chr3:181,707,992–181,708,401

chr3 : 181,707,992 – 181,708,401

409 bp 140 TFs 5 linked genes

This 409 bp open chromatin element is linked to 5 target genes and is bound by 140 transcription factors.

Linked Genes

5 genes

Gene	Expression	Dist. to TSS	Distance	Link type
SOX2-OT		2.7 kb	Proximal	Proximity
ENSG00000289435		3.3 kb	Proximal	Proximity
SOX2		3.5 kb	Proximal	Proximity
ENSG00000239381		7.4 kb	Proximal	Proximity
ENSG00000276690		8.4 kb	Proximal	Proximity

Chromatin Accessibility

Genome Browser

Genomic view centred on this element. Tracks include ATAC-seq accessibility, RNA-seq expression, TF binding peaks, and element-to-gene loop arcs across the ESC → DE time course.

Transcription factors with ChIP-seq peak overlap or TOBIAS motif footprint evidence at this element.

TF Binding

140 transcription factors

ChIP WTC11 ENCFF556XTF 397 bp overlap

Motif DE_12h DE_12h-ALX3_MA0634.2 6 bp overlap

ARGFX 1 dataset

Motif DE_12h DE_12h-ARGFX_MA1463.2 8 bp overlap

ARID1A 1 dataset

ChIP HAP1 GSE108387.ARID1A.HAP1 323 bp overlap

ASH2L 1 dataset

ChIP WA01 ENCSR850KIP.ASH2L.WA01 365 bp overlap

ATF2 2 datasets

ChIP H1 ENCFF295GZO 409 bp overlap

ChIP WA01 ENCSR000BQU.ATF2.WA01 287 bp overlap

Motif DE_12h DE_12h-Alx1_MA0854.2 8 bp overlap

Motif DE_12h DE_12h-Alx4_MA0853.2 12 bp overlap

Motif DE_12h DE_12h-Arx_MA0874.2 10 bp overlap

BCL11A 3 datasets

ChIP H1 ENCFF833IPY 145 bp overlap

ChIP WA01 ENCSR000BMJ.BCL11A.WA01 193 bp overlap

ChIP WA01 ENCSR000BIP.BCL11A.WA01 198 bp overlap

ChIP cortical-interneuron_KCl-pos_JQ1-neg GSE117508.BRD4.cortical-interneuron_KCl-pos_JQ1-neg 250 bp overlap

Bach1::Mafk 2 datasets

Motif DE_12h DE_12h-Bach1Mafk_MA0591.2 12 bp overlap

Motif DE_12h DE_12h-Bach1Mafk_MA0591.2 12 bp overlap

CHD7 3 datasets

ChIP H1 ENCFF126NLU 409 bp overlap

ChIP WA01 ENCSR000AVA.CHD7.WA01 383 bp overlap

ChIP hiPSC_derived_lt-NES GSE108506.CHD7.hiPSC_derived_lt-NES 302 bp overlap

CTCF 2 datasets

Motif DE_12h DE_12h-CTCF_MA1930.2 33 bp overlap

ChIP dorsolateral prefrontal cortex ENCFF338KEP 105 bp overlap

ChIP BIN-67_lentivirus-SMARCA4-T910M GSE117734.DPF2.BIN-67_lentivirus-SMARCA4-T910M 271 bp overlap

Motif DE_12h DE_12h-DRGX_MA1481.2 6 bp overlap

Motif DE_12h DE_12h-EMX1_MA0612.3 6 bp overlap

Motif DE_12h DE_12h-EMX2_MA0886.2 6 bp overlap

Motif DE_12h DE_12h-EN1_MA0027.3 6 bp overlap

Motif DE_12h DE_12h-EN2_MA0642.3 7 bp overlap

EOMES 1 dataset

ChIP hESC GSE26097.EOMES.hESC 275 bp overlap

EP300 3 datasets

ChIP WA01 ENCSR000BKK.EP300.WA01 176 bp overlap

ChIP hESC GSE17917.EP300.hESC 409 bp overlap

ChIP osteoblast ENCSR000AUD.EP300.osteoblast 217 bp overlap

Motif DE_12h DE_12h-ESX1_MA0644.3 7 bp overlap

ChIP hESC ENCSR534VHI.ETS1.hESC 120 bp overlap

ChIP WTC11 ENCFF812SCD 362 bp overlap

Motif DE_12h DE_12h-EVX1_MA0887.2 6 bp overlap

Motif DE_12h DE_12h-EVX2_MA0888.2 6 bp overlap

EZH2 2 datasets

ChIP SF8628 GSE94834.EZH2.SF8628 409 bp overlap

ChIP hepatocyte ENCSR384LYW.EZH2.hepatocyte 288 bp overlap

ChIP A-673_1_KRAB_GFP GSE106914.FLI1.A-673_1_KRAB_GFP 286 bp overlap

FOXN3 1 dataset

Motif DE_12h DE_12h-FOXN3_MA1489.1 8 bp overlap

FOXP1 1 dataset

ChIP H9 GSE31006.FOXP1.H9 157 bp overlap

GATA6 5 datasets

ChIP DE_D1 S09-DE-d1-GATA6-exp1 409 bp overlap

ChIP DE_D1 S14-DE-d1-GATA6-exp1 409 bp overlap

ChIP DE_D1 S41-DE-d1-GATA6-exp2 409 bp overlap

ChIP DE_D2 S55-DE-d2-GATA6-exp2 386 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.GATA6.HUES-8_DE_ctrl 409 bp overlap

Motif DE_12h DE_12h-GBX1_MA0889.2 7 bp overlap

Motif DE_12h DE_12h-GSX1_MA0892.2 6 bp overlap

Motif DE_12h DE_12h-GSX2_MA0893.3 7 bp overlap

HAND2 1 dataset

Motif DE_12h DE_12h-HAND2_MA1638.2 6 bp overlap

HDAC2 2 datasets

ChIP H1 ENCFF939VKA 237 bp overlap

ChIP WA01 ENCSR000BNR.HDAC2.WA01 217 bp overlap

HOXA1 1 dataset

Motif DE_12h DE_12h-HOXA1_MA1495.2 6 bp overlap

HOXA2 1 dataset

Motif DE_12h DE_12h-HOXA2_MA0900.3 6 bp overlap

HOXA3 1 dataset

Motif DE_12h DE_12h-HOXA3_MA2119.1 7 bp overlap

HOXA5 1 dataset

Motif DE_12h DE_12h-HOXA5_MA0158.2 8 bp overlap

HOXB1 1 dataset

Motif DE_12h DE_12h-HOXB1_MA2093.1 7 bp overlap

HOXB2 1 dataset

Motif DE_12h DE_12h-HOXB2_MA0902.3 6 bp overlap

HOXB3 1 dataset

Motif DE_12h DE_12h-HOXB3_MA0903.2 6 bp overlap

HOXB5 1 dataset

Motif DE_12h DE_12h-HOXB5_MA0904.3 6 bp overlap

HOXC11 1 dataset

Motif DE_12h DE_12h-HOXC11_MA0651.3 11 bp overlap

HOXC12 1 dataset

Motif DE_12h DE_12h-HOXC12_MA0906.2 10 bp overlap

HOXC13 1 dataset

Motif DE_12h DE_12h-HOXC13_MA0907.2 9 bp overlap

HOXC8 1 dataset

Motif DE_12h DE_12h-HOXC8_MA1505.2 6 bp overlap

HOXD3 1 dataset

Motif DE_12h DE_12h-HOXD3_MA0912.2 8 bp overlap

Motif DE_12h DE_12h-ISX_MA0654.2 6 bp overlap

ChIP DE_D1 S40-DE-d1-JUN-exp2 366 bp overlap

ChIP DE_D2 S02-DE-d2-JUN-exp1 340 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.JUN.HUES-8_DE_ctrl 409 bp overlap

KDM1A 1 dataset

ChIP H1 ENCFF696SGD 401 bp overlap

ChIP WA09 GSE105028.KLF4.WA09 371 bp overlap

Motif DE_12h DE_12h-LBX1_MA0618.2 7 bp overlap

Motif DE_12h DE_12h-LHX5_MA1519.2 7 bp overlap

Motif DE_12h DE_12h-LHX6_MA0658.2 8 bp overlap

Motif DE_12h DE_12h-LHX9_MA0701.3 7 bp overlap

LMX1A 1 dataset

Motif DE_12h DE_12h-LMX1A_MA0702.3 7 bp overlap

LMX1B 1 dataset

Motif DE_12h DE_12h-LMX1B_MA0703.3 8 bp overlap

Motif DE_12h DE_12h-Lhx1_MA1518.3 10 bp overlap

Motif DE_12h DE_12h-Lhx4_MA0704.2 6 bp overlap

Motif DE_12h DE_12h-Lhx8_MA0705.2 6 bp overlap

Motif DE_12h DE_12h-MAZ_MA1522.2 8 bp overlap

ChIP hESC_PRIMED GSE69646.MED1.hESC_PRIMED 377 bp overlap

MEOX1 1 dataset

Motif DE_12h DE_12h-MEOX1_MA0661.2 7 bp overlap

MEOX2 1 dataset

Motif DE_12h DE_12h-MEOX2_MA0706.2 7 bp overlap

MIXL1 1 dataset

Motif DE_12h DE_12h-MIXL1_MA0662.2 6 bp overlap

Motif DE_12h DE_12h-MNX1_MA0707.3 6 bp overlap

NANOG 9 datasets

ChIP GM23338 ENCFF065NZG 305 bp overlap

ChIP GM23338 ENCSR061DGF.NANOG.GM23338 297 bp overlap

ChIP HUES-8 GSE109524.NANOG.HUES-8 409 bp overlap

ChIP WA01 ERP004238.NANOG.WA01 405 bp overlap

ChIP WA01 ENCSR000BMT.NANOG.WA01 236 bp overlap

ChIP WA01_3IL ERP004238.NANOG.WA01_3IL 409 bp overlap

ChIP WA09_heat-shock GSE105028.NANOG.WA09_heat-shock 409 bp overlap

ChIP hESC GSE20650.NANOG.hESC 261 bp overlap

ChIP hESC GSE18292.NANOG.hESC 304 bp overlap

NFATC3 1 dataset

Motif DE_12h DE_12h-NFATC3_MA0625.3 6 bp overlap

NIPBL 1 dataset

ChIP hESC_WNT3A GSE64758.NIPBL.hESC_WNT3A 195 bp overlap

NKX2-2 1 dataset

Motif DE_12h DE_12h-NKX2-2_MA1645.2 8 bp overlap

NKX2-5 1 dataset

Motif DE_12h DE_12h-NKX2-5_MA0063.3 7 bp overlap

NKX6-2 1 dataset

Motif DE_12h DE_12h-NKX6-2_MA0675.2 6 bp overlap

Motif DE_12h DE_12h-NOTO_MA0710.2 7 bp overlap

NUTM1 1 dataset

ChIP NUT_DMSO GSE133122.NUTM1.NUT_DMSO 388 bp overlap

Nfatc1 1 dataset

Motif DE_12h DE_12h-Nfatc1_MA0624.3 6 bp overlap

Nfatc2 1 dataset

Motif DE_12h DE_12h-Nfatc2_MA0152.3 8 bp overlap

ChIP WTC11 ENCFF634NAO 245 bp overlap

Motif DE_12h DE_12h-PAX4_MA0068.2 8 bp overlap

Motif DE_12h DE_12h-PDX1_MA0132.3 6 bp overlap

POU1F1 2 datasets

Motif DE_12h DE_12h-POU1F1_MA0784.3 14 bp overlap

Motif DE_12h DE_12h-POU1F1_MA0784.3 14 bp overlap

POU2F1 1 dataset

Motif DE_12h DE_12h-POU2F1_MA0785.2 9 bp overlap

POU2F1::SOX2 2 datasets

Motif DE_12h DE_12h-POU2F1SOX2_MA1962.1 17 bp overlap

Motif DE_12h DE_12h-POU2F1SOX2_MA1962.1 17 bp overlap

POU2F2 2 datasets

Motif DE_12h DE_12h-POU2F2_MA0507.3 13 bp overlap

Motif DE_12h DE_12h-POU2F2_MA0507.3 13 bp overlap

POU2F3 1 dataset

Motif DE_12h DE_12h-POU2F3_MA0627.3 9 bp overlap

POU3F1 1 dataset

Motif DE_12h DE_12h-POU3F1_MA0786.2 10 bp overlap

POU3F2 1 dataset

Motif DE_12h DE_12h-POU3F2_MA0787.1 12 bp overlap

POU3F3 2 datasets

Motif DE_12h DE_12h-POU3F3_MA0788.1 13 bp overlap

Motif DE_12h DE_12h-POU3F3_MA0788.1 13 bp overlap

POU3F4 1 dataset

Motif DE_12h DE_12h-POU3F4_MA0789.1 9 bp overlap

POU4F2 1 dataset

Motif DE_12h DE_12h-POU4F2_MA0683.2 15 bp overlap

POU5F1 11 datasets

ChIP DE_D1 DED1-OCT4_Batch_II 283 bp overlap

ChIP GM23338 ENCFF333SNB 277 bp overlap

ChIP HUES-8 GSE109524.POU5F1.HUES-8 409 bp overlap

ChIP NCCIT GSE36134.POU5F1.NCCIT 409 bp overlap

ChIP NCCIT_SNF5 GSE36134.POU5F1.NCCIT_SNF5 409 bp overlap

ChIP WA09 GSE105028.POU5F1.WA09 379 bp overlap

ChIP WA09_heat-shock GSE105028.POU5F1.WA09_heat-shock 319 bp overlap

ChIP hESC ENCSR264RJX.POU5F1.hESC 294 bp overlap

ChIP hESC_NAIVE GSE69646.POU5F1.hESC_NAIVE 369 bp overlap

ChIP hESC_PRIMED GSE69646.POU5F1.hESC_PRIMED 409 bp overlap

ChIP hiPSC GSE56567.POU5F1.hiPSC 256 bp overlap

POU5F1B 1 dataset

Motif DE_12h DE_12h-POU5F1B_MA0792.1 9 bp overlap

POU6F1 1 dataset

Motif DE_12h DE_12h-POU6F1_MA0628.2 6 bp overlap

POU6F2 1 dataset

Motif DE_12h DE_12h-POU6F2_MA0793.2 9 bp overlap

PRDM6 1 dataset

ChIP HEK293 ENCSR892QHR.PRDM6.HEK293 152 bp overlap

PRRX1 1 dataset

Motif DE_12h DE_12h-PRRX1_MA0716.2 6 bp overlap

PRRX2 1 dataset

Motif DE_12h DE_12h-PRRX2_MA0075.4 7 bp overlap

Pou5f1::Sox2 2 datasets

Motif DE_12h DE_12h-Pou5f1Sox2_MA0142.1 15 bp overlap

Motif DE_12h DE_12h-Pou5f1Sox2_MA0142.1 15 bp overlap

Prdm5 1 dataset

Motif DE_12h DE_12h-Prdm5_MA1999.2 11 bp overlap

ChIP hiPSC_D4 GSE109172.RARA.hiPSC_D4 193 bp overlap

Motif DE_12h DE_12h-RAX2_MA0717.2 6 bp overlap

RBBP5 1 dataset

ChIP WA01 ENCSR000AQC.RBBP5.WA01 149 bp overlap

RNF2 3 datasets

ChIP A-549 ENCSR798EGJ.RNF2.A-549 159 bp overlap

ChIP SYO-1_shRING1A-B GSE139053.RNF2.SYO-1_shRING1A-B 409 bp overlap

ChIP fibroblast GSE139053.RNF2.fibroblast 409 bp overlap

Motif DE_12h DE_12h-SHOX_MA0630.2 6 bp overlap

SMAD2-3 3 datasets

ChIP HUES-8_DE GSE109524.SMAD2-3.HUES-8_DE 269 bp overlap

ChIP HUES-8_DE_JNKi GSE109524.SMAD2-3.HUES-8_DE_JNKi 409 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.SMAD2-3.HUES-8_DE_ctrl 409 bp overlap

SMAD2_3 4 datasets

ChIP DE_D1 S07-DE-d1-SMAD2_3-exp1 393 bp overlap

ChIP DE_D1 S12-DE-d1-SMAD2_3-exp1 352 bp overlap

ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 366 bp overlap

ChIP DE_D2 S53-DE-d2-SMAD2_3-exp2 282 bp overlap

SMAD3 1 dataset

ChIP BG03 GSE21614.SMAD3.BG03 195 bp overlap

SMARCA4 9 datasets

ChIP BIN-67_lentivirus-SMARCA4-K785R GSE117734.SMARCA4.BIN-67_lentivirus-SMARCA4-K785R 246 bp overlap

ChIP BIN-67_lentivirus-SMARCA4-T910M GSE117734.SMARCA4.BIN-67_lentivirus-SMARCA4-T910M 288 bp overlap

ChIP HS-SY-2_HA-tagged GSE108926.SMARCA4.HS-SY-2_HA-tagged 195 bp overlap

ChIP NPC_siCT GSE122631.SMARCA4.NPC_siCT 268 bp overlap

ChIP NPC_siSOX GSE122631.SMARCA4.NPC_siSOX 334 bp overlap

ChIP WA09 GSE105028.SMARCA4.WA09 303 bp overlap

ChIP WA09_heat-shock GSE105028.SMARCA4.WA09_heat-shock 409 bp overlap

ChIP hiPSC GSE124903.SMARCA4.hiPSC 409 bp overlap

ChIP hiPSC_WT GSE124903.SMARCA4.hiPSC_WT 409 bp overlap

SMARCB1 2 datasets

ChIP hiPSC GSE124903.SMARCB1.hiPSC 388 bp overlap

ChIP hiPSC_WT GSE124903.SMARCB1.hiPSC_WT 409 bp overlap

SMARCC1 6 datasets

ChIP BIN-67_lentivirus-SMARCA4-T910M GSE117734.SMARCC1.BIN-67_lentivirus-SMARCA4-T910M 207 bp overlap

ChIP DE_D1 S10-DE-d1-BAF155-exp1 329 bp overlap

ChIP DE_D1 S15-DE-d1-BAF155-exp1 409 bp overlap

ChIP HS-SY-2 GSE108025.SMARCC1.HS-SY-2 386 bp overlap

ChIP hiPSC GSE124903.SMARCC1.hiPSC 400 bp overlap

ChIP hiPSC_WT GSE124903.SMARCC1.hiPSC_WT 409 bp overlap

SOX2 3 datasets

ChIP HNSC GSE69479.SOX2.HNSC 127 bp overlap

ChIP hESC GSE18292.SOX2.hESC 270 bp overlap

ChIP hiPSC GSE56567.SOX2.hiPSC 266 bp overlap

SOX21 1 dataset

Motif DE_12h DE_12h-SOX21_MA0866.1 15 bp overlap

ChIP H1 ENCFF263FUH 294 bp overlap

ChIP WA01 ENCSR000BIR.SP1.WA01 273 bp overlap

ChIP WA01 ENCSR000BQV.SP4.WA01 192 bp overlap

ChIP DC_LPS GSE123347.SPI1.DC_LPS 105 bp overlap

SS18 2 datasets

ChIP BIN-67_lentivirus-SMARCA4-K785R GSE117734.SS18.BIN-67_lentivirus-SMARCA4-K785R 114 bp overlap

ChIP SYO-1_shCt GSE139053.SS18.SYO-1_shCt 326 bp overlap

Shox2 1 dataset

Motif DE_12h DE_12h-Shox2_MA0720.2 6 bp overlap

Stat4 1 dataset

Motif DE_12h DE_12h-Stat4_MA0518.2 10 bp overlap

ChIP H9_ENDODERM GSE60606.T.H9_ENDODERM 376 bp overlap

ChIP H9_MESODERM GSE60606.T.H9_MESODERM 183 bp overlap

ChIP WA01 ENCSR000BHO.TAF1.WA01 163 bp overlap

ChIP hESC GSE122298.TBP.hESC 140 bp overlap

ChIP hESC_2h GSE122298.TBP.hESC_2h 299 bp overlap

ChIP hESC_8h GSE122298.TBP.hESC_8h 131 bp overlap

TCF12 1 dataset

ChIP WA01 ENCSR000BIT.TCF12.WA01 112 bp overlap

TEAD1 2 datasets

Motif DE_12h DE_12h-TEAD1_MA0090.4 9 bp overlap

ChIP WTC11 ENCFF502QUV 321 bp overlap

TEAD4 4 datasets

Motif DE_12h DE_12h-TEAD4_MA0809.3 8 bp overlap

ChIP ESC S26-ESC-d0-TEAD4-exp1 320 bp overlap

ChIP H1 ENCFF778PAX 234 bp overlap

ChIP hESC GSE99202.TEAD4.hESC 185 bp overlap

Motif DE_12h DE_12h-TLX2_MA1577.2 6 bp overlap

ChIP H9_ectoderm GSE142050.TP53.H9_ectoderm 364 bp overlap

Motif DE_12h DE_12h-UNCX_MA0721.2 6 bp overlap

Motif DE_12h DE_12h-VAX1_MA0722.2 7 bp overlap

Motif DE_12h DE_12h-VAX2_MA0723.3 6 bp overlap

Motif DE_12h DE_12h-VSX1_MA0725.2 7 bp overlap

Motif DE_12h DE_12h-VSX2_MA0726.2 7 bp overlap

ZBTB7B 1 dataset

Motif DE_12h DE_12h-ZBTB7B_MA0694.2 10 bp overlap

ZBTB7C 1 dataset

Motif DE_12h DE_12h-ZBTB7C_MA0695.2 8 bp overlap

ZNF148 1 dataset

Motif DE_12h DE_12h-ZNF148_MA1653.2 10 bp overlap

ZNF207 1 dataset

ChIP WA09 GSE118632.ZNF207.WA09 223 bp overlap

ZNF680 1 dataset

Motif DE_12h DE_12h-ZNF680_MA1729.2 11 bp overlap

ZNF816 1 dataset

Motif DE_12h DE_12h-ZNF816_MA1719.2 15 bp overlap

ZSCAN4 1 dataset

Motif DE_12h DE_12h-ZSCAN4_MA1155.1 15 bp overlap