chr3 : 128,675,353 – 128,676,166
813 bp 103 TFs 4 linked genes
This 813 bp open chromatin element is linked to 4 target genes and is bound by 103 transcription factors.
Linked Genes
4 genes
Gene↕ Expression Dist. to TSS↑ Distance↕ Link type↕
RPN1 25.1 kb Distal Multiome
RAB7A 50.2 kb Distal Multiome
ENSG00000290241 174.6 kb Distal Multiome
ACAD9 203.7 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.
chr3:128,670,353 – 128,681,166
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
103 transcription factors
Source
Cell type
Arx 2 datasets
Motif DE_48h DE_48h-Arx_MA0874.2 10 bp overlap
Motif DE_72h DE_72h-Arx_MA0874.2 10 bp overlap
BARX1 2 datasets
Motif DE_48h DE_48h-BARX1_MA0875.2 6 bp overlap
Motif DE_72h DE_72h-BARX1_MA0875.2 6 bp overlap
BATF 1 dataset
ChIP GM12878 ENCFF954REE 231 bp overlap
BCL11A 1 dataset
ChIP GM12878 ENCSR000BHA.BCL11A.GM12878 172 bp overlap
BCL6 2 datasets
ChIP OCI-Ly1 GSE29282.BCL6.OCI-Ly1 201 bp overlap
ChIP SU-DHL-4 GSE119038.BCL6.SU-DHL-4 225 bp overlap
BCOR 1 dataset
ChIP B-cell_GERMINAL_CENTER GSE43350.BCOR.B-cell_GERMINAL_CENTER 272 bp overlap
BRD2 3 datasets
ChIP THP-1_iBET GSE138084.BRD2.THP-1_iBET 293 bp overlap
ChIP THP-1_iBET-BD1 GSE138084.BRD2.THP-1_iBET-BD1 364 bp overlap
ChIP THP-1_iBET-BD2 GSE138084.BRD2.THP-1_iBET-BD2 414 bp overlap
BRD3 2 datasets
ChIP MV4-11_DMSO GSE120715.BRD3.MV4-11_DMSO 281 bp overlap
ChIP MV4-11_IBET151_500nM GSE120715.BRD3.MV4-11_IBET151_500nM 139 bp overlap
BRD4 6 datasets
ChIP MOLM-14_DMSO GSE65138.BRD4.MOLM-14_DMSO 199 bp overlap
ChIP MV4-11-B_DMSO GSE101821.BRD4.MV4-11-B_DMSO 303 bp overlap
ChIP MV4-11_DMSO GSE71776.BRD4.MV4-11_DMSO 295 bp overlap
ChIP THP-1_DMSO GSE138084.BRD4.THP-1_DMSO 217 bp overlap
ChIP THP-1_DMSO-PMA GSE138084.BRD4.THP-1_DMSO-PMA 258 bp overlap
ChIP THP-1_iBET-BD2 GSE138084.BRD4.THP-1_iBET-BD2 257 bp overlap
BSX 2 datasets
Motif DE_48h DE_48h-BSX_MA0876.2 6 bp overlap
Motif DE_72h DE_72h-BSX_MA0876.2 6 bp overlap
CBX5 2 datasets
ChIP GM12878 ENCFF542UDC 82 bp overlap
ChIP GM12878 ENCFF542UDC 281 bp overlap
CHD7 1 dataset
ChIP H1 ENCFF126NLU 514 bp overlap
CTCF 2 datasets
ChIP DOHH2 ENCSR084RDK.CTCF.DOHH2 234 bp overlap
ChIP GM12868 ENCSR000DRI.CTCF.GM12868 103 bp overlap
DLX1 2 datasets
Motif DE_48h DE_48h-DLX1_MA0879.3 6 bp overlap
Motif DE_72h DE_72h-DLX1_MA0879.3 6 bp overlap
DLX6 2 datasets
Motif DE_48h DE_48h-DLX6_MA0882.2 6 bp overlap
Motif DE_72h DE_72h-DLX6_MA0882.2 6 bp overlap
Dlx3 2 datasets
Motif DE_48h DE_48h-Dlx3_MA0880.2 6 bp overlap
Motif DE_72h DE_72h-Dlx3_MA0880.2 6 bp overlap
Dlx4 2 datasets
Motif DE_48h DE_48h-Dlx4_MA0881.2 6 bp overlap
Motif DE_72h DE_72h-Dlx4_MA0881.2 6 bp overlap
Dmrt1 1 dataset
Motif DE_72h DE_72h-Dmrt1_MA1603.2 9 bp overlap
E2F8 1 dataset
ChIP GM12878 ENCSR793HVL.E2F8.GM12878 183 bp overlap
EBF1 2 datasets
ChIP GM12878 ENCFF813OXE 265 bp overlap
ChIP MUTUL GSE75503.EBF1.MUTUL 251 bp overlap
EED 1 dataset
ChIP GM12878 ENCFF266FYW 466 bp overlap
EGR1 1 dataset
ChIP GM12878 ENCFF092DJY 207 bp overlap
ELF1 2 datasets
ChIP GM12878 ENCFF692SMY 67 bp overlap
ChIP GM12878 ENCSR000BMB.ELF1.GM12878 159 bp overlap
EN2 2 datasets
Motif DE_48h DE_48h-EN2_MA0642.3 7 bp overlap
Motif DE_72h DE_72h-EN2_MA0642.3 7 bp overlap
ESR1 1 dataset
ChIP MCF-7_E2 GSE14664.ESR1.MCF-7_E2 94 bp overlap
ETV6 1 dataset
ChIP WTC11 ENCFF812SCD 437 bp overlap
ETV7 2 datasets
Motif DE_48h DE_48h-ETV7_MA1708.2 9 bp overlap
Motif DE_72h DE_72h-ETV7_MA1708.2 9 bp overlap
FEZF1 1 dataset
ChIP HEK293 GSE76494.FEZF1.HEK293 184 bp overlap
FOXA2 2 datasets
ChIP DE DE-FOXA2-1 660 bp overlap
ChIP DE DE-FOXA2-2 627 bp overlap
GATA4 5 datasets
ChIP DE DE-GATA4-1 630 bp overlap
ChIP DE DE-GATA4-2 811 bp overlap
Motif DE_48h DE_48h-GATA4_MA0482.3 8 bp overlap
Motif DE_72h DE_72h-GATA4_MA0482.3 8 bp overlap
ChIP pancreatic-progenitor_PP1 GSE104840.GATA4.pancreatic-progenitor_PP1 252 bp overlap
GATA5 2 datasets
Motif DE_48h DE_48h-GATA5_MA0766.3 8 bp overlap
Motif DE_72h DE_72h-GATA5_MA0766.3 8 bp overlap
GATA6 8 datasets
ChIP DE DE-GATA6-1 462 bp overlap
ChIP DE DE-GATA6-2 813 bp overlap
ChIP DE_D1 S09-DE-d1-GATA6-exp1 770 bp overlap
ChIP DE_D1 S14-DE-d1-GATA6-exp1 813 bp overlap
ChIP DE_D1 S41-DE-d1-GATA6-exp2 734 bp overlap
ChIP DE_D2 S55-DE-d2-GATA6-exp2 812 bp overlap
ChIP HUES-8_DE_JNKi GSE109524.GATA6.HUES-8_DE_JNKi 813 bp overlap
ChIP HUES-8_DE_ctrl GSE109524.GATA6.HUES-8_DE_ctrl 770 bp overlap
GBX1 2 datasets
Motif DE_48h DE_48h-GBX1_MA0889.2 7 bp overlap
Motif DE_72h DE_72h-GBX1_MA0889.2 7 bp overlap
GBX2 2 datasets
Motif DE_48h DE_48h-GBX2_MA0890.2 6 bp overlap
Motif DE_72h DE_72h-GBX2_MA0890.2 6 bp overlap
GLIS1 3 datasets
ChIP HEK293 ENCFF299RSE 146 bp overlap
ChIP HEK293 ENCFF299RSE 457 bp overlap
ChIP HEK293 ENCSR482BBZ.GLIS1.HEK293 328 bp overlap
GTF3C2 1 dataset
ChIP H9 GSE94418.GTF3C2.H9 330 bp overlap
HESX1 2 datasets
Motif DE_48h DE_48h-HESX1_MA0894.2 6 bp overlap
Motif DE_72h DE_72h-HESX1_MA0894.2 6 bp overlap
HNF4A 1 dataset
Motif DE_72h DE_72h-HNF4A_MA0114.5 9 bp overlap
HNF4G 1 dataset
Motif DE_72h DE_72h-HNF4G_MA0484.3 9 bp overlap
HOXA7 2 datasets
Motif DE_48h DE_48h-HOXA7_MA1498.3 6 bp overlap
Motif DE_72h DE_72h-HOXA7_MA1498.3 6 bp overlap
HOXC13 1 dataset
Motif DE_72h DE_72h-HOXC13_MA0907.2 9 bp overlap
Hmx2 2 datasets
Motif DE_48h DE_48h-Hmx2_MA0897.2 15 bp overlap
Motif DE_72h DE_72h-Hmx2_MA0897.2 15 bp overlap
IKZF2 1 dataset
ChIP GM12878 ENCFF918AID 155 bp overlap
IRF4 1 dataset
ChIP T-cell GSE136853.IRF4.T-cell 192 bp overlap
JUN 5 datasets
ChIP DE_D1 S08-DE-d1-JUN-exp1 781 bp overlap
ChIP DE_D1 S13-DE-d1-JUN-exp1 349 bp overlap
ChIP DE_D1 S40-DE-d1-JUN-exp2 792 bp overlap
ChIP DE_D2 S02-DE-d2-JUN-exp1 813 bp overlap
ChIP HUES-8_DE_ctrl GSE109524.JUN.HUES-8_DE_ctrl 461 bp overlap
KDM1A 3 datasets
ChIP NB4_DMSO GSE128528.KDM1A.NB4_DMSO 301 bp overlap
ChIP OCI-Ly1 GSE107920.KDM1A.OCI-Ly1 116 bp overlap
ChIP pancreatic-progenitor_PP1 GSE104840.KDM1A.pancreatic-progenitor_PP1 317 bp overlap
KMT2A 1 dataset
ChIP CCRF-CEM GSE83671.KMT2A.CCRF-CEM 289 bp overlap
LBX1 2 datasets
Motif DE_48h DE_48h-LBX1_MA0618.2 7 bp overlap
Motif DE_72h DE_72h-LBX1_MA0618.2 7 bp overlap
LBX2 2 datasets
Motif DE_48h DE_48h-LBX2_MA0699.2 6 bp overlap
Motif DE_72h DE_72h-LBX2_MA0699.2 6 bp overlap
LHX2 2 datasets
Motif DE_48h DE_48h-LHX2_MA0700.3 6 bp overlap
Motif DE_72h DE_72h-LHX2_MA0700.3 6 bp overlap
LHX9 2 datasets
Motif DE_48h DE_48h-LHX9_MA0701.3 7 bp overlap
Motif DE_72h DE_72h-LHX9_MA0701.3 7 bp overlap
MAFF 2 datasets
Motif DE_48h DE_48h-MAFF_MA0495.4 11 bp overlap
Motif DE_72h DE_72h-MAFF_MA0495.4 11 bp overlap
MAX 1 dataset
ChIP P493-6 GSE36354.MAX.P493-6 171 bp overlap
MLLT1 1 dataset
ChIP GM12878 ENCSR552XSN.MLLT1.GM12878 384 bp overlap
MSX1 2 datasets
Motif DE_48h DE_48h-MSX1_MA0666.3 6 bp overlap
Motif DE_72h DE_72h-MSX1_MA0666.3 6 bp overlap
MSX2 2 datasets
Motif DE_48h DE_48h-MSX2_MA0708.3 6 bp overlap
Motif DE_72h DE_72h-MSX2_MA0708.3 6 bp overlap
MYC 2 datasets
ChIP P493-6 GSE77061.MYC.P493-6 246 bp overlap
ChIP P493-6_MST-312 GSE77061.MYC.P493-6_MST-312 239 bp overlap
Mafb 2 datasets
Motif DE_48h DE_48h-Mafb_MA0117.3 11 bp overlap
Motif DE_72h DE_72h-Mafb_MA0117.3 11 bp overlap
Msx3 2 datasets
Motif DE_48h DE_48h-Msx3_MA0709.2 6 bp overlap
Motif DE_72h DE_72h-Msx3_MA0709.2 6 bp overlap
NANOG 4 datasets
ChIP GM23338 ENCFF065NZG 311 bp overlap
ChIP HUES-8 GSE109524.NANOG.HUES-8 255 bp overlap
ChIP WA01_3IL ERP004238.NANOG.WA01_3IL 531 bp overlap
ChIP hESC GSE18292.NANOG.hESC 151 bp overlap
NBN 2 datasets
ChIP GM12878 ENCFF213ZNN 237 bp overlap
ChIP GM12878 ENCSR278SQL.NBN.GM12878 382 bp overlap
NR2F1 1 dataset
Motif DE_72h DE_72h-NR2F1_MA0017.3 12 bp overlap
NRL 2 datasets
Motif DE_48h DE_48h-NRL_MA0842.3 12 bp overlap
Motif DE_72h DE_72h-NRL_MA0842.3 12 bp overlap
Nobox 2 datasets
Motif DE_48h DE_48h-Nobox_MA0125.2 6 bp overlap
Motif DE_72h DE_72h-Nobox_MA0125.2 6 bp overlap
PAX5 1 dataset
ChIP GM12878 ENCSR000BHD.PAX5.GM12878 171 bp overlap
PML 1 dataset
ChIP GM12878 ENCFF160JQZ 83 bp overlap
POLR2A 3 datasets
ChIP GM12892 ENCFF506PGQ 95 bp overlap
ChIP GM18505 ENCFF311CYB 192 bp overlap
ChIP Raji ENCFF613VGX 325 bp overlap
POU2F2 2 datasets
ChIP GM12878 ENCFF207RKY 249 bp overlap
ChIP GM12891 ENCFF166YPP 231 bp overlap
POU2F3 1 dataset
ChIP NCI-H1048 GSE115123.POU2F3.NCI-H1048 136 bp overlap
POU5F1 2 datasets
ChIP DE_D1 DED1-OCT4_Batch_II 375 bp overlap
ChIP hESC_NAIVE GSE69646.POU5F1.hESC_NAIVE 317 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
PRRX2 2 datasets
Motif DE_48h DE_48h-PRRX2_MA0075.4 7 bp overlap
Motif DE_72h DE_72h-PRRX2_MA0075.4 7 bp overlap
Pou5f1::Sox2 2 datasets
Motif DE_48h DE_48h-Pou5f1Sox2_MA0142.1 15 bp overlap
Motif DE_72h DE_72h-Pou5f1Sox2_MA0142.1 15 bp overlap
RARA::RXRG 1 dataset
Motif DE_72h DE_72h-RARARXRG_MA1149.2 17 bp overlap
RAX 2 datasets
Motif DE_48h DE_48h-RAX_MA0718.2 6 bp overlap
Motif DE_72h DE_72h-RAX_MA0718.2 6 bp overlap
RELB 1 dataset
ChIP GM12878 ENCSR387QUV.RELB.GM12878 307 bp overlap
RUNX1 1 dataset
ChIP Jurkat GSE68976.RUNX1.Jurkat 242 bp overlap
RUNX1T1 1 dataset
ChIP Kasumi-1 GSE115115.RUNX1T1.Kasumi-1 346 bp overlap
RUNX3 1 dataset
ChIP GM12878 ENCFF395WHA 326 bp overlap
SKIL 1 dataset
ChIP GM12878 ENCSR212YKD.SKIL.GM12878 151 bp overlap
SMAD2-3 2 datasets
ChIP HUES-8_DE GSE109524.SMAD2-3.HUES-8_DE 627 bp overlap
ChIP HUES-8_DE_ctrl GSE109524.SMAD2-3.HUES-8_DE_ctrl 619 bp overlap
SMAD2_3 5 datasets
ChIP DE_D1 S07-DE-d1-SMAD2_3-exp1 602 bp overlap
ChIP DE_D1 S12-DE-d1-SMAD2_3-exp1 751 bp overlap
ChIP DE_D1 S39-DE-d1-SMAD2_3-exp2 800 bp overlap
ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 813 bp overlap
ChIP DE_D2 S53-DE-d2-SMAD2_3-exp2 402 bp overlap
SMARCA4 1 dataset
ChIP hiPSC GSE124903.SMARCA4.hiPSC 159 bp overlap
SMARCC1 1 dataset
ChIP DE_D1 S15-DE-d1-BAF155-exp1 276 bp overlap
SOX11 1 dataset
ChIP GRANT-A519 GSE52146.SOX11.GRANT-A519 138 bp overlap
SOX14 1 dataset
Motif DE_72h DE_72h-SOX14_MA1562.2 9 bp overlap
SOX17 1 dataset
ChIP DE_D2 DED2-SOX17_Batch_II 255 bp overlap
SOX17_M 2 datasets
ChIP DE_D2 DED2-SOX17-M_Batch_II 202 bp overlap
ChIP DE_D2 DED2-SOX17-M_Batch_II 272 bp overlap
SOX8 1 dataset
Motif DE_72h DE_72h-SOX8_MA0868.3 7 bp overlap
SP1 1 dataset
ChIP GM12878 ENCSR000BHK.SP1.GM12878 135 bp overlap
SREBP2 2 datasets
ChIP monocyte GSE129202.SREBP2.monocyte 296 bp overlap
ChIP monocyte_TNF GSE129202.SREBP2.monocyte_TNF 357 bp overlap
Sox5 1 dataset
Motif DE_72h DE_72h-Sox5_MA0087.3 8 bp overlap
TAF1 1 dataset
ChIP GM12878 ENCSR000BGS.TAF1.GM12878 152 bp overlap
TCF3 2 datasets
ChIP GM12878 ENCSR000BQT.TCF3.GM12878 158 bp overlap
ChIP Kasumi-1 GSE43834.TCF3.Kasumi-1 296 bp overlap
TCF7L2 2 datasets
Motif DE_48h DE_48h-TCF7L2_MA0523.2 9 bp overlap
Motif DE_72h DE_72h-TCF7L2_MA0523.2 9 bp overlap
TRIM28 1 dataset
ChIP WIBR3_NAIVE GSE84382.TRIM28.WIBR3_NAIVE 242 bp overlap
ZBTB33 1 dataset
ChIP K-562 ENCSR876GXA.ZBTB33.K-562 83 bp overlap
ZEB1 1 dataset
ChIP GM12878 ENCSR000BND.ZEB1.GM12878 126 bp overlap
ZNF143 1 dataset
ChIP GM12878 ENCSR936XTK.ZNF143.GM12878 333 bp overlap
ZNF281 2 datasets
Motif DE_48h DE_48h-ZNF281_MA1630.3 10 bp overlap
Motif DE_72h DE_72h-ZNF281_MA1630.3 10 bp overlap
ZNF341 1 dataset
ChIP HIES_EBV-B_ZNF341_isoform1 GSE113194.ZNF341.HIES_EBV-B_ZNF341_isoform1 195 bp overlap
ZNF652 2 datasets
Motif DE_48h DE_48h-ZNF652_MA1657.2 9 bp overlap
Motif DE_72h DE_72h-ZNF652_MA1657.2 9 bp overlap
ZSCAN16 2 datasets
Motif DE_48h DE_48h-ZSCAN16_MA2100.1 18 bp overlap
Motif DE_72h DE_72h-ZSCAN16_MA2100.1 18 bp overlap
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