chr3 : 25,420,047 – 25,420,725
678 bp 92 TFs 1 linked gene
This 678 bp open chromatin element is linked to RARB and is bound by 92 transcription factors.
Linked Genes
1 gene
Gene↕ Expression Dist. to TSS↑ Distance↕ Link type↕
RARB 7.4 kb Proximal Proximity
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.
chr3:25,415,047 – 25,425,725
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
92 transcription factors
Source
Cell type
ARID1A 1 dataset
ChIP HAP1 GSE108387.ARID1A.HAP1 354 bp overlap
ASH2L 2 datasets
ChIP H1 ENCFF399KAM 515 bp overlap
ChIP WA01 ENCSR850KIP.ASH2L.WA01 678 bp overlap
ATF2 1 dataset
ChIP WA01 ENCSR000BQU.ATF2.WA01 295 bp overlap
BCL11A 1 dataset
ChIP WA01 ENCSR000BIP.BCL11A.WA01 131 bp overlap
BRD2 1 dataset
ChIP SK-MEL-147 GSE94488.BRD2.SK-MEL-147 150 bp overlap
CEBPB 1 dataset
ChIP WA01 ENCSR000EBV.CEBPB.WA01 133 bp overlap
CHD1 1 dataset
ChIP WA01 ENCSR000AQK.CHD1.WA01 185 bp overlap
CHD7 3 datasets
ChIP H1 ENCFF126NLU 597 bp overlap
ChIP WA01 ENCSR000AVA.CHD7.WA01 266 bp overlap
ChIP hiPSC_derived_lt-NES GSE108506.CHD7.hiPSC_derived_lt-NES 582 bp overlap
CTBP1 1 dataset
ChIP MCF-7 ENCSR636EYA.CTBP1.MCF-7 87 bp overlap
CTCF 1 dataset
ChIP HAP1_clone21_CTCF-CRISPR GSE152721.CTCF.HAP1_clone21_CTCF-CRISPR 518 bp overlap
Cebpa 1 dataset
ChIP BLaER1 ENCFF093OYK 116 bp overlap
EBF3 2 datasets
Motif DE_12h DE_12h-EBF3_MA1637.2 9 bp overlap
Motif ES_0h ES_0h-EBF3_MA1637.2 9 bp overlap
EP300 2 datasets
ChIP H1 ENCFF927IYK 297 bp overlap
ChIP WA01 ENCSR000BKK.EP300.WA01 279 bp overlap
Ebf2 2 datasets
Motif DE_12h DE_12h-Ebf2_MA1604.2 9 bp overlap
Motif ES_0h ES_0h-Ebf2_MA1604.2 9 bp overlap
Elf5 2 datasets
Motif DE_12h DE_12h-Elf5_MA0136.4 8 bp overlap
Motif ES_0h ES_0h-Elf5_MA0136.4 8 bp overlap
Foxl2 2 datasets
Motif DE_12h DE_12h-Foxl2_MA1607.2 10 bp overlap
Motif ES_0h ES_0h-Foxl2_MA1607.2 10 bp overlap
GATA2 1 dataset
ChIP WA09 GSE105081.GATA2.WA09 135 bp overlap
GRHL1 2 datasets
Motif DE_12h DE_12h-GRHL1_MA0647.2 10 bp overlap
Motif ES_0h ES_0h-GRHL1_MA0647.2 10 bp overlap
GRHL2 2 datasets
Motif DE_12h DE_12h-GRHL2_MA1105.3 8 bp overlap
Motif ES_0h ES_0h-GRHL2_MA1105.3 8 bp overlap
HOXB4 2 datasets
Motif DE_12h DE_12h-HOXB4_MA1499.2 6 bp overlap
Motif ES_0h ES_0h-HOXB4_MA1499.2 6 bp overlap
HOXC4 2 datasets
Motif DE_12h DE_12h-HOXC4_MA1504.2 6 bp overlap
Motif ES_0h ES_0h-HOXC4_MA1504.2 6 bp overlap
HOXD4 2 datasets
Motif DE_12h DE_12h-HOXD4_MA1507.2 6 bp overlap
Motif ES_0h ES_0h-HOXD4_MA1507.2 6 bp overlap
Hnf1A 4 datasets
Motif DE_12h DE_12h-Hnf1A_MA1991.2 10 bp overlap
Motif DE_12h DE_12h-Hnf1A_MA1991.2 10 bp overlap
Motif DE_12h DE_12h-Hnf1A_MA1991.2 10 bp overlap
Motif ES_0h ES_0h-Hnf1A_MA1991.2 10 bp overlap
IRF2 2 datasets
Motif DE_12h DE_12h-IRF2_MA0051.2 16 bp overlap
Motif ES_0h ES_0h-IRF2_MA0051.2 16 bp overlap
IRF3 2 datasets
Motif DE_12h DE_12h-IRF3_MA1418.2 17 bp overlap
Motif ES_0h ES_0h-IRF3_MA1418.2 17 bp overlap
Irf1 2 datasets
Motif DE_12h DE_12h-Irf1_MA0050.4 11 bp overlap
Motif ES_0h ES_0h-Irf1_MA0050.4 11 bp overlap
JUND 1 dataset
ChIP WA01 ENCSR000EBZ.JUND.WA01 363 bp overlap
MEIS1 2 datasets
Motif DE_12h DE_12h-MEIS1_MA1639.2 9 bp overlap
Motif ES_0h ES_0h-MEIS1_MA1639.2 9 bp overlap
MEIS2 2 datasets
Motif DE_12h DE_12h-MEIS2_MA1640.2 9 bp overlap
Motif ES_0h ES_0h-MEIS2_MA1640.2 9 bp overlap
NANOG 8 datasets
ChIP GM23338 ENCSR061DGF.NANOG.GM23338 208 bp overlap
ChIP HUES-8 GSE109524.NANOG.HUES-8 635 bp overlap
ChIP WA01 ERP004238.NANOG.WA01 405 bp overlap
ChIP WA01 ENCSR000BMT.NANOG.WA01 117 bp overlap
ChIP WA01_3IL ERP004238.NANOG.WA01_3IL 678 bp overlap
ChIP WA09 GSE105028.NANOG.WA09 589 bp overlap
ChIP WA09_heat-shock GSE105028.NANOG.WA09_heat-shock 584 bp overlap
ChIP hESC GSE20650.NANOG.hESC 247 bp overlap
NFYB 1 dataset
Motif DE_12h DE_12h-NFYB_MA0502.3 9 bp overlap
NIPBL 1 dataset
ChIP hESC_WNT3A GSE64758.NIPBL.hESC_WNT3A 248 bp overlap
NR1H2::RXRA 1 dataset
Motif DE_12h DE_12h-NR1H2RXRA_MA0115.1 17 bp overlap
NR2C1 1 dataset
Motif DE_12h DE_12h-NR2C1_MA1535.2 6 bp overlap
NR2C2 1 dataset
Motif DE_12h DE_12h-NR2C2_MA1536.2 6 bp overlap
NR2F1 2 datasets
Motif DE_12h DE_12h-NR2F1_MA0017.3 12 bp overlap
Motif DE_12h DE_12h-NR2F1_MA1538.1 15 bp overlap
NR2F2 1 dataset
Motif DE_12h DE_12h-NR2F2_MA1111.2 7 bp overlap
NR4A2 1 dataset
Motif DE_12h DE_12h-NR4A2_MA0160.3 8 bp overlap
NR6A1 1 dataset
Motif DE_12h DE_12h-NR6A1_MA1541.2 14 bp overlap
Nr1H2 1 dataset
Motif DE_12h DE_12h-Nr1H2_MA1996.2 6 bp overlap
Nr1H4 1 dataset
Motif DE_12h DE_12h-Nr1H4_MA1110.3 6 bp overlap
Nr1h3 1 dataset
Motif DE_12h DE_12h-Nr1h3_MA2337.1 6 bp overlap
PAX5 1 dataset
ChIP fetal_testis GSE100639.PAX5.fetal_testis 222 bp overlap
PBX2 2 datasets
Motif DE_12h DE_12h-PBX2_MA1113.3 9 bp overlap
Motif ES_0h ES_0h-PBX2_MA1113.3 9 bp overlap
PDX1 1 dataset
ChIP hiPSC GSE125768.PDX1.hiPSC 297 bp overlap
POU1F1 2 datasets
Motif DE_12h DE_12h-POU1F1_MA0784.3 14 bp overlap
Motif ES_0h ES_0h-POU1F1_MA0784.3 14 bp overlap
POU2F1 2 datasets
Motif DE_12h DE_12h-POU2F1_MA0785.2 9 bp overlap
Motif ES_0h ES_0h-POU2F1_MA0785.2 9 bp overlap
POU2F1::SOX2 4 datasets
Motif DE_12h DE_12h-POU2F1SOX2_MA1962.1 17 bp overlap
Motif DE_12h DE_12h-POU2F1SOX2_MA1962.1 17 bp overlap
Motif ES_0h ES_0h-POU2F1SOX2_MA1962.1 17 bp overlap
Motif ES_0h ES_0h-POU2F1SOX2_MA1962.1 17 bp overlap
POU2F2 2 datasets
Motif DE_12h DE_12h-POU2F2_MA0507.3 13 bp overlap
Motif ES_0h ES_0h-POU2F2_MA0507.3 13 bp overlap
POU3F1 2 datasets
Motif DE_12h DE_12h-POU3F1_MA0786.2 10 bp overlap
Motif ES_0h ES_0h-POU3F1_MA0786.2 10 bp overlap
POU3F2 2 datasets
Motif DE_12h DE_12h-POU3F2_MA0787.1 12 bp overlap
Motif ES_0h ES_0h-POU3F2_MA0787.1 12 bp overlap
POU3F3 2 datasets
Motif DE_12h DE_12h-POU3F3_MA0788.1 13 bp overlap
Motif ES_0h ES_0h-POU3F3_MA0788.1 13 bp overlap
POU3F4 2 datasets
Motif DE_12h DE_12h-POU3F4_MA0789.1 9 bp overlap
Motif ES_0h ES_0h-POU3F4_MA0789.1 9 bp overlap
POU5F1 13 datasets
Motif DE_12h DE_12h-POU5F1_MA1115.2 7 bp overlap
Motif ES_0h ES_0h-POU5F1_MA1115.2 7 bp overlap
ChIP GM23338 ENCFF333SNB 311 bp overlap
ChIP HUES-8 GSE109524.POU5F1.HUES-8 678 bp overlap
ChIP NCCIT_SNF5 GSE36134.POU5F1.NCCIT_SNF5 516 bp overlap
ChIP WA01 ENCSR000BMU.POU5F1.WA01 153 bp overlap
ChIP WA09 GSE105028.POU5F1.WA09 425 bp overlap
ChIP WA09_heat-shock GSE105028.POU5F1.WA09_heat-shock 318 bp overlap
ChIP hESC ENCSR264RJX.POU5F1.hESC 202 bp overlap
ChIP hESC_NAIVE GSE69646.POU5F1.hESC_NAIVE 678 bp overlap
ChIP hESC_PRIMED GSE69646.POU5F1.hESC_PRIMED 666 bp overlap
ChIP hiPSC GSE56567.POU5F1.hiPSC 322 bp overlap
ChIP hiPSC_3s2 GSE81899.POU5F1.hiPSC_3s2 146 bp overlap
POU5F1B 2 datasets
Motif DE_12h DE_12h-POU5F1B_MA0792.1 9 bp overlap
Motif ES_0h ES_0h-POU5F1B_MA0792.1 9 bp overlap
PRDM1 1 dataset
ChIP fetal_testis GSE100639.PRDM1.fetal_testis 220 bp overlap
Pou5f1::Sox2 4 datasets
Motif DE_12h DE_12h-Pou5f1Sox2_MA0142.1 15 bp overlap
Motif DE_12h DE_12h-Pou5f1Sox2_MA0142.1 15 bp overlap
Motif ES_0h ES_0h-Pou5f1Sox2_MA0142.1 15 bp overlap
Motif ES_0h ES_0h-Pou5f1Sox2_MA0142.1 15 bp overlap
Ppara 1 dataset
Motif DE_12h DE_12h-Ppara_MA2338.1 7 bp overlap
Prdm15 2 datasets
Motif DE_12h DE_12h-Prdm15_MA1616.2 11 bp overlap
Motif ES_0h ES_0h-Prdm15_MA1616.2 11 bp overlap
RAD21 4 datasets
ChIP HAP1 GSE126634.RAD21.HAP1 597 bp overlap
ChIP HAP1 GSE152721.RAD21.HAP1 443 bp overlap
ChIP HAP1_CTCF GSE126634.RAD21.HAP1_CTCF 487 bp overlap
ChIP HAP1_clone25 GSE152721.RAD21.HAP1_clone25 355 bp overlap
RARA 2 datasets
Motif DE_12h DE_12h-RARA_MA0729.1 18 bp overlap
Motif ES_0h ES_0h-RARA_MA0729.1 18 bp overlap
RELA 2 datasets
Motif DE_12h DE_12h-RELA_MA0107.1 10 bp overlap
Motif ES_0h ES_0h-RELA_MA0107.1 10 bp overlap
RFX7 2 datasets
Motif DE_12h DE_12h-RFX7_MA1554.2 8 bp overlap
Motif ES_0h ES_0h-RFX7_MA1554.2 8 bp overlap
RORA 2 datasets
Motif DE_12h DE_12h-RORA_MA0071.1 10 bp overlap
Motif DE_12h DE_12h-RORA_MA0072.2 11 bp overlap
RORB 1 dataset
Motif DE_12h DE_12h-RORB_MA1150.2 10 bp overlap
Rarb 2 datasets
Motif DE_12h DE_12h-Rarb_MA0857.1 16 bp overlap
Motif ES_0h ES_0h-Rarb_MA0857.1 16 bp overlap
SCRT1 2 datasets
Motif DE_12h DE_12h-SCRT1_MA0743.3 10 bp overlap
Motif ES_0h ES_0h-SCRT1_MA0743.3 10 bp overlap
SMAD3 1 dataset
ChIP BG03 GSE21614.SMAD3.BG03 170 bp overlap
SMARCA4 6 datasets
ChIP NPC GSE122631.SMARCA4.NPC 189 bp overlap
ChIP NPC_siCT GSE122631.SMARCA4.NPC_siCT 633 bp overlap
ChIP NPC_siSOX GSE122631.SMARCA4.NPC_siSOX 399 bp overlap
ChIP NSC GSE125033.SMARCA4.NSC 522 bp overlap
ChIP hiPSC GSE124903.SMARCA4.hiPSC 674 bp overlap
ChIP hiPSC_WT GSE124903.SMARCA4.hiPSC_WT 504 bp overlap
SMARCB1 2 datasets
ChIP hiPSC GSE124903.SMARCB1.hiPSC 578 bp overlap
ChIP hiPSC_WT GSE124903.SMARCB1.hiPSC_WT 255 bp overlap
SMARCC1 3 datasets
ChIP ESC S25-ESC-d0-BAF155-exp1 371 bp overlap
ChIP hiPSC GSE124903.SMARCC1.hiPSC 417 bp overlap
ChIP hiPSC_WT GSE124903.SMARCC1.hiPSC_WT 349 bp overlap
SOX2 4 datasets
ChIP HNSC GSE69479.SOX2.HNSC 596 bp overlap
ChIP LK2_GFP GSE137459.SOX2.LK2_GFP 214 bp overlap
ChIP NPC GSE122631.SOX2.NPC 270 bp overlap
ChIP hiPSC GSE56567.SOX2.hiPSC 299 bp overlap
SP1 2 datasets
ChIP H1 ENCFF263FUH 321 bp overlap
ChIP WA01 ENCSR000BIR.SP1.WA01 479 bp overlap
Six4 2 datasets
Motif DE_12h DE_12h-Six4_MA2001.2 7 bp overlap
Motif ES_0h ES_0h-Six4_MA2001.2 7 bp overlap
TCF12 1 dataset
ChIP H1 ENCFF203EBH 251 bp overlap
TCF3 1 dataset
ChIP NPC GSE154479.TCF3.NPC 299 bp overlap
TCF7L1 5 datasets
Motif DE_12h DE_12h-TCF7L1_MA1421.1 12 bp overlap
Motif DE_12h DE_12h-TCF7L1_MA1421.1 12 bp overlap
Motif DE_12h DE_12h-TCF7L1_MA1421.1 12 bp overlap
Motif ES_0h ES_0h-TCF7L1_MA1421.1 12 bp overlap
Motif ES_0h ES_0h-TCF7L1_MA1421.1 12 bp overlap
TEAD2 2 datasets
Motif DE_12h DE_12h-TEAD2_MA1121.2 7 bp overlap
Motif ES_0h ES_0h-TEAD2_MA1121.2 7 bp overlap
TEAD4 4 datasets
Motif DE_12h DE_12h-TEAD4_MA0809.3 8 bp overlap
Motif ES_0h ES_0h-TEAD4_MA0809.3 8 bp overlap
ChIP H1 ENCFF778PAX 245 bp overlap
ChIP hESC GSE99202.TEAD4.hESC 243 bp overlap
TP63 1 dataset
ChIP foreskin GSE126390.TP63.foreskin 137 bp overlap
TRIM28 1 dataset
ChIP WIBR3_NAIVE GSE84382.TRIM28.WIBR3_NAIVE 381 bp overlap
Tfcp2l1 2 datasets
Motif DE_12h DE_12h-Tfcp2l1_MA0145.2 14 bp overlap
Motif ES_0h ES_0h-Tfcp2l1_MA0145.2 14 bp overlap
YBX1 1 dataset
ChIP HEL GSE146717.YBX1.HEL 144 bp overlap
ZBTB1 1 dataset
ChIP Jurkat_ZBTB1-KO_cDNA GSE145783.ZBTB1.Jurkat_ZBTB1-KO_cDNA 123 bp overlap
ZNF114 1 dataset
ChIP GM23338 ENCFF631OSW 249 bp overlap
ZNF140 2 datasets
Motif DE_12h DE_12h-ZNF140_MA1589.2 19 bp overlap
Motif ES_0h ES_0h-ZNF140_MA1589.2 19 bp overlap
ZNF366 2 datasets
ChIP HEK293 ENCFF799ATK 199 bp overlap
ChIP HEK293 ENCSR106EBH.ZNF366.HEK293 114 bp overlap
ZNF418 2 datasets
Motif DE_12h DE_12h-ZNF418_MA1980.1 15 bp overlap
Motif ES_0h ES_0h-ZNF418_MA1980.1 15 bp overlap
ZNF462 3 datasets
ChIP GM23338 ENCFF896CCA 251 bp overlap
ChIP GM23338 ENCFF896CCA 139 bp overlap
ChIP GM23338 ENCSR334UWP.ZNF462.GM23338 380 bp overlap
ZNF530 2 datasets
Motif DE_12h DE_12h-ZNF530_MA1981.2 14 bp overlap
Motif ES_0h ES_0h-ZNF530_MA1981.2 14 bp overlap
ZNF547 2 datasets
Motif DE_12h DE_12h-ZNF547_MA2334.1 13 bp overlap
Motif ES_0h ES_0h-ZNF547_MA2334.1 13 bp overlap
ZNF667 2 datasets
Motif DE_12h DE_12h-ZNF667_MA1984.2 11 bp overlap
Motif ES_0h ES_0h-ZNF667_MA1984.2 11 bp overlap
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