chr3:120,604,594–120,605,753

chr3 : 120,604,594 – 120,605,753

1,159 bp 62 TFs 5 linked genes

This 1.2 kb open chromatin element is linked to 5 target genes and is bound by 62 transcription factors.

Linked Genes

5 genes

Gene	Expression	Dist. to TSS	Distance	Link type
NDUFB4		8.3 kb	Proximal	Proximity
RABL3		137.3 kb	Distal	Multiome+HiCAR
GTF2E1		137.5 kb	Distal	Multiome+HiCAR
FSTL1		154.2 kb	Distal	Multiome
LRRC58		255.9 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.

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

TF Binding

62 transcription factors

ChIP LNCaP GSE80256.AR.LNCaP 326 bp overlap

ARNT2 1 dataset

Motif DE_36h DE_36h-ARNT2_MA1464.2 8 bp overlap

ARNT::HIF1A 1 dataset

Motif DE_36h DE_36h-ARNTHIF1A_MA0259.2 5 bp overlap

Motif DE_36h DE_36h-Arnt_MA0004.1 6 bp overlap

ChIP THP-1_iBET-BD1 GSE138084.BRD2.THP-1_iBET-BD1 352 bp overlap

ChIP K-562_iBET-IFNG GSE138084.BRD4.K-562_iBET-IFNG 180 bp overlap

ChIP H9_Activin GSE94418.BRF1.H9_Activin 133 bp overlap

CLOCK 1 dataset

Motif DE_36h DE_36h-CLOCK_MA0819.3 7 bp overlap

ChIP retina_Hu20 GSE137311.CRX.retina_Hu20 155 bp overlap

ChIP retina_Hu3 GSE137311.CRX.retina_Hu3 206 bp overlap

ChIP retina_Hu6 GSE137311.CRX.retina_Hu6 286 bp overlap

CTCF 19 datasets

ChIP BE2C ENCFF757SRF 317 bp overlap

ChIP GM04648 GSE148179.CTCF.GM04648 207 bp overlap

ChIP GM12866 ENCSR000DRF.CTCF.GM12866 100 bp overlap

ChIP HEC-1-B_F-mutation GSE140868.CTCF.HEC-1-B_F-mutation 84 bp overlap

ChIP HEC-1-B_FFRR-insertion GSE140868.CTCF.HEC-1-B_FFRR-insertion 113 bp overlap

ChIP HEC-1-B_R1-mutation GSE140868.CTCF.HEC-1-B_R1-mutation 55 bp overlap

ChIP HEC-1-B_WT GSE140868.CTCF.HEC-1-B_WT 303 bp overlap

ChIP HeLa-S3 ENCSR000AOA.CTCF.HeLa-S3 260 bp overlap

ChIP LNCaP_Ctrl GSE125639.CTCF.LNCaP_Ctrl 246 bp overlap

ChIP MCF-7 ENCFF139NQI 277 bp overlap

ChIP MCF-7 ENCSR000DWH.CTCF.MCF-7 144 bp overlap

ChIP WA01_NEUR GSE52457.CTCF.WA01_NEUR 139 bp overlap

ChIP endodermal cell ENCFF471YCZ 461 bp overlap

ChIP heart_left-ventricle ENCSR544APK.CTCF.heart_left-ventricle 230 bp overlap

ChIP hiPSC_IB7 GSE106870.CTCF.hiPSC_IB7 121 bp overlap

ChIP hiPSC_IV8 GSE106870.CTCF.hiPSC_IV8 176 bp overlap

ChIP retina_Hu22 GSE137311.CTCF.retina_Hu22 147 bp overlap

ChIP retina_Hu25 GSE137311.CTCF.retina_Hu25 223 bp overlap

ChIP retina_Hu6 GSE137311.CTCF.retina_Hu6 213 bp overlap

Creb3l2 1 dataset

Motif DE_36h DE_36h-Creb3l2_MA0608.1 9 bp overlap

Motif DE_36h DE_36h-EGR2_MA0472.2 11 bp overlap

EOMES 1 dataset

ChIP hESC GSE26097.EOMES.hESC 359 bp overlap

ESR1 2 datasets

ChIP MCF-7_E2+4OHT_SRC-3 GSE119702.ESR1.MCF-7_E2+4OHT_SRC-3 136 bp overlap

ChIP MCF-7_SRC3_OHT GSE119702.ESR1.MCF-7_SRC3_OHT 136 bp overlap

FOXA2 2 datasets

ChIP DE DE-FOXA2-1 726 bp overlap

ChIP DE DE-FOXA2-2 731 bp overlap

GATA1 2 datasets

ChIP K-562 ENCSR000EWM.GATA1.K-562 159 bp overlap

ChIP K-562_enCRISPRi-LK GSE132212.GATA1.K-562_enCRISPRi-LK 145 bp overlap

GATA3_Nter 1 dataset

ChIP T-47D_CR3flp GSE99479.GATA3_Nter.T-47D_CR3flp 153 bp overlap

GATA4 2 datasets

ChIP DE DE-GATA4-1 512 bp overlap

ChIP DE DE-GATA4-2 704 bp overlap

GATA6 9 datasets

ChIP DE DE-GATA6-1 521 bp overlap

ChIP DE DE-GATA6-2 805 bp overlap

ChIP DE_D1 S09-DE-d1-GATA6-exp1 299 bp overlap

ChIP DE_D1 S14-DE-d1-GATA6-exp1 366 bp overlap

ChIP DE_D1 S41-DE-d1-GATA6-exp2 468 bp overlap

ChIP DE_D2 S55-DE-d2-GATA6-exp2 379 bp overlap

ChIP HUES-8_DE_JNKi GSE109524.GATA6.HUES-8_DE_JNKi 492 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.GATA6.HUES-8_DE_ctrl 490 bp overlap

ChIP endoderm_KO GSE117136.GATA6.endoderm_KO 323 bp overlap

Motif DE_36h DE_36h-HES1_MA1099.3 8 bp overlap

Motif DE_36h DE_36h-HES5_MA0821.2 10 bp overlap

Motif DE_36h DE_36h-HES6_MA1493.1 10 bp overlap

Motif DE_36h DE_36h-HEY1_MA0823.1 10 bp overlap

Motif DE_36h DE_36h-HEY2_MA0649.2 9 bp overlap

HNF4A 1 dataset

ChIP gastric-epithelial-cell_OE GSE114018.HNF4A.gastric-epithelial-cell_OE 277 bp overlap

ChIP CD4_Th1 GSE72266.MAF.CD4_Th1 194 bp overlap

Motif DE_36h DE_36h-MAX_MA0058.4 6 bp overlap

MED26 1 dataset

ChIP HEK293T GSE121024.MED26.HEK293T 236 bp overlap

MEF2D 3 datasets

ChIP retina_Hu13 GSE137311.MEF2D.retina_Hu13 193 bp overlap

ChIP retina_Hu21 GSE137311.MEF2D.retina_Hu21 103 bp overlap

ChIP retina_Hu25 GSE137311.MEF2D.retina_Hu25 129 bp overlap

ChIP A-549_MGA-OE GSE112188.MGA.A-549_MGA-OE 308 bp overlap

MITF 6 datasets

ChIP 501-mel GSE137522.MITF.501-mel 233 bp overlap

ChIP 501-mel GSE61965.MITF.501-mel 190 bp overlap

ChIP 501-mel_20ng_K243R GSE137522.MITF.501-mel_20ng_K243R 253 bp overlap

ChIP 501-mel_K243Q GSE137522.MITF.501-mel_K243Q 234 bp overlap

ChIP K-562 ENCSR797SWM.MITF.K-562 232 bp overlap

ChIP K562 ENCFF731XJJ 273 bp overlap

MLXIPL 1 dataset

Motif DE_36h DE_36h-MLXIPL_MA0664.2 8 bp overlap

Motif DE_36h DE_36h-MNT_MA0825.2 6 bp overlap

Motif DE_36h DE_36h-MYC_MA0147.4 8 bp overlap

MYCN 2 datasets

Motif DE_36h DE_36h-MYCN_MA0104.5 8 bp overlap

ChIP LA-N-5 GSE138295.MYCN.LA-N-5 158 bp overlap

Mlxip 1 dataset

Motif DE_36h DE_36h-Mlxip_MA0622.2 6 bp overlap

NEUROD1 2 datasets

ChIP D283-Med GSE92582.NEUROD1.D283-Med 206 bp overlap

ChIP D283-Med_shNEUROD1-1579 GSE92582.NEUROD1.D283-Med_shNEUROD1-1579 116 bp overlap

Npas2 1 dataset

Motif DE_36h DE_36h-Npas2_MA0626.2 8 bp overlap

ChIP retina_Hu7 GSE137311.OTX2.retina_Hu7 211 bp overlap

ChIP NALM-6 GSE126300.PAX5.NALM-6 188 bp overlap

PHF19 1 dataset

ChIP DU145_SH4 GSE135623.PHF19.DU145_SH4 465 bp overlap

PITX3 1 dataset

ChIP SH-SY5Y GSE93275.PITX3.SH-SY5Y 201 bp overlap

RAD21 1 dataset

ChIP H1 ENCFF698EWO 241 bp overlap

ChIP retina_Hu22 GSE137311.RORB.retina_Hu22 201 bp overlap

ChIP kidney_fetal_17w GSE75948.SIX2.kidney_fetal_17w 214 bp overlap

SMAD2 1 dataset

ChIP endoderm GSE29422.SMAD2.endoderm 226 bp overlap

SMAD2-3 3 datasets

ChIP HUES-8_DE GSE109524.SMAD2-3.HUES-8_DE 790 bp overlap

ChIP HUES-8_DE_JNKi GSE109524.SMAD2-3.HUES-8_DE_JNKi 655 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.SMAD2-3.HUES-8_DE_ctrl 964 bp overlap

SMAD2_3 5 datasets

ChIP DE_D1 S07-DE-d1-SMAD2_3-exp1 554 bp overlap

ChIP DE_D1 S12-DE-d1-SMAD2_3-exp1 573 bp overlap

ChIP DE_D1 S39-DE-d1-SMAD2_3-exp2 627 bp overlap

ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 585 bp overlap

ChIP DE_D2 S53-DE-d2-SMAD2_3-exp2 634 bp overlap

SMAD3 1 dataset

ChIP BG03_DIFF_48H GSE36578.SMAD3.BG03_DIFF_48H 150 bp overlap

SMAD4 1 dataset

ChIP endoderm GSE29422.SMAD4.endoderm 363 bp overlap

SMARCA4 1 dataset

ChIP 501-mel_SHSOX10 GSE61965.SMARCA4.501-mel_SHSOX10 264 bp overlap

SMARCC1 2 datasets

ChIP BIN-67_lentivirus-SMARCA4-K785R GSE117734.SMARCC1.BIN-67_lentivirus-SMARCA4-K785R 234 bp overlap

ChIP TTC-549_Dox GSE71504.SMARCC1.TTC-549_Dox 238 bp overlap

ChIP HeLa-Kyoto_PDS5-depleted GSE102884.SMC3.HeLa-Kyoto_PDS5-depleted 160 bp overlap

SNAI2 1 dataset

ChIP SMS-CTR_shSNAI2 GSE137168.SNAI2.SMS-CTR_shSNAI2 185 bp overlap

SOX17_M 1 dataset

ChIP DE_D2 DED2-SOX17-M_Batch_II 336 bp overlap

ChIP hiPSC GSE56567.SOX2.hiPSC 178 bp overlap

SUPT5H 2 datasets

ChIP DLD-1_NELFCD-AID GSE144786.SUPT5H.DLD-1_NELFCD-AID 135 bp overlap

ChIP U2OS_siCtrl GSE115365.SUPT5H.U2OS_siCtrl 104 bp overlap

ChIP H9_ENDODERM GSE60606.T.H9_ENDODERM 286 bp overlap

TEAD4 5 datasets

ChIP H1 ENCFF778PAX 245 bp overlap

ChIP MCF-7_BLRP_WT_E2 GSE125594.TEAD4.MCF-7_BLRP_WT_E2 283 bp overlap

ChIP MCF-7_BLRP_WT_Veh GSE125594.TEAD4.MCF-7_BLRP_WT_Veh 338 bp overlap

ChIP T-47D_Veh GSE125594.TEAD4.T-47D_Veh 343 bp overlap

ChIP hMSC-TERT4 GSE140782.TEAD4.hMSC-TERT4 245 bp overlap

ChIP SK-N-SH ENCSR000BMF.USF1.SK-N-SH 116 bp overlap

ZBTB7A 1 dataset

ChIP VCaP_FBS GSE123089.ZBTB7A.VCaP_FBS 241 bp overlap

ZNF490 1 dataset

ChIP HEK293 GSE76494.ZNF490.HEK293 247 bp overlap