chr3:47,024,824–47,025,334

chr3 : 47,024,824 – 47,025,334

510 bp 51 TFs 6 linked genes

This 510 bp open chromatin element is linked to 6 target genes and is bound by 51 transcription factors.

Linked Genes

6 genes

Gene	Expression	Dist. to TSS	Distance	Link type
NBEAL2		45.4 kb	Distal	Multiome
CCDC12		45.5 kb	Distal	Multiome
SETD2		138.8 kb	Distal	Multiome
KIF9-AS1		139.1 kb	Distal	Multiome
KIF9		257.7 kb	Distal	Multiome+HiCAR
KLHL18		257.8 kb	Distal	Multiome+HiCAR

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

51 transcription factors

ChIP HCT-116_CAMP GSE74355.ATF3.HCT-116_CAMP 121 bp overlap

ChIP GM12878 ENCFF954REE 231 bp overlap

BRD4 2 datasets

ChIP K-562_JQ1_2h GSE99178.BRD4.K-562_JQ1_2h 135 bp overlap

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

CTCF 103 datasets

ChIP AG04449 ENCFF248MBD 181 bp overlap

ChIP AG09319 ENCFF401ZTN 277 bp overlap

ChIP ASC GSE21366.CTCF.ASC 177 bp overlap

ChIP BJ ENCFF434HEC 311 bp overlap

ChIP D54 ENCSR000DKN.CTCF.D54 162 bp overlap

ChIP DND41 ENCSR000AQU.CTCF.DND41 132 bp overlap

ChIP FT282 GSE131931.CTCF.FT282 184 bp overlap

ChIP FT282_EV GSE131931.CTCF.FT282_EV 155 bp overlap

ChIP GM06077 GSE148179.CTCF.GM06077 170 bp overlap

ChIP GM09237_B-lymphocytes GSE111170.CTCF.GM09237_B-lymphocytes 198 bp overlap

ChIP GM12869 ENCSR000DRJ.CTCF.GM12869 98 bp overlap

ChIP GM12878 ENCFF635MMB 217 bp overlap

ChIP GM12878 ENCSR000DZN.CTCF.GM12878 151 bp overlap

ChIP GM17942 GSE76922.CTCF.GM17942 323 bp overlap

ChIP GM23338 ENCFF772DML 201 bp overlap

ChIP H1 ENCFF764RHO 277 bp overlap

ChIP H54 ENCFF255TVO 225 bp overlap

ChIP HAP1 GSE152721.CTCF.HAP1 215 bp overlap

ChIP HAP1_clone21_CTCF-CRISPR GSE152721.CTCF.HAP1_clone21_CTCF-CRISPR 290 bp overlap

ChIP HAP1_clone21_CTCF-TSS-CRISPR_2 GSE152721.CTCF.HAP1_clone21_CTCF-TSS-CRISPR_2 177 bp overlap

ChIP HEC-1-B GSE139679.CTCF.HEC-1-B 156 bp overlap

ChIP HEC-1-B_F-insertion GSE140868.CTCF.HEC-1-B_F-insertion 74 bp overlap

ChIP HEC-1-B_FFRR-insertion GSE140868.CTCF.HEC-1-B_FFRR-insertion 90 bp overlap

ChIP HEC-1-B_R1-insertion GSE140868.CTCF.HEC-1-B_R1-insertion 87 bp overlap

ChIP HEC-1-B_R1-mutation GSE140868.CTCF.HEC-1-B_R1-mutation 122 bp overlap

ChIP HEC-1-B_WT GSE140868.CTCF.HEC-1-B_WT 295 bp overlap

ChIP HeLa-S3 ENCFF565UFR 161 bp overlap

ChIP HeLa-S3 ENCSR000DLO.CTCF.HeLa-S3 92 bp overlap

ChIP ID00014 GSE76922.CTCF.ID00014 315 bp overlap

ChIP IMR-90 ENCSR000EFI.CTCF.IMR-90 237 bp overlap

ChIP IMR-90 GSE43070.CTCF.IMR-90 162 bp overlap

ChIP IMR-90_Ctrl GSE125639.CTCF.IMR-90_Ctrl 218 bp overlap

ChIP K-562 ENCSR000DMA.CTCF.K-562 136 bp overlap

ChIP K-562 GSE70764.CTCF.K-562 185 bp overlap

ChIP LNCaP ENCSR315NAC.CTCF.LNCaP 263 bp overlap

ChIP LNCaP ENCSR000DMF.CTCF.LNCaP 131 bp overlap

ChIP LNCaP clone FGC ENCFF519YVI 181 bp overlap

ChIP LNCaP clone FGC ENCFF957KCI 181 bp overlap

ChIP Loucy ENCFF359TVQ 444 bp overlap

ChIP Loucy ENCSR464DKE.CTCF.Loucy 217 bp overlap

ChIP MCF-7 ENCFF198DQX 231 bp overlap

ChIP MCF-7 ENCFF494VXA 231 bp overlap

ChIP MCF-7 ENCSR560BUE.CTCF.MCF-7 265 bp overlap

ChIP MCF-7 ENCSR000DMR.CTCF.MCF-7 168 bp overlap

ChIP MCF-7 ENCSR000DMS.CTCF.MCF-7 127 bp overlap

ChIP MCF-7L_t0 GSE108787.CTCF.MCF-7L_t0 242 bp overlap

ChIP MCF-7L_t24 GSE108787.CTCF.MCF-7L_t24 223 bp overlap

ChIP MCF-7_HYPOXIA GSE78113.CTCF.MCF-7_HYPOXIA 263 bp overlap

ChIP MCF-7_NORMOXIA GSE78113.CTCF.MCF-7_NORMOXIA 310 bp overlap

ChIP MDA-MB-435_Asynchronous GSE102019.CTCF.MDA-MB-435_Asynchronous 360 bp overlap

ChIP OCI-Ly3 ENCSR756ZKG.CTCF.OCI-Ly3 304 bp overlap

ChIP OVCAR-8 GSE70764.CTCF.OVCAR-8 233 bp overlap

ChIP Peyers-patch ENCSR375VXU.CTCF.Peyers-patch 241 bp overlap

ChIP SK-N-SH ENCSR541AMF.CTCF.SK-N-SH 282 bp overlap

ChIP SK-N-SH ENCSR000BLX.CTCF.SK-N-SH 137 bp overlap

ChIP ascending-aorta ENCSR846JKO.CTCF.ascending-aorta 171 bp overlap

ChIP astrocyte of the spinal cord ENCFF213GKL 261 bp overlap

ChIP astrocyte_spinal_cord ENCSR000DSU.CTCF.astrocyte_spinal_cord 226 bp overlap

ChIP bonchial_epithelial ENCSR000DXI.CTCF.bonchial_epithelial 110 bp overlap

ChIP choroid plexus epithelial cell ENCFF407YNR 277 bp overlap

ChIP choroid-plexus_epithelial ENCSR000DTL.CTCF.choroid-plexus_epithelial 189 bp overlap

ChIP dorsolateral prefrontal cortex ENCFF841TWE 397 bp overlap

ChIP endodermal cell ENCFF471YCZ 435 bp overlap

ChIP endothelial_brain-microvascular ENCSR000DTA.CTCF.endothelial_brain-microvascular 162 bp overlap

ChIP epithelial cell of prostate ENCFF086GTI 482 bp overlap

ChIP epithelial_kidney ENCSR000DVH.CTCF.epithelial_kidney 148 bp overlap

ChIP epithelial_proximal_tubule ENCSR000DXD.CTCF.epithelial_proximal_tubule 156 bp overlap

ChIP epithelial_retinal_pigment ENCSR000DVI.CTCF.epithelial_retinal_pigment 172 bp overlap

ChIP fibroblast of dermis ENCFF986DNJ 297 bp overlap

ChIP fibroblast of lung ENCFF084DUH 317 bp overlap

ChIP fibroblast of lung ENCFF356FDN 317 bp overlap

ChIP fibroblast of pulmonary artery ENCFF742RSV 297 bp overlap

ChIP fibroblast_DERMAL ENCSR000APM.CTCF.fibroblast_DERMAL 270 bp overlap

ChIP fibroblast_FORESKIN ENCSR000DUH.CTCF.fibroblast_FORESKIN 223 bp overlap

ChIP fibroblast_FORESKIN ENCSR000DWQ.CTCF.fibroblast_FORESKIN 176 bp overlap

ChIP fibroblast_GINGIVA ENCSR000DPS.CTCF.fibroblast_GINGIVA 194 bp overlap

ChIP fibroblast_LUNG ENCSR000DWY.CTCF.fibroblast_LUNG 152 bp overlap

ChIP fibroblast_LUNG ENCSR000DPM.CTCF.fibroblast_LUNG 143 bp overlap

ChIP fibroblast_PULMONARY_ARTERY ENCSR000DUX.CTCF.fibroblast_PULMONARY_ARTERY 156 bp overlap

ChIP fibroblast_SKIN_LEG ENCSR000DPG.CTCF.fibroblast_SKIN_LEG 111 bp overlap

ChIP foreskin fibroblast ENCFF671HLG 321 bp overlap

ChIP foreskin keratinocyte ENCFF980OWR 203 bp overlap

ChIP hepatocyte ERP000395.CTCF.hepatocyte 133 bp overlap

ChIP hepatocyte ENCSR252QYR.CTCF.hepatocyte 186 bp overlap

ChIP hiPSC_IB7 GSE106870.CTCF.hiPSC_IB7 224 bp overlap

ChIP hiPSC_IIA11 GSE106870.CTCF.hiPSC_IIA11 213 bp overlap

ChIP hiPSC_IV8 GSE106870.CTCF.hiPSC_IV8 196 bp overlap

ChIP hiPSC_parental-line GSE106870.CTCF.hiPSC_parental-line 213 bp overlap

ChIP islet ERP004003.CTCF.islet 344 bp overlap

ChIP keratinocyte ENCFF046PBT 185 bp overlap

ChIP keratinocyte ENCFF291YDC 185 bp overlap

ChIP keratinocyte GSE154221.CTCF.keratinocyte 330 bp overlap

ChIP keratinocyte ENCSR000ALJ.CTCF.keratinocyte 339 bp overlap

ChIP keratinocyte ENCSR000DNC.CTCF.keratinocyte 170 bp overlap

ChIP keratinocyte ENCSR000DWX.CTCF.keratinocyte 147 bp overlap

ChIP mammary epithelial cell ENCFF164SPU 265 bp overlap

ChIP myotube ENCSR000ANS.CTCF.myotube 193 bp overlap

ChIP osteoblast ENCFF491ZJZ 175 bp overlap

ChIP osteoblast ENCSR000APF.CTCF.osteoblast 316 bp overlap

ChIP primary-epidermal-keratinocyte_diff_d0 GSE84657.CTCF.primary-epidermal-keratinocyte_diff_d0 263 bp overlap

ChIP primary-epidermal-keratinocyte_diff_d3 GSE84657.CTCF.primary-epidermal-keratinocyte_diff_d3 147 bp overlap

ChIP primary-epidermal-keratinocyte_diff_d6 GSE84657.CTCF.primary-epidermal-keratinocyte_diff_d6 282 bp overlap

ChIP retinal pigment epithelial cell ENCFF810AAG 257 bp overlap

DPF2 2 datasets

ChIP BIN-67_lentivirus-SMARCA4-K785R GSE117734.DPF2.BIN-67_lentivirus-SMARCA4-K785R 322 bp overlap

ChIP BIN-67_lentivirus-SMARCA4-T910M GSE117734.DPF2.BIN-67_lentivirus-SMARCA4-T910M 510 bp overlap

EOMES 1 dataset

ChIP hESC GSE26097.EOMES.hESC 456 bp overlap

ESRRA 4 datasets

ChIP BT-474 GSE81651.ESRRA.BT-474 182 bp overlap

ChIP BT-474_AICAR GSE75876.ESRRA.BT-474_AICAR 101 bp overlap

ChIP BT-474_EGF GSE81651.ESRRA.BT-474_EGF 210 bp overlap

ChIP BT-474_HRG GSE81651.ESRRA.BT-474_HRG 216 bp overlap

ChIP ProEs GSE59087.EZH1.ProEs 139 bp overlap

FOXA2 3 datasets

ChIP BJ1-hTERT_CDT1 GSE92491.FOXA2.BJ1-hTERT_CDT1 330 bp overlap

ChIP DE DE-FOXA2-1 510 bp overlap

ChIP DE DE-FOXA2-2 510 bp overlap

GABPA 1 dataset

ChIP VCaP GSE49091.GABPA.VCaP 223 bp overlap

GATA4 3 datasets

ChIP DE DE-GATA4-1 510 bp overlap

ChIP DE DE-GATA4-2 510 bp overlap

ChIP foregut GSE117136.GATA4.foregut 437 bp overlap

GATA6 9 datasets

ChIP DE DE-GATA6-1 510 bp overlap

ChIP DE DE-GATA6-2 510 bp overlap

ChIP DE_D1 S09-DE-d1-GATA6-exp1 375 bp overlap

ChIP DE_D1 S14-DE-d1-GATA6-exp1 488 bp overlap

ChIP DE_D1 S41-DE-d1-GATA6-exp2 459 bp overlap

ChIP DE_D2 S55-DE-d2-GATA6-exp2 510 bp overlap

ChIP HUES-8_DE_JNKi GSE109524.GATA6.HUES-8_DE_JNKi 482 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.GATA6.HUES-8_DE_ctrl 495 bp overlap

ChIP endoderm_KO GSE117136.GATA6.endoderm_KO 466 bp overlap

ChIP K-562 ENCSR197ALX.HDGF.K-562 184 bp overlap

HOXB8 1 dataset

ChIP CFPAC-1_HOXB8-OE GSE119930.HOXB8.CFPAC-1_HOXB8-OE 510 bp overlap

HOXC6 1 dataset

ChIP 22Rv1 GSE129951.HOXC6.22Rv1 510 bp overlap

ChIP K-562 ENCSR005NMT.ID3.K-562 422 bp overlap

IRF4 3 datasets

ChIP GM12878 ENCFF769ZDL 321 bp overlap

ChIP GM12878 ENCSR000BGY.IRF4.GM12878 238 bp overlap

ChIP T-cell GSE136853.IRF4.T-cell 510 bp overlap

ChIP DE_D1 S08-DE-d1-JUN-exp1 464 bp overlap

ChIP DE_D1 S40-DE-d1-JUN-exp2 475 bp overlap

ChIP DE_D2 S02-DE-d2-JUN-exp1 403 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.JUN.HUES-8_DE_ctrl 485 bp overlap

ChIP Karpas-299 GSE151413.JUN.Karpas-299 403 bp overlap

ChIP T-cell GSE136853.JUN.T-cell 224 bp overlap

JUNB 2 datasets

ChIP GM12878 ENCFF667EJQ 419 bp overlap

ChIP Karpas-299 GSE151413.JUNB.Karpas-299 157 bp overlap

ChIP K-562 ENCSR000EGN.JUND.K-562 155 bp overlap

ChIP BJ_INDUCED GSE36570.KLF4.BJ_INDUCED 159 bp overlap

ChIP islet ERP004003.MAFB.islet 169 bp overlap

ChIP hMSC-TERT4_4h GSE104537.MED1.hMSC-TERT4_4h 158 bp overlap

MYOD1 1 dataset

ChIP RD_shSNAI2 GSE137168.MYOD1.RD_shSNAI2 177 bp overlap

NANOG 1 dataset

ChIP WA01_3IL ERP004238.NANOG.WA01_3IL 414 bp overlap

NR3C1 1 dataset

ChIP A-549 ENCSR000BHE.NR3C1.A-549 127 bp overlap

RAD21 22 datasets

ChIP GP5D GSE51234.RAD21.GP5D 304 bp overlap

ChIP H1 ENCFF698EWO 241 bp overlap

ChIP H1 ENCFF967OJF 245 bp overlap

ChIP HAP1 GSE152721.RAD21.HAP1 265 bp overlap

ChIP HEC-1-B_RF-insertion GSE140868.RAD21.HEC-1-B_RF-insertion 202 bp overlap

ChIP HepG2 ENCFF906QIS 225 bp overlap

ChIP IMR-90 ENCFF752PTH 237 bp overlap

ChIP IMR-90 ENCSR000EFJ.RAD21.IMR-90 228 bp overlap

ChIP Ishikawa ENCSR000BTU.RAD21.Ishikawa 126 bp overlap

ChIP K-562 ENCSR000BKV.RAD21.K-562 121 bp overlap

ChIP K562 ENCFF169SQI 171 bp overlap

ChIP K562 ENCFF634XYR 365 bp overlap

ChIP MCF-7 ENCFF694KOM 337 bp overlap

ChIP MCF-7 GSE72082.RAD21.MCF-7 179 bp overlap

ChIP MCF-7 ENCSR000BTQ.RAD21.MCF-7 178 bp overlap

ChIP MCF-7 ENCSR703TNG.RAD21.MCF-7 161 bp overlap

ChIP MCF-7 ERP000209.RAD21.MCF-7 124 bp overlap

ChIP MCF-7_E2 ERP000209.RAD21.MCF-7_E2 123 bp overlap

ChIP hiPSC_IIA11 GSE106870.RAD21.hiPSC_IIA11 195 bp overlap

ChIP hiPSC_IIA12 GSE106870.RAD21.hiPSC_IIA12 175 bp overlap

ChIP hiPSC_IV8 GSE106870.RAD21.hiPSC_IV8 206 bp overlap

ChIP hiPSC_parental-line GSE106870.RAD21.hiPSC_parental-line 241 bp overlap

ChIP K-562 ENCSR506CVF.RB1.K-562 110 bp overlap

RCOR1 1 dataset

ChIP keratinocyte_diff GSE57702.RCOR1.keratinocyte_diff 192 bp overlap

ChIP K-562 ENCSR000BMW.REST.K-562 94 bp overlap

SMAD2 1 dataset

ChIP endoderm GSE29422.SMAD2.endoderm 289 bp overlap

SMAD2-3 4 datasets

ChIP HGrC1_WT GSE138496.SMAD2-3.HGrC1_WT 139 bp overlap

ChIP HUES-8_DE GSE109524.SMAD2-3.HUES-8_DE 510 bp overlap

ChIP HUES-8_DE_JNKi GSE109524.SMAD2-3.HUES-8_DE_JNKi 313 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.SMAD2-3.HUES-8_DE_ctrl 397 bp overlap

SMAD2_3 4 datasets

ChIP DE_D1 S07-DE-d1-SMAD2_3-exp1 364 bp overlap

ChIP DE_D1 S39-DE-d1-SMAD2_3-exp2 335 bp overlap

ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 510 bp overlap

ChIP DE_D2 S53-DE-d2-SMAD2_3-exp2 510 bp overlap

SMAD3 1 dataset

ChIP endoderm GSE29422.SMAD3.endoderm 318 bp overlap

SMAD4 1 dataset

ChIP endoderm GSE29422.SMAD4.endoderm 281 bp overlap

SMARCA4 6 datasets

ChIP A-549_AG15677 GSE132290.SMARCA4.A-549_AG15677 110 bp overlap

ChIP A-549_AG15725 GSE132290.SMARCA4.A-549_AG15725 157 bp overlap

ChIP BIN-67_lentivirus-SMARCA4 GSE117734.SMARCA4.BIN-67_lentivirus-SMARCA4 261 bp overlap

ChIP BIN-67_lentivirus-SMARCA4-K785R GSE117734.SMARCA4.BIN-67_lentivirus-SMARCA4-K785R 510 bp overlap

ChIP BIN-67_lentivirus-SMARCA4-T910M GSE117734.SMARCA4.BIN-67_lentivirus-SMARCA4-T910M 510 bp overlap

ChIP NPC_K755R-siAP GSE122631.SMARCA4.NPC_K755R-siAP 207 bp overlap

SMARCB1 1 dataset

ChIP proliferating-human-fibroblast GSE131711.SMARCB1.proliferating-human-fibroblast 305 bp overlap

SMARCC1 3 datasets

ChIP BIN-67_lentivirus-SMARCA4 GSE117734.SMARCC1.BIN-67_lentivirus-SMARCA4 173 bp overlap

ChIP BIN-67_lentivirus-SMARCA4-K785R GSE117734.SMARCC1.BIN-67_lentivirus-SMARCA4-K785R 369 bp overlap

ChIP BIN-67_lentivirus-SMARCA4-T910M GSE117734.SMARCC1.BIN-67_lentivirus-SMARCA4-T910M 510 bp overlap

SMC1A 1 dataset

ChIP primary-epidermal-keratinocyte_diff_d0 GSE84657.SMC1A.primary-epidermal-keratinocyte_diff_d0 390 bp overlap

SMC3 4 datasets

ChIP GP5D GSE51234.SMC3.GP5D 401 bp overlap

ChIP HeLa GSE126990.SMC3.HeLa 158 bp overlap

ChIP HeLa-Kyoto GSE102884.SMC3.HeLa-Kyoto 158 bp overlap

ChIP HeLa-Kyoto GSE138405.SMC3.HeLa-Kyoto 158 bp overlap

SOX17 1 dataset

ChIP DE_D2 DED2-SOX17_Batch_II 510 bp overlap

SOX17_M 1 dataset

ChIP DE_D2 DED2-SOX17-M_Batch_II 510 bp overlap

SOX2 2 datasets

ChIP LK2_DNp63 GSE137459.SOX2.LK2_DNp63 301 bp overlap

ChIP LK2_GFP GSE137459.SOX2.LK2_GFP 374 bp overlap

ChIP K-562 ENCSR788RSW.SOX6.K-562 466 bp overlap

SS18 3 datasets

ChIP BIN-67_lentivirus-SMARCA4 GSE117734.SS18.BIN-67_lentivirus-SMARCA4 347 bp overlap

ChIP BIN-67_lentivirus-SMARCA4-K785R GSE117734.SS18.BIN-67_lentivirus-SMARCA4-K785R 438 bp overlap

ChIP BIN-67_lentivirus-SMARCA4-T910M GSE117734.SS18.BIN-67_lentivirus-SMARCA4-T910M 510 bp overlap

STAG1 5 datasets

ChIP HeLa GSE126990.STAG1.HeLa 177 bp overlap

ChIP HeLa-Kyoto GSE138405.STAG1.HeLa-Kyoto 177 bp overlap

ChIP Hep-G2 ENCSR167MTG.STAG1.Hep-G2 129 bp overlap

ChIP MCF-7 ERP000209.STAG1.MCF-7 200 bp overlap

ChIP MCF-7_E2 ERP000209.STAG1.MCF-7_E2 167 bp overlap

STAG2 1 dataset

ChIP HMEC-1 GSE101921.STAG2.HMEC-1 140 bp overlap

TARDBP 1 dataset

ChIP GM12878 ENCSR412QBS.TARDBP.GM12878 144 bp overlap

ZBTB2 1 dataset

ChIP GM12878 GSE97661.ZBTB2.GM12878 114 bp overlap

ZNF528 1 dataset

ChIP HEK293 GSE76494.ZNF528.HEK293 154 bp overlap

ZNF654 2 datasets

ChIP HEK293 ENCFF636WIC 106 bp overlap

ChIP HEK293 ENCSR504VDV.ZNF654.HEK293 302 bp overlap