chr3 : 57,546,064 – 57,547,149
1,085 bp 113 TFs 5 linked genes
This 1.1 kb open chromatin element is linked to 5 target genes and is bound by 113 transcription factors.
Linked Genes
5 genes
Distance
Link type
Gene↕ Expression Dist. to TSS↑ Distance↕ Link type↕
DNAH12 1.7 kb Proximal Proximity
ENSG00000287502 8.9 kb Proximal Proximity
PDE12 9.1 kb Proximal Proximity
ARF4 50.6 kb Distal Multiome
DENND6A 146.3 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.
chr3:57,541,064 – 57,552,149
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
113 transcription factors
Source
Cell type
ARID1B 1 dataset
ChIP K-562 ENCSR822CCM.ARID1B.K-562 296 bp overlap
ATF3 1 dataset
ChIP K-562 ENCSR028UIU.ATF3.K-562 376 bp overlap
ATF4 1 dataset
ChIP K-562 ENCSR145TSJ.ATF4.K-562 261 bp overlap
Atf3 1 dataset
Motif DE_72h DE_72h-Atf3_MA1988.2 7 bp overlap
BACH1 1 dataset
Motif DE_72h DE_72h-BACH1_MA1633.2 9 bp overlap
BATF 1 dataset
Motif DE_72h DE_72h-BATF_MA1634.2 7 bp overlap
BATF3 1 dataset
Motif DE_72h DE_72h-BATF3_MA0835.3 7 bp overlap
BATF::JUN 1 dataset
Motif DE_72h DE_72h-BATFJUN_MA0462.3 7 bp overlap
BCL6 1 dataset
ChIP HepG2 ENCFF423EJH 171 bp overlap
BNC2 1 dataset
Motif DE_72h DE_72h-BNC2_MA1928.2 7 bp overlap
CBFA2T3 1 dataset
ChIP K-562 ENCSR697YLJ.CBFA2T3.K-562 217 bp overlap
CREBBP 1 dataset
ChIP retina_Hu33 GSE137311.CREBBP.retina_Hu33 303 bp overlap
CRX 4 datasets
ChIP retina_Hu20 GSE137311.CRX.retina_Hu20 473 bp overlap
ChIP retina_Hu21 GSE137311.CRX.retina_Hu21 245 bp overlap
ChIP retina_Hu3 GSE137311.CRX.retina_Hu3 487 bp overlap
ChIP retina_Hu6 GSE137311.CRX.retina_Hu6 492 bp overlap
CTCF 3 datasets
ChIP retina_Hu22 GSE137311.CTCF.retina_Hu22 332 bp overlap
ChIP retina_Hu25 GSE137311.CTCF.retina_Hu25 589 bp overlap
ChIP retina_Hu6 GSE137311.CTCF.retina_Hu6 482 bp overlap
Cebpa 1 dataset
ChIP BLaER1 ENCFF364PUR 251 bp overlap
Crx 1 dataset
Motif DE_72h DE_72h-Crx_MA0467.3 6 bp overlap
DPRX 2 datasets
Motif DE_48h DE_48h-DPRX_MA1480.2 9 bp overlap
Motif DE_72h DE_72h-DPRX_MA1480.2 9 bp overlap
DUX4 1 dataset
Motif DE_72h DE_72h-DUX4_MA0468.1 11 bp overlap
DUXA 1 dataset
Motif DE_72h DE_72h-DUXA_MA0884.2 13 bp overlap
Dux 1 dataset
Motif DE_72h DE_72h-Dux_MA0611.3 11 bp overlap
EOMES 1 dataset
ChIP hESC GSE26097.EOMES.hESC 292 bp overlap
ESR2 2 datasets
Motif DE_48h DE_48h-ESR2_MA0258.2 15 bp overlap
Motif DE_72h DE_72h-ESR2_MA0258.2 15 bp overlap
ESRRA 2 datasets
Motif DE_48h DE_48h-ESRRA_MA0592.4 9 bp overlap
Motif DE_72h DE_72h-ESRRA_MA0592.4 9 bp overlap
ESRRB 2 datasets
Motif DE_48h DE_48h-ESRRB_MA0141.4 10 bp overlap
Motif DE_72h DE_72h-ESRRB_MA0141.4 10 bp overlap
ETS1 1 dataset
ChIP cardiomyocyte_D2 GSE129986.ETS1.cardiomyocyte_D2 172 bp overlap
EZH2 1 dataset
ChIP neural progenitor cell ENCFF018MKA 800 bp overlap
EZH2_phosphoT487 1 dataset
ChIP neural_progenitor ENCSR656MXA.EZH2_phosphoT487.neural_progenitor 232 bp overlap
Esrrg 2 datasets
Motif DE_48h DE_48h-Esrrg_MA0643.2 9 bp overlap
Motif DE_72h DE_72h-Esrrg_MA0643.2 9 bp overlap
FOSL2 3 datasets
ChIP Hep-G2 ENCSR000BHP.FOSL2.Hep-G2 110 bp overlap
ChIP HepG2 ENCFF548CXY 128 bp overlap
ChIP HepG2 ENCFF796NIA 146 bp overlap
FOXA2 3 datasets
ChIP BJ1-hTERT_GATA4 GSE90454.FOXA2.BJ1-hTERT_GATA4 208 bp overlap
ChIP DE DE-FOXA2-1 641 bp overlap
ChIP DE DE-FOXA2-2 623 bp overlap
FOXB1 1 dataset
Motif DE_72h DE_72h-FOXB1_MA0845.1 11 bp overlap
FOXD2 2 datasets
Motif DE_60h DE_60h-FOXD2_MA0847.4 11 bp overlap
Motif DE_72h DE_72h-FOXD2_MA0847.4 11 bp overlap
FOXE1 2 datasets
Motif DE_60h DE_60h-FOXE1_MA1487.3 12 bp overlap
Motif DE_72h DE_72h-FOXE1_MA1487.3 12 bp overlap
GATA1 5 datasets
ChIP CD34_ERYTH_BIO GSE29194.GATA1.CD34_ERYTH_BIO 147 bp overlap
Motif DE_60h DE_60h-GATA1_MA0035.5 7 bp overlap
Motif DE_72h DE_72h-GATA1_MA0035.5 7 bp overlap
ChIP HUDEP-2_30min GSE104676.GATA1.HUDEP-2_30min 84 bp overlap
ChIP K-562_enCRISPRi-LK GSE132212.GATA1.K-562_enCRISPRi-LK 170 bp overlap
GATA1::TAL1 2 datasets
Motif DE_60h DE_60h-GATA1TAL1_MA0140.3 17 bp overlap
Motif DE_72h DE_72h-GATA1TAL1_MA0140.3 17 bp overlap
GATA4 7 datasets
ChIP BJ1-hTERT_FOXA2_GATA4_Coexp GSE92491.GATA4.BJ1-hTERT_FOXA2_GATA4_Coexp 289 bp overlap
ChIP DE DE-GATA4-1 942 bp overlap
ChIP DE DE-GATA4-2 1063 bp overlap
ChIP Hep-G2 GSE135714.GATA4.Hep-G2 272 bp overlap
ChIP pancreatic-progenitor GSE117136.GATA4.pancreatic-progenitor 133 bp overlap
ChIP pancreatic-progenitor GSE117136.GATA4.pancreatic-progenitor 468 bp overlap
ChIP pancreatic-progenitor_PP1 GSE104840.GATA4.pancreatic-progenitor_PP1 642 bp overlap
GATA6 4 datasets
ChIP DE DE-GATA6-1 913 bp overlap
ChIP DE DE-GATA6-2 1085 bp overlap
ChIP DE_D2 S55-DE-d2-GATA6-exp2 770 bp overlap
ChIP endoderm_KO GSE117136.GATA6.endoderm_KO 539 bp overlap
GFI1B 1 dataset
ChIP K-562 ENCSR509GDT.GFI1B.K-562 185 bp overlap
GSC 1 dataset
Motif DE_72h DE_72h-GSC_MA0648.2 6 bp overlap
GSC2 1 dataset
Motif DE_72h DE_72h-GSC2_MA0891.2 6 bp overlap
HDAC1 1 dataset
ChIP K-562 ENCSR387UWP.HDAC1.K-562 372 bp overlap
HNF4A 4 datasets
ChIP Hep-G2 ENCSR469FBY.HNF4A.Hep-G2 86 bp overlap
ChIP Hep-G2 ENCSR000BLF.HNF4A.Hep-G2 86 bp overlap
ChIP IM95 GSE114018.HNF4A.IM95 61 bp overlap
ChIP KATO-III GSE114018.HNF4A.KATO-III 90 bp overlap
HOXA3 2 datasets
Motif DE_60h DE_60h-HOXA3_MA2119.1 7 bp overlap
Motif DE_72h DE_72h-HOXA3_MA2119.1 7 bp overlap
HOXA4 2 datasets
Motif DE_60h DE_60h-HOXA4_MA1496.2 7 bp overlap
Motif DE_72h DE_72h-HOXA4_MA1496.2 7 bp overlap
HOXB4 2 datasets
Motif DE_60h DE_60h-HOXB4_MA1499.2 6 bp overlap
Motif DE_72h DE_72h-HOXB4_MA1499.2 6 bp overlap
HOXB9 2 datasets
Motif DE_60h DE_60h-HOXB9_MA1503.2 9 bp overlap
Motif DE_72h DE_72h-HOXB9_MA1503.2 9 bp overlap
HOXC10 2 datasets
Motif DE_60h DE_60h-HOXC10_MA0905.2 9 bp overlap
Motif DE_72h DE_72h-HOXC10_MA0905.2 9 bp overlap
HOXC4 2 datasets
Motif DE_60h DE_60h-HOXC4_MA1504.2 6 bp overlap
Motif DE_72h DE_72h-HOXC4_MA1504.2 6 bp overlap
HOXC9 2 datasets
Motif DE_60h DE_60h-HOXC9_MA0485.3 9 bp overlap
Motif DE_72h DE_72h-HOXC9_MA0485.3 9 bp overlap
HOXD12 2 datasets
Motif DE_60h DE_60h-HOXD12_MA0873.2 10 bp overlap
Motif DE_72h DE_72h-HOXD12_MA0873.2 10 bp overlap
HOXD4 2 datasets
Motif DE_60h DE_60h-HOXD4_MA1507.2 6 bp overlap
Motif DE_72h DE_72h-HOXD4_MA1507.2 6 bp overlap
Hoxa11 2 datasets
Motif DE_60h DE_60h-Hoxa11_MA0911.2 9 bp overlap
Motif DE_72h DE_72h-Hoxa11_MA0911.2 9 bp overlap
JUN 1 dataset
ChIP HAEC_TNFa_4h GSE89970.JUN.HAEC_TNFa_4h 112 bp overlap
JUN::JUNB 1 dataset
Motif DE_72h DE_72h-JUNJUNB_MA1132.2 8 bp overlap
JUNB 1 dataset
ChIP HAEC GSE89970.JUNB.HAEC 102 bp overlap
JUND 1 dataset
ChIP HepG2 ENCFF869OPW 166 bp overlap
Jun 1 dataset
Motif DE_72h DE_72h-Jun_MA0489.3 8 bp overlap
KDM1A 1 dataset
ChIP pancreatic-progenitor_PP2-KDM1A-inh GSE104840.KDM1A.pancreatic-progenitor_PP2-KDM1A-inh 300 bp overlap
LDB1 1 dataset
ChIP HEP GSE52637.LDB1.HEP 138 bp overlap
Lhx3 2 datasets
Motif DE_60h DE_60h-Lhx3_MA0135.2 12 bp overlap
Motif DE_72h DE_72h-Lhx3_MA0135.2 12 bp overlap
MEF2D 3 datasets
ChIP retina_Hu13 GSE137311.MEF2D.retina_Hu13 384 bp overlap
ChIP retina_Hu21 GSE137311.MEF2D.retina_Hu21 335 bp overlap
ChIP retina_Hu25 GSE137311.MEF2D.retina_Hu25 423 bp overlap
MEIS1 5 datasets
Motif DE_48h DE_48h-MEIS1_MA0498.3 5 bp overlap
Motif DE_60h DE_60h-MEIS1_MA1639.2 9 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_MA1639.2 9 bp overlap
MEIS2 4 datasets
Motif DE_60h DE_60h-MEIS2_MA1640.2 9 bp overlap
Motif DE_72h DE_72h-MEIS2_MA1640.2 9 bp overlap
ChIP K-562 ENCSR851BNE.MEIS2.K-562 309 bp overlap
ChIP K562 ENCFF320GSD 104 bp overlap
Mecom 1 dataset
Motif DE_72h DE_72h-Mecom_MA0029.2 11 bp overlap
NEUROD1 5 datasets
ChIP D283-Med GSE92582.NEUROD1.D283-Med 432 bp overlap
ChIP D283-Med_shNEUROD1-1579 GSE92582.NEUROD1.D283-Med_shNEUROD1-1579 405 bp overlap
ChIP D341-Med_shGFP GSE92582.NEUROD1.D341-Med_shGFP 350 bp overlap
ChIP D341-Med_shNEUROD1-1154 GSE92582.NEUROD1.D341-Med_shNEUROD1-1154 274 bp overlap
ChIP D341-Med_shNEUROD1-1579 GSE92582.NEUROD1.D341-Med_shNEUROD1-1579 264 bp overlap
NFYB 1 dataset
ChIP Hep-G2 ENCSR935GZV.NFYB.Hep-G2 105 bp overlap
NKX6-1 2 datasets
Motif DE_60h DE_60h-NKX6-1_MA0674.2 7 bp overlap
Motif DE_72h DE_72h-NKX6-1_MA0674.2 7 bp overlap
NKX6-3 2 datasets
Motif DE_60h DE_60h-NKX6-3_MA1530.2 8 bp overlap
Motif DE_72h DE_72h-NKX6-3_MA1530.2 8 bp overlap
NR5A1 2 datasets
Motif DE_48h DE_48h-NR5A1_MA1540.3 12 bp overlap
Motif DE_72h DE_72h-NR5A1_MA1540.3 12 bp overlap
NRL 1 dataset
ChIP retina_Hu13 GSE137311.NRL.retina_Hu13 422 bp overlap
OLIG2 1 dataset
ChIP brain-prefrontal-cortex_2017014 GSE129039.OLIG2.brain-prefrontal-cortex_2017014 101 bp overlap
ONECUT1 2 datasets
Motif DE_48h DE_48h-ONECUT1_MA0679.3 9 bp overlap
Motif DE_72h DE_72h-ONECUT1_MA0679.3 9 bp overlap
ONECUT2 4 datasets
Motif DE_48h DE_48h-ONECUT2_MA0756.3 8 bp overlap
Motif DE_72h DE_72h-ONECUT2_MA0756.3 8 bp overlap
ChIP PC-3_hypoxia GSE106305.ONECUT2.PC-3_hypoxia 310 bp overlap
ChIP PC-3_normoxia GSE106305.ONECUT2.PC-3_normoxia 229 bp overlap
OTX1 1 dataset
Motif DE_72h DE_72h-OTX1_MA0711.2 6 bp overlap
OTX2 2 datasets
Motif DE_72h DE_72h-OTX2_MA0712.3 7 bp overlap
ChIP retina_Hu7 GSE137311.OTX2.retina_Hu7 507 bp overlap
PBX1 2 datasets
Motif DE_48h DE_48h-PBX1_MA0070.2 9 bp overlap
Motif DE_72h DE_72h-PBX1_MA0070.2 9 bp overlap
PBX2 2 datasets
Motif DE_60h DE_60h-PBX2_MA1113.3 9 bp overlap
Motif DE_72h DE_72h-PBX2_MA1113.3 9 bp overlap
PDX1 4 datasets
ChIP hESC GSE58685.PDX1.hESC 203 bp overlap
ChIP hiPSC GSE125768.PDX1.hiPSC 223 bp overlap
ChIP hiPSC_derived_PPs GSE106949.PDX1.hiPSC_derived_PPs 276 bp overlap
ChIP pancreatic-progenitor GSE117136.PDX1.pancreatic-progenitor 497 bp overlap
PHOX2B 1 dataset
Motif DE_72h DE_72h-PHOX2B_MA0681.3 12 bp overlap
PITX1 1 dataset
Motif DE_72h DE_72h-PITX1_MA0682.3 6 bp overlap
PITX3 1 dataset
Motif DE_72h DE_72h-PITX3_MA0714.2 6 bp overlap
POU2F1::SOX2 1 dataset
Motif DE_72h DE_72h-POU2F1SOX2_MA1962.1 17 bp overlap
PPARG 2 datasets
Motif DE_48h DE_48h-PPARG_MA0066.2 19 bp overlap
Motif DE_72h DE_72h-PPARG_MA0066.2 19 bp overlap
PROP1 1 dataset
Motif DE_72h DE_72h-PROP1_MA0715.1 11 bp overlap
RELA 6 datasets
ChIP HAEC_TNFa_4h GSE89970.RELA.HAEC_TNFa_4h 54 bp overlap
ChIP aortic-endothelial-cell_IL1B_D14 GSE139377.RELA.aortic-endothelial-cell_IL1B_D14 108 bp overlap
ChIP aortic-endothelial-cell_IL1B_D45 GSE139377.RELA.aortic-endothelial-cell_IL1B_D45 130 bp overlap
ChIP aortic-endothelial-cell_IL1B_D47 GSE139377.RELA.aortic-endothelial-cell_IL1B_D47 111 bp overlap
ChIP aortic-endothelial-cell_IL1B_D53 GSE139377.RELA.aortic-endothelial-cell_IL1B_D53 57 bp overlap
ChIP aortic-endothelial-cell_IL1B_D6 GSE139377.RELA.aortic-endothelial-cell_IL1B_D6 96 bp overlap
RHOXF1 1 dataset
Motif DE_72h DE_72h-RHOXF1_MA0719.2 6 bp overlap
RORA 2 datasets
Motif DE_48h DE_48h-RORA_MA0072.2 11 bp overlap
Motif DE_72h DE_72h-RORA_MA0072.2 11 bp overlap
RORB 1 dataset
ChIP retina_Hu22 GSE137311.RORB.retina_Hu22 467 bp overlap
Rhox11 2 datasets
Motif DE_60h DE_60h-Rhox11_MA0629.2 9 bp overlap
Motif DE_72h DE_72h-Rhox11_MA0629.2 9 bp overlap
SMAD2-3 2 datasets
ChIP HGrC1_EV GSE138496.SMAD2-3.HGrC1_EV 113 bp overlap
ChIP HUES-8_DE GSE109524.SMAD2-3.HUES-8_DE 504 bp overlap
SMAD2_3 1 dataset
ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 261 bp overlap
SMARCA4 1 dataset
ChIP BT-16_Dox GSE71504.SMARCA4.BT-16_Dox 56 bp overlap
SOX11 1 dataset
ChIP GRANT-A519 GSE52146.SOX11.GRANT-A519 90 bp overlap
SOX17 1 dataset
ChIP DE_D2 DED2-SOX17_Batch_II 410 bp overlap
SOX17_M 1 dataset
ChIP DE_D2 DED2-SOX17-M_Batch_II 690 bp overlap
T 1 dataset
ChIP H9_ENDODERM GSE60606.T.H9_ENDODERM 280 bp overlap
TAL1 3 datasets
ChIP K-562 ENCSR106FRG.TAL1.K-562 318 bp overlap
ChIP K-562_sgGal4 GSE132212.TAL1.K-562_sgGal4 157 bp overlap
ChIP K562 ENCFF620GMX 385 bp overlap
TCF12 1 dataset
ChIP SK-N-SH ENCFF147AHB 247 bp overlap
ZBTB24 1 dataset
Motif DE_72h DE_72h-ZBTB24_MA2330.1 10 bp overlap
ZFP36 1 dataset
ChIP K-562 ENCSR776CYN.ZFP36.K-562 141 bp overlap
ZFP42 1 dataset
Motif DE_72h DE_72h-ZFP42_MA1651.2 13 bp overlap
ZNF10 2 datasets
ChIP HEK293 ENCFF611ZJI 385 bp overlap
ChIP HEK293 ENCSR019WUS.ZNF10.HEK293 279 bp overlap
ZNF134 2 datasets
ChIP K-562 ENCSR553NTC.ZNF134.K-562 431 bp overlap
ChIP K562 ENCFF502NWS 286 bp overlap
ZNF217 1 dataset
ChIP Hep-G2 ENCSR055FQB.ZNF217.Hep-G2 83 bp overlap
ZNF354C 2 datasets
Motif DE_48h DE_48h-ZNF354C_MA0130.1 6 bp overlap
Motif DE_72h DE_72h-ZNF354C_MA0130.1 6 bp overlap
ZNF549 1 dataset
Motif DE_72h DE_72h-ZNF549_MA1728.2 8 bp overlap
ZNF605 1 dataset
ChIP HepG2 ENCFF640NFJ 117 bp overlap
ZNF680 5 datasets
Motif DE_48h DE_48h-ZNF680_MA1729.2 11 bp overlap
Motif DE_72h DE_72h-ZNF680_MA1729.2 11 bp overlap
ChIP HEK293 ENCFF418WHE 175 bp overlap
ChIP HEK293 ENCSR307CKC.ZNF680.HEK293 432 bp overlap
ChIP HEK293 GSE76494.ZNF680.HEK293 345 bp overlap
ZNF85 3 datasets
Motif DE_60h DE_60h-ZNF85_MA1720.2 12 bp overlap
Motif DE_72h DE_72h-ZNF85_MA1720.2 12 bp overlap
Motif DE_72h DE_72h-ZNF85_MA1720.2 12 bp overlap
ZSCAN16 1 dataset
ChIP HEK293 GSE76494.ZSCAN16.HEK293 90 bp overlap
Zfp809 1 dataset
Motif DE_72h DE_72h-Zfp809_MA2125.1 9 bp overlap
Zic2 2 datasets
Motif DE_60h DE_60h-Zic2_MA1629.2 9 bp overlap
Motif DE_72h DE_72h-Zic2_MA1629.2 9 bp overlap
Znf423 1 dataset
Motif DE_72h DE_72h-Znf423_MA0116.1 15 bp overlap
Huangfu Lab · Publications · Resources · Contact