chr3 : 126,933,925 126,934,641
716 bp 84 TFs 3 linked genes
This 716 bp open chromatin element is linked to PLXNA1, CHCHD6, and TXNRD3 and is bound by 84 transcription factors.
Linked Genes
3 genes
Link type
Gene Expression Dist. to TSS Distance Link type
PLXNA1 48.3 kb Distal Multiome+HiCAR
CHCHD6 230.1 kb Distal Multiome
TXNRD3 279.3 kb Distal Multiome
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.

View limited to ±500 kb around this element.
For the full data, please see the UCSC track linked below.
chr3:126,928,925 – 126,939,641
This element Other elements Gene links ATAC-seq RNA-seq

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

TF Binding
84 transcription factors
Source
Cell type
AR 1 dataset
ChIP epididymis_HEE_R1881 GSE109061.AR.epididymis_HEE_R1881 147 bp overlap
BNC2 2 datasets
ChIP SK-N-SH ENCFF174EMC 425 bp overlap
ChIP SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour ENCSR754GYI.BNC2.SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour 517 bp overlap
BRD4 6 datasets
ChIP Kelly_resistant GSE103030.BRD4.Kelly_resistant 611 bp overlap
ChIP Kelly_resistant_JQ1 GSE103030.BRD4.Kelly_resistant_JQ1 247 bp overlap
ChIP Kelly_sensitive GSE103030.BRD4.Kelly_sensitive 247 bp overlap
ChIP retina_AB1-FW15 GSE86981.BRD4.retina_AB1-FW15 559 bp overlap
ChIP retina_AB1-FW20 GSE86981.BRD4.retina_AB1-FW20 385 bp overlap
ChIP retina_AB1-FW23 GSE86981.BRD4.retina_AB1-FW23 266 bp overlap
CDX2 2 datasets
ChIP Caco-2_DIFF GSE23436.CDX2.Caco-2_DIFF 186 bp overlap
ChIP Caco-2_PROLIF GSE23436.CDX2.Caco-2_PROLIF 305 bp overlap
CHD2 1 dataset
ChIP SK-N-SH ENCSR274SLQ.CHD2.SK-N-SH 177 bp overlap
CHD7 2 datasets
ChIP hiPSC_derived_lt-NES GSE108506.CHD7.hiPSC_derived_lt-NES 279 bp overlap
ChIP hiPSC_derived_neural-crest-cell GSE108506.CHD7.hiPSC_derived_neural-crest-cell 362 bp overlap
CREB5 2 datasets
ChIP SK-N-SH ENCFF144PMI 345 bp overlap
ChIP SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour ENCSR758GOA.CREB5.SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour 349 bp overlap
CREBBP 1 dataset
ChIP fibroblast_proliferating GSE106146.CREBBP.fibroblast_proliferating 327 bp overlap
CTCFL 1 dataset
ChIP FT282 GSE131931.CTCFL.FT282 168 bp overlap
EOMES 1 dataset
ChIP hESC GSE26097.EOMES.hESC 224 bp overlap
EP300 7 datasets
ChIP SK-N-SH ENCFF829RWA 377 bp overlap
ChIP SK-N-SH ENCSR000EHV.EP300.SK-N-SH 191 bp overlap
ChIP SK-N-SH ENCSR000BUA.EP300.SK-N-SH 221 bp overlap
ChIP fibroblast_proliferating GSE106146.EP300.fibroblast_proliferating 441 bp overlap
ChIP neural ENCSR843ZUP.EP300.neural 296 bp overlap
ChIP neural cell ENCFF442QNK 517 bp overlap
ChIP neural cell ENCFF442QNK 383 bp overlap
ESR1 1 dataset
ChIP Ishikawa ENCSR000BIY.ESR1.Ishikawa 151 bp overlap
ESRRG 1 dataset
ChIP cardiomyocyte GSE113760.ESRRG.cardiomyocyte 279 bp overlap
ETS1 2 datasets
ChIP cardiomyocyte_D9 GSE129986.ETS1.cardiomyocyte_D9 150 bp overlap
ChIP cardiomyocyte_D9 GSE129986.ETS1.cardiomyocyte_D9 240 bp overlap
EZH2 1 dataset
ChIP hepatocyte ENCFF118DKH 357 bp overlap
FOSL2 2 datasets
ChIP NPC_R1159Q GSE122631.FOSL2.NPC_R1159Q 219 bp overlap
ChIP SK-N-SH ENCSR000BVB.FOSL2.SK-N-SH 286 bp overlap
FOXA1 1 dataset
ChIP pancreatic-progenitor_PP1 GSE104840.FOXA1.pancreatic-progenitor_PP1 378 bp overlap
FOXA2 5 datasets
ChIP BJ1-hTERT_FOXA2_GATA4_Coexp GSE92491.FOXA2.BJ1-hTERT_FOXA2_GATA4_Coexp 367 bp overlap
ChIP Caco-2 GSE66218.FOXA2.Caco-2 303 bp overlap
ChIP DE DE-FOXA2-1 698 bp overlap
ChIP DE DE-FOXA2-2 625 bp overlap
ChIP pancreatic-progenitor_PP1 GSE104840.FOXA2.pancreatic-progenitor_PP1 311 bp overlap
GATA2 1 dataset
ChIP dermal-fibroblast_alone GSE51025.GATA2.dermal-fibroblast_alone 188 bp overlap
GATA3 2 datasets
ChIP CLB-Ga GSE90683.GATA3.CLB-Ga 238 bp overlap
ChIP Kelly GSE65664.GATA3.Kelly 171 bp overlap
GATA4 7 datasets
ChIP BJ1-hTERT GSE92491.GATA4.BJ1-hTERT 333 bp overlap
ChIP BJ1-hTERT_FOXA2_GATA4_Coexp GSE92491.GATA4.BJ1-hTERT_FOXA2_GATA4_Coexp 190 bp overlap
ChIP DE DE-GATA4-1 617 bp overlap
ChIP DE DE-GATA4-2 668 bp overlap
ChIP foregut GSE117136.GATA4.foregut 319 bp overlap
ChIP pancreatic-progenitor GSE117136.GATA4.pancreatic-progenitor 555 bp overlap
ChIP pancreatic-progenitor_PP1 GSE104840.GATA4.pancreatic-progenitor_PP1 402 bp overlap
GATA6 14 datasets
ChIP Caco-2_PROLIF GSE23436.GATA6.Caco-2_PROLIF 237 bp overlap
ChIP DE DE-GATA6-1 577 bp overlap
ChIP DE DE-GATA6-2 574 bp overlap
ChIP DE_D1 S09-DE-d1-GATA6-exp1 517 bp overlap
ChIP DE_D1 S14-DE-d1-GATA6-exp1 530 bp overlap
ChIP DE_D1 S41-DE-d1-GATA6-exp2 499 bp overlap
ChIP DE_D2 S55-DE-d2-GATA6-exp2 547 bp overlap
ChIP HUES-8_DE_JNKi GSE109524.GATA6.HUES-8_DE_JNKi 552 bp overlap
ChIP HUES-8_DE_ctrl GSE109524.GATA6.HUES-8_DE_ctrl 624 bp overlap
ChIP endoderm_KO GSE117136.GATA6.endoderm_KO 363 bp overlap
ChIP foregut GSE117136.GATA6.foregut 342 bp overlap
ChIP pancreatic-progenitor GSE117136.GATA6.pancreatic-progenitor 499 bp overlap
ChIP pancreatic-progenitor_KO GSE117136.GATA6.pancreatic-progenitor_KO 454 bp overlap
ChIP pancreatic-progenitor_PP1 GSE104840.GATA6.pancreatic-progenitor_PP1 371 bp overlap
HAND2 2 datasets
ChIP CLB-Ga GSE90683.HAND2.CLB-Ga 477 bp overlap
ChIP SK-N-BE2-C GSE94822.HAND2.SK-N-BE2-C 372 bp overlap
HIF1A 1 dataset
ChIP U2OS_trough_DMOG GSE85096.HIF1A.U2OS_trough_DMOG 173 bp overlap
HOXA3 1 dataset
Motif DE_60h DE_60h-HOXA3_MA2119.1 7 bp overlap
HOXA4 1 dataset
Motif DE_60h DE_60h-HOXA4_MA1496.2 7 bp overlap
HOXA5 1 dataset
Motif DE_60h DE_60h-HOXA5_MA0158.2 8 bp overlap
HOXB4 1 dataset
Motif DE_60h DE_60h-HOXB4_MA1499.2 6 bp overlap
HOXC4 1 dataset
Motif DE_60h DE_60h-HOXC4_MA1504.2 6 bp overlap
HOXD3 1 dataset
Motif DE_60h DE_60h-HOXD3_MA0912.2 8 bp overlap
HOXD4 1 dataset
Motif DE_60h DE_60h-HOXD4_MA1507.2 6 bp overlap
ISL1 2 datasets
ChIP SK-N-BE2-C GSE94822.ISL1.SK-N-BE2-C 325 bp overlap
ChIP SK-N-SH ENCFF285GEQ 319 bp overlap
JUN 4 datasets
ChIP DE_D1 S08-DE-d1-JUN-exp1 357 bp overlap
ChIP DE_D1 S40-DE-d1-JUN-exp2 351 bp overlap
ChIP DE_D2 S02-DE-d2-JUN-exp1 553 bp overlap
ChIP HUES-8_DE_ctrl GSE109524.JUN.HUES-8_DE_ctrl 420 bp overlap
JUND 1 dataset
ChIP SK-N-SH ENCSR000BSK.JUND.SK-N-SH 209 bp overlap
KDM1A 1 dataset
ChIP pancreatic-progenitor_PP2-KDM1A-inh GSE104840.KDM1A.pancreatic-progenitor_PP2-KDM1A-inh 348 bp overlap
MAX 2 datasets
ChIP NCI-H2171 GSE41105.MAX.NCI-H2171 259 bp overlap
ChIP SK-N-SH ENCSR000BVD.MAX.SK-N-SH 123 bp overlap
MEIS1 7 datasets
Motif DE_60h DE_60h-MEIS1_MA0498.3 5 bp overlap
Motif DE_60h DE_60h-MEIS1_MA0498.3 5 bp overlap
Motif DE_60h DE_60h-MEIS1_MA0498.3 5 bp overlap
Motif DE_72h DE_72h-MEIS1_MA0498.3 5 bp overlap
Motif DE_72h DE_72h-MEIS1_MA0498.3 5 bp overlap
Motif DE_72h DE_72h-MEIS1_MA0498.3 5 bp overlap
Motif DE_72h DE_72h-MEIS1_MA0498.3 5 bp overlap
MEIS3 2 datasets
Motif DE_60h DE_60h-MEIS3_MA0775.2 7 bp overlap
Motif DE_72h DE_72h-MEIS3_MA0775.2 7 bp overlap
MXI1 1 dataset
ChIP SK-N-SH ENCFF746HVJ 434 bp overlap
MYC 3 datasets
ChIP CD34 GSE85488.MYC.CD34 113 bp overlap
ChIP NCI-H128 GSE41105.MYC.NCI-H128 202 bp overlap
ChIP NCI-H2171 GSE36354.MYC.NCI-H2171 320 bp overlap
MYCN 3 datasets
ChIP Kelly GSE94822.MYCN.Kelly 190 bp overlap
ChIP Kelly_sensitive GSE115249.MYCN.Kelly_sensitive 157 bp overlap
ChIP NB-1643 GSE138295.MYCN.NB-1643 237 bp overlap
MYOD1 4 datasets
ChIP IMR-90_GM GSE128527.MYOD1.IMR-90_GM 245 bp overlap
ChIP RH30_DMSO GSE85169.MYOD1.RH30_DMSO 218 bp overlap
ChIP RH4 GSE83726.MYOD1.RH4 172 bp overlap
ChIP rhabdomyosarcoma GSE50413.MYOD1.rhabdomyosarcoma 163 bp overlap
NKX2-1 1 dataset
ChIP H9_derived-cIN GSE99937.NKX2-1.H9_derived-cIN 178 bp overlap
NKX3-1 1 dataset
ChIP islet ERP004003.NKX3-1.islet 191 bp overlap
NR1D1 2 datasets
Motif DE_60h DE_60h-NR1D1_MA1531.2 14 bp overlap
Motif DE_72h DE_72h-NR1D1_MA1531.2 14 bp overlap
NR1D2 2 datasets
Motif DE_60h DE_60h-NR1D2_MA1532.2 15 bp overlap
Motif DE_72h DE_72h-NR1D2_MA1532.2 15 bp overlap
NR2F2 3 datasets
ChIP liver ENCFF565JGD 491 bp overlap
ChIP liver ENCSR168SMX.NR2F2.liver 380 bp overlap
ChIP liver ENCSR338MMB.NR2F2.liver 199 bp overlap
NR3C1 2 datasets
ChIP Ishikawa ENCSR000BJC.NR3C1.Ishikawa 101 bp overlap
ChIP Ishikawa ENCSR000BJC.NR3C1.Ishikawa 177 bp overlap
PBX3 1 dataset
ChIP SK-N-SH ENCFF876BMC 317 bp overlap
PDX1 5 datasets
ChIP hESC GSE58685.PDX1.hESC 404 bp overlap
ChIP hiPSC GSE125768.PDX1.hiPSC 418 bp overlap
ChIP hiPSC_derived_PPs GSE106949.PDX1.hiPSC_derived_PPs 520 bp overlap
ChIP islet ERP001456.PDX1.islet 121 bp overlap
ChIP pancreatic-progenitor GSE117136.PDX1.pancreatic-progenitor 670 bp overlap
PHOX2B 1 dataset
ChIP CLB-Ga GSE90683.PHOX2B.CLB-Ga 378 bp overlap
PITX3 1 dataset
ChIP SH-SY5Y GSE93275.PITX3.SH-SY5Y 351 bp overlap
POLR2A 1 dataset
ChIP spleen ENCFF044PYR 222 bp overlap
RARA 4 datasets
ChIP hiPSC_D2 GSE132532.RARA.hiPSC_D2 328 bp overlap
ChIP hiPSC_D3 GSE109172.RARA.hiPSC_D3 293 bp overlap
ChIP hiPSC_D4 GSE109172.RARA.hiPSC_D4 377 bp overlap
ChIP hiPSC_D5 GSE132532.RARA.hiPSC_D5 592 bp overlap
RBBP4 1 dataset
ChIP SCMC GSE155861.RBBP4.SCMC 271 bp overlap
RCOR1 1 dataset
ChIP SK-N-SH ENCSR009TKN.RCOR1.SK-N-SH 319 bp overlap
RELA 2 datasets
ChIP IMR-90_TNF GSE43070.RELA.IMR-90_TNF 258 bp overlap
ChIP IMR-90_TNF GSE43070.RELA.IMR-90_TNF 173 bp overlap
REST 1 dataset
ChIP neural ENCSR000BTV.REST.neural 137 bp overlap
RXRA 2 datasets
ChIP liver ENCFF077DAP 465 bp overlap
ChIP liver ENCFF807CIA 121 bp overlap
SIN3A 1 dataset
ChIP SK-N-SH ENCSR000BPB.SIN3A.SK-N-SH 300 bp overlap
SMAD2 1 dataset
ChIP endoderm GSE29422.SMAD2.endoderm 190 bp overlap
SMAD2-3 3 datasets
ChIP HUES-8_DE GSE109524.SMAD2-3.HUES-8_DE 553 bp overlap
ChIP HUES-8_DE_JNKi GSE109524.SMAD2-3.HUES-8_DE_JNKi 457 bp overlap
ChIP HUES-8_DE_ctrl GSE109524.SMAD2-3.HUES-8_DE_ctrl 439 bp overlap
SMAD2_3 5 datasets
ChIP DE_D1 S07-DE-d1-SMAD2_3-exp1 417 bp overlap
ChIP DE_D1 S12-DE-d1-SMAD2_3-exp1 383 bp overlap
ChIP DE_D1 S39-DE-d1-SMAD2_3-exp2 388 bp overlap
ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 489 bp overlap
ChIP DE_D2 S53-DE-d2-SMAD2_3-exp2 587 bp overlap
SMAD4 2 datasets
ChIP Caco-2 GSE112946.SMAD4.Caco-2 123 bp overlap
ChIP endoderm GSE29422.SMAD4.endoderm 189 bp overlap
SMARCA2 1 dataset
ChIP NPC_R1159Q_ab GSE122631.SMARCA2.NPC_R1159Q_ab 204 bp overlap
SMARCA4 3 datasets
ChIP NPC_siSOX GSE122631.SMARCA4.NPC_siSOX 252 bp overlap
ChIP NSC GSE125033.SMARCA4.NSC 154 bp overlap
ChIP hiPSC GSE124903.SMARCA4.hiPSC 159 bp overlap
SMC3 1 dataset
ChIP neural ENCSR404BPV.SMC3.neural 291 bp overlap
SNAI2 1 dataset
ChIP SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour ENCSR106GVM.SNAI2.SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour 190 bp overlap
SOX17 1 dataset
ChIP DE_D2 DED2-SOX17_Batch_II 229 bp overlap
SOX17_M 1 dataset
ChIP DE_D2 DED2-SOX17-M_Batch_II 564 bp overlap
SP1 1 dataset
ChIP liver ENCFF769YSM 508 bp overlap
SS18-SSX 1 dataset
ChIP fibroblast_6aa GSE139053.SS18-SSX.fibroblast_6aa 227 bp overlap
TBX2 2 datasets
ChIP Kelly GSE94822.TBX2.Kelly 288 bp overlap
ChIP SK-N-BE2-C GSE94822.TBX2.SK-N-BE2-C 236 bp overlap
TBX5 2 datasets
ChIP G296S_4 GSE85628.TBX5.G296S_4 261 bp overlap
ChIP hiPSC GSE81585.TBX5.hiPSC 205 bp overlap
TEAD1 1 dataset
ChIP pancreas_12D ERP008682.TEAD1.pancreas_12D 349 bp overlap
TEAD4 3 datasets
ChIP BE2C GSE84389.TEAD4.BE2C 303 bp overlap
ChIP Ishikawa ENCSR000BSW.TEAD4.Ishikawa 138 bp overlap
ChIP SK-N-BE2 GSE84389.TEAD4.SK-N-BE2 303 bp overlap
TFAP2B 1 dataset
ChIP SK-N-SH ENCFF869XXQ 441 bp overlap
TSHZ2 2 datasets
ChIP SK-N-SH ENCFF182EBB 381 bp overlap
ChIP SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour ENCSR282NLQ.TSHZ2.SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour 257 bp overlap
ZFP3 2 datasets
ChIP SK-N-SH ENCFF981MBE 441 bp overlap
ChIP SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour ENCSR581GUY.ZFP3.SK-N-SH_all-trans-retinoic-acid_6-uM_48-hour 364 bp overlap
ZNF384 2 datasets
ChIP HEK293T ENCFF019DZX 334 bp overlap
ChIP HEK293T ENCSR882ICT.ZNF384.HEK293T 300 bp overlap
ZNF534 1 dataset
ChIP HEK293T GSE78099.ZNF534.HEK293T 108 bp overlap