1

cytochrome b5 reductase 1

NM_001013126

protein-coding

Cyba

cytochrome b-245, alpha polypeptide

NM_024160

protein-coding

Ddb1

damage-specific DNA binding protein 1, 127 kDa

NM_171995

protein-coding

Ddb2

damage specific DNA binding protein 2

NM_001271346

protein-coding

Ddias

DNA damage-induced apoptosis suppressor

NM_001126294

protein-coding

Ddit4l2

DNA-damage-inducible transcript 4-like 2

NM_080399

protein-coding

Ddx55

DEAD (Asp-Glu-Ala-Asp) box polypeptide 55

NM_001271326

protein-coding

Ddx56

DEAD (Asp-Glu-Ala-Asp) box helicase 56

NM_001004211

protein-coding

Dhdds

dehydrodolichyl diphosphate synthase subunit

NM_001011978

protein-coding

Dmrtc2

DMRT-like family C2

NM_001109140

protein-coding

Dnaja1

DnaJ (Hsp40) homolog, subfamily A, member 1

NM_022934

protein-coding

Eif3e

eukaryotic translation initiation factor 3, subunit E

NM_001011990

protein-coding

Emc3

ER membrane protein complex subunit 3

NM_001008355

protein-coding

Emd

emerin

NM_012948

protein-coding

Entpd6

ectonucleoside triphosphate diphosphohydrolase 6

NM_053498

protein-coding

Eny2

enhancer of yellow 2 homolog (Drosophila)

NM_001130580

protein-coding

Ephx2

epoxide hydrolase 2, cytoplasmic

NM_022936

protein-coding

Fam151a

family with sequence similarity 151, member A

NM_001005558

protein-coding

Fam178b

family with sequence similarity 178, member B

NM_001122653

protein-coding

Fam192a

family with sequence similarity 192, member A

NM_001014014

protein-coding

Fanca

Fanconi anemia, complementation group A

NM_001108455

protein-coding

Fbxo44

F-box protein 44

NM_001191576

protein-coding

Fdxr

ferredoxin reductase

NM_024153

protein-coding

Fgfr1op2

FGFR1 oncogene partner 2

NM_201421

protein-coding

Fkbp6

FK506 binding protein 6

NM_001105922

protein-coding

Foxm1

forkhead box M1

NM_031633

protein-coding

Fyco1

FYVE and coiled-coil domain containing 1

NM_001106870

protein-coding

Gamt

guanidinoacetate N-methyltransferase

NM_012793

protein-coding

Gdf1

growth differentiation factor 1

NM_001044240

protein-coding

Gja4

gap junction protein, alpha 4

NM_021654

protein-coding

Gjd4

gap junction protein, delta 4

NM_001100487

protein-coding

Gna15

guanine nucleotide binding protein, alpha 15

NM_053542

protein-coding

Gng5

guanine nucleotide binding protein (G protein), gamma 5

NM_024377

protein-coding

Gnmt

glycine N-methyltransferase

NM_017084

protein-coding

Gnpat

glyceronephosphate O-acyltransferase

NM_053410

protein-coding

Gosr2

golgi SNAP receptor complex member 2

NM_031685

protein-coding

Gpalpp1

GPALPP motifs containing 1

NM_001024875

protein-coding

Gtf2e1

general transcription factor IIE, polypeptide 1, alpha

NM_001100556

protein-coding

Gtsf1

gametocyte specific factor 1

NM_001079707

protein-coding

Gzf1

GDNF-inducible zinc finger protein 1

NM_001107788

protein-coding

Hcfc1r1

host cell factor C1 regulator 1 (XPO1-dependent)

NM_001100492

protein-coding

Higd2a

HIG1 hypoxia inducible domain family, member 2 A

NM_001106102

protein-coding

Hist3h2a

histone cluster 3, H2a

NM_021840

protein-coding

Hist3h2bb

histone cluster 3, H2bb

NM_001109641

protein-coding

Hoxc8

homeobox C8

NM_001177326

protein-coding

Hoxd10

homeo box D10

NM_001107094

protein-coding

Hrg

histidine-rich glycoprotein

NM_133428

protein-coding

Icam1

intercellular adhesion molecule 1

NM_012967

protein-coding

Idua

iduronidase, alpha-L-

NM_001172084

protein-coding

Ift122

intraflagellar transport 122

NM_001009416

protein-coding

Ikzf5

IKAROS family zinc finger 5

NM_001107555

protein-coding

Il17rb

interleukin 17 receptor B

NM_001107290

protein-coding

Itga4

integrin, alpha 4

NM_001107737

protein-coding

Jagn1

jagunal homolog 1

NM_001044272

protein-coding

Jtb

jumping translocation breakpoint

NM_019213

protein-coding

Kb15

type II keratin Kb15

NM_001008825

protein-coding

Kcne5

potassium channel, voltage-gated Isk-related subfamily E regulatory beta subunit 5

NM_001101003

protein-coding

Kdelr1

KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 1

NM_001017385

protein-coding

Kiaa0895l

hypothetical protein LOC688736

NM_001044292

protein-coding

Kif11

kinesin family member 11

NM_001169112

protein-coding

Kif18b

kinesin family member 18B

NM_001039019

protein-coding

Klrd1

killer cell lectin-like receptor, subfamily D, member 1

NM_012745

protein-coding

Krt33b

keratin 33B

NM_001008819

protein-coding

Lars2

leucyl-tRNA synthetase 2, mitochondrial

NM_001108787

protein-coding

Leng1

leukocyte receptor cluster (LRC) member 1

NM_001106218

protein-coding

Lhx1

LIM homeobox 1

NM_145880

protein-coding

LOC100912214

uncharacterized LOC100912214

NR_131101

ncRNA

LOC103689982

lysophospholipid acyltransferase 7

NM_001313940

protein-coding

LOC288913

similar to LEYDIG CELL TUMOR 10 KD PROTEIN

NM_198728

protein-coding

LOC498154

hypothetical protein LOC498154

NM_001025033

protein-coding

LOC688925

similar to Glutathione S-transferase alpha-4

NM_001270386

protein-coding

Lrrc14

leucine rich repeat containing 14

NM_001024354

protein-coding

Lrrc27

leucine rich repeat containing 27

NM_001113789

protein-coding

Lrrc36

leucine rich repeat containing 36

NM_001004088

protein-coding

Lrrc51

leucine rich repeat containing 51

NM_001106284

protein-coding

Lypd3

Ly6/Plaur domain containing 3

NM_021759

protein-coding

Lzic

leucine zipper and CTNNBIP1 domain containing

NM_001013241

protein-coding

Lztfl1

leucine zipper transcription factor-like 1

NM_001024266

protein-coding

Maf1

MAF1 homolog, negative regulator of RNA polymerase III

NM_001014085

protein-coding

Mag

myelin-associated glycoprotein

NM_017190

protein-coding

Mal

mal, T-cell differentiation protein

NM_012798

protein-coding

Mboat7

membrane bound O-acyltransferase domain containing 7

NM_001134978

protein-coding

Mcemp1

mast cell-expressed membrane protein 1

NM_001134602

protein-coding

Mea1

male-enhanced antigen 1

NM_001044286

protein-coding

Med11

mediator complex subunit 11

NM_001105799

protein-coding

Mir137

microRNA 137

NR_031883

ncRNA

Mir207

microRNA 207

NR_032107

ncRNA

Mir338

microRNA 338

NR_031783

ncRNA

Mir3562

microRNA 3562

NR_037344

ncRNA

Misp

mitotic spindle positioning

NM_001109284

protein-coding

Mrpl43

mitochondrial ribosomal protein L43

NM_001107598

protein-coding

Mrps18b

mitochondrial ribosomal protein S18B

NM_212534

protein-coding

Mrps25

mitochondrial ribosomal protein S25

NM_001025408

protein-coding

Mt2A

metallothionein 2A

NM_001137564

protein-coding

Mt3

metallothionein 3

NM_053968

protein-coding

Mterf3

mitochondrial transcription termination factor 3

NM_199387

protein-coding

Mtf1

metal-regulatory transcription factor 1

NM_001108677

protein-coding

Mtf2

metal response element binding transcription factor 2

NM_001100898

protein-coding

Myeov2

myeloma overexpressed 2

NM_001109044

protein-coding

Naa38

N(alpha)-acetyltransferase 38, NatC auxiliary subunit

NM_001105794

protein-coding

Ncbp1

nuclear cap binding protein subunit 1

NM_001014785

protein-coding

Ncoa4

nuclear receptor coactivator 4

NM_001034007

protein-coding

Ndor1

NADPH dependent diflavin oxidoreductase 1

NM_001107818

protein-coding

Ndufb8

NADH dehydrogenase (ubiquinone) 1 beta subcomplex 8

NM_001106360

protein-coding

Ndufs5

NADH dehydrogenase (ubiquinone) Fe-S protein 5

NM_001030052

protein-coding

Ndufv3

NADH dehydrogenase (ubiquinone) flavoprotein 3

NM_022607

protein-coding

Nipsnap1

nipsnap homolog 1 (C. elegans)

NM_001100730

protein-coding

Nme3

NME/NM23 nucleoside diphosphate kinase 3

NM_053507

protein-coding

Nmi

N-myc (and STAT) interactor

NM_001034148

protein-coding

Nmu

neuromedin U

NM_022239

protein-coding

Nob1

NIN1/RPN12 binding protein 1 homolog

NM_199086

protein-coding

Nolc1

nucleolar and coiled-body phosphoprotein 1

NM_022869

protein-coding

Nr2c2ap

nuclear receptor 2C2-associated protein

NM_001047104

protein-coding

Nsl1

NSL1, MIS12 kinetochore complex component

NM_001109083

protein-coding

Ntpcr

nucleoside-triphosphatase, cancer-related

NM_001134573

protein-coding

Ntsr1

neurotensin receptor 1

NM_001108967

protein-coding

Nubp2

nucleotide binding protein 2

NM_001011891

protein-coding

Nudt2

nudix (nucleoside diphosphate linked moiety X)-type motif 2

NM_207596

protein-coding

Olr437

olfactory receptor 437

NM_001109347

protein-coding

Olr760

olfactory receptor 760

NM_001001069

protein-coding

Ovca2

ovarian tumor suppressor candidate 2

NM_001109036

protein-coding

Pcdha3

protocadherin alpha 3

NM_053941

protein-coding

Pctp

phosphatidylcholine transfer protein

NM_017225

protein-coding

Pex1

peroxisomal biogenesis factor 1

NM_001109220

protein-coding

Phlda2

pleckstrin homology-like domain, family A, member 2

NM_001100521

protein-coding

Phldb3

pleckstrin homology-like domain, family B, member 3

NM_001191622

protein-coding

Pigp

phosphatidylinositol glycan anchor biosynthesis, class P

NM_001099758

protein-coding

Plcxd2

phosphatidylinositol-specific phospholipase C, X domain containing 2

NM_001134481

protein-coding

Plp2

proteolipid protein 2 (colonic epithelium-enriched)

NM_207601

protein-coding

Pmf1

polyamine-modulated factor 1

NM_001191568

protein-coding

Pnldc1

poly(A)-specific ribonuclease (PARN)-like domain containing 1

NM_001025724

protein-coding

Polr3d

polymerase (RNA) III (DNA directed) polypeptide D

NM_001031653

protein-coding

Pou6f1

POU class 6 homeobox 1

NM_001105746

protein-coding

Ppp1r11

protein phosphatase 1, regulatory (inhibitor) subunit 11

NM_212542

protein-coding

Ppt2

palmitoyl-protein thioesterase 2

NM_019367

protein-coding

Psmg4

proteasome (prosome, macropain) assembly chaperone 4

NM_001109543

protein-coding

Ptcd1

pentatricopeptide repeat domain 1

NM_001109665

protein-coding

Ptk2b

protein tyrosine kinase 2 beta

NM_017318

protein-coding

Qk

quaking

NM_001115021

protein-coding

Rab3gap2

RAB3 GTPase activating protein subunit 2

NM_001008294

protein-coding

Rab5c

RAB5C, member RAS oncogene family

NM_001105840

protein-coding

Rad51ap1

RAD51 associated protein 1

NM_001079711

protein-coding

Ranbp10

RAN binding protein 10

NM_001135875

protein-coding

Rec8

REC8 meiotic recombination protein

NM_001011916

protein-coding

Rfc2

replication factor C (activator 1) 2

NM_053786

protein-coding

RGD1307443

similar to mKIAA0319 protein

NM_001197023

protein-coding

RGD1309188

similar to hypothetical protein BC011833

NM_001108129

protein-coding

RGD1309676

similar to RIKEN cDNA 5730469M10

NM_001014140

protein-coding

RGD1311703

similar to sid2057p

NM_001013898

protein-coding

RGD1359334

similar to hypothetical protein FLJ20519

NM_001007638

protein-coding

RGD1559909

RGD1559909

NM_001108678

protein-coding

RGD1560608

similar to novel protein

NM_001109280

protein-coding

RGD1562683

RGD1562683

NM_001108314

protein-coding

RGD1563714

RGD1563714

NM_001126297

protein-coding

RGD1564036

similar to RIKEN cDNA 3010026O09

NM_001109030

protein-coding

Ribc2

RIB43 A domain with coiled-coils 2

NM_001013949

protein-coding

Rnf40

ring finger protein 40, E3 ubiquitin protein ligase

NM_153471

protein-coding

Rph3a

rabphilin 3A

NM_133518

protein-coding

Rpl27

ribosomal protein L27

NM_022514

protein-coding

Rpl27a

ribosomal protein L27a

NM_001106290

protein-coding

Rspry1

ring finger and SPRY domain containing 1

NM_001100945

protein-coding

Rxfp3

relaxin/insulin-like family peptide receptor 3

NM_001008310

protein-coding

Sart3

squamous cell carcinoma antigen recognized by T-cells 3

NM_001107156

protein-coding

Scly

selenocysteine lyase

NM_001007755

protein-coding

Sert1

Sertoli cell protein 1

NR_130708

ncRNA

Sfxn3

sideroflexin 3

NM_022948

protein-coding

Skap2

src kinase associated phosphoprotein 2

NM_130413

protein-coding

Slc19a2

solute carrier family 19 (thiamine transporter), member 2

NM_001030024

protein-coding

Slc25a54

solute carrier family 25, member 54

NM_001109640

protein-coding

Slc43a3

solute carrier family 43, member 3

NM_001107743

protein-coding

Slc5a6

solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6

NM_130746

protein-coding

Slc6a20

solute carrier family 6 (proline IMINO transporter), member 20

NM_133296

protein-coding

Slc6a3

solute carrier family 6 (neurotransmitter transporter), member 3

NM_012694

protein-coding

Snrnp35

small nuclear ribonucleoprotein 35 (U11/U12)

NM_001014127

protein-coding

Snrpb2

small nuclear ribonucleoprotein polypeptide B”

NM_001108592

protein-coding

Spag7

sperm associated antigen 7

NM_001107016

protein-coding

Spata33

spermatogenesis associated 33

NM_001106195

protein-coding

Spata5

spermatogenesis associated 5

NM_001108549

protein-coding

Spic

Spi-C transcription factor (Spi-1/PU.1 related)

NM_001108080

protein-coding

Stam

signal transducing adaptor molecule (SH3 domain and ITAM motif) 1

NM_001109121

protein-coding

Stk19

serine/threonine kinase 19

NM_001013197

protein-coding

Susd3

sushi domain containing 3

NM_001107341

protein-coding

Tada3

transcriptional adaptor 3

NM_001025734

protein-coding

Taf6l

TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor

NM_001107575

protein-coding

Tax1bp3

Tax1 (human T-cell leukemia virus type I) binding protein 3

NM_001025419

protein-coding

Tbc1d25

TBC1 domain family, member 25

NM_001106955

protein-coding

Tbcb

tubulin folding cofactor B

NM_001040180

protein-coding

Them4

thioesterase superfamily member 4

NM_001025017

protein-coding

Tmem109

transmembrane protein 109

NM_001007736

protein-coding

Tmem126a

transmembrane protein 126 A

NM_001011557

protein-coding

Tnxa-ps1

tenascin XA, pseudogene 1

NR_024118

pseudo

Trappc1

trafficking protein particle complex 1

NM_001039378

protein-coding

Trim23

tripartite motif-containing 23

NM_001100637

protein-coding

Trip13

thyroid hormone receptor interactor 13

NM_001011930

protein-coding

Trip4

thyroid hormone receptor interactor 4

NM_001134981

protein-coding

Trmt112

tRNA methyltransferase 11-2 homolog (S. cerevisiae)

NM_001106330

protein-coding

Tsc2

tuberous sclerosis 2

NM_012680

protein-coding

Tstd2

thiosulfate sulfurtransferase (rhodanese)-like domain containing 2

NM_001108663

protein-coding

Ttc3

tetratricopeptide repeat domain 3

NM_001108315

protein-coding

Tuba3a

tubulin, alpha 3A

NM_001040008

protein-coding

Tuba4a

tubulin, alpha 4A

NM_001007004

protein-coding

Tubb2b

tubulin, beta 2B class IIb

NM_001013886

protein-coding

Ufsp2

UFM1-specific peptidase 2

NM_001014142

protein-coding

Vmp1

vacuole membrane protein 1

NM_138839

protein-coding

Vwa7

von Willebrand factor A domain containing 7

NM_212499

protein-coding

Zbtb26

zinc finger and BTB domain containing 26

NM_001107840

protein-coding

Zfp142

zinc finger protein 142

NM_001108225

protein-coding

Zfp597

zinc finger protein 597

NM_153732

protein-coding

Zscan21

zinc finger and SCAN domain containing 21

NM_001012021

protein-coding