chr3 : 16,302,010 16,302,566
556 bp 117 TFs 3 linked genes
This 556 bp open chromatin element is linked to OXNAD1, DPH3, and RFTN1 and is bound by 117 transcription factors.
Linked Genes
3 genes
Link type
Gene Expression Dist. to TSS Distance Link type
OXNAD1 37.1 kb Distal Multiome
DPH3 37.3 kb Distal Multiome
RFTN1 211.4 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.

View limited to ±500 kb around this element.
For the full data, please see the UCSC track linked below.
chr3:16,297,010 – 16,307,566
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
117 transcription factors
Source
Cell type
ARID2 1 dataset
ChIP Aska-SS_shSSX GSE108025.ARID2.Aska-SS_shSSX 122 bp overlap
ASCL1 1 dataset
Motif ES_0h ES_0h-ASCL1_MA1100.3 8 bp overlap
ASH2L 1 dataset
ChIP WA01 ENCSR850KIP.ASH2L.WA01 214 bp overlap
ATF2 1 dataset
ChIP WA01 ENCSR000BQU.ATF2.WA01 334 bp overlap
Ascl2 1 dataset
Motif ES_0h ES_0h-Ascl2_MA0816.1 10 bp overlap
BARX1 1 dataset
Motif ES_0h ES_0h-BARX1_MA0875.2 6 bp overlap
BARX2 1 dataset
Motif ES_0h ES_0h-BARX2_MA1471.2 9 bp overlap
BCL11A 2 datasets
Motif ES_0h ES_0h-BCL11A_MA2324.1 7 bp overlap
ChIP WA01 ENCSR000BIP.BCL11A.WA01 128 bp overlap
BCL11B 1 dataset
ChIP thymus_CD34neg GSE84677.BCL11B.thymus_CD34neg 280 bp overlap
BCOR 2 datasets
ChIP WA01_KDM2B_KO GSE104690.BCOR.WA01_KDM2B_KO 276 bp overlap
ChIP WA01_RNF2-R_Doxycyclin GSE104690.BCOR.WA01_RNF2-R_Doxycyclin 263 bp overlap
BHLHE22 2 datasets
ChIP CAL-1 GSE43876.BHLHE22.CAL-1 291 bp overlap
Motif ES_0h ES_0h-BHLHE22_MA1635.2 6 bp overlap
BRD4 7 datasets
ChIP DND41 GSE54379.BRD4.DND41 517 bp overlap
ChIP DND41_E GSE54379.BRD4.DND41_E 277 bp overlap
ChIP MOLT-4_DMSO GSE79288.BRD4.MOLT-4_DMSO 410 bp overlap
ChIP cortical-interneuron_KCl-pos_JQ1-neg GSE117508.BRD4.cortical-interneuron_KCl-pos_JQ1-neg 503 bp overlap
ChIP cortical-interneuron_R133C_KCl-neg_JQ1-neg GSE117508.BRD4.cortical-interneuron_R133C_KCl-neg_JQ1-neg 243 bp overlap
ChIP cortical-interneuron_R133C_KCl-neg_JQ1-pos GSE117508.BRD4.cortical-interneuron_R133C_KCl-neg_JQ1-pos 376 bp overlap
ChIP cortical-interneuron_R133C_KCl-pos_JQ1-neg GSE117508.BRD4.cortical-interneuron_R133C_KCl-pos_JQ1-neg 326 bp overlap
BSX 1 dataset
Motif ES_0h ES_0h-BSX_MA0876.2 6 bp overlap
CDK9 2 datasets
ChIP MOLT-4_DMSO GSE79288.CDK9.MOLT-4_DMSO 490 bp overlap
ChIP MOLT-4_JQ1 GSE79288.CDK9.MOLT-4_JQ1 483 bp overlap
CHD7 1 dataset
ChIP WA01 ENCSR000AVA.CHD7.WA01 313 bp overlap
CREB1 2 datasets
ChIP GM23338 ENCFF432ZEW 305 bp overlap
ChIP GM23338 ENCSR214ZAV.CREB1.GM23338 187 bp overlap
CTCF 2 datasets
ChIP DND-41 ENCFF913MRA 222 bp overlap
ChIP DND-41 ENCFF913MRA 317 bp overlap
Cebpa 1 dataset
ChIP BLaER1 ENCFF844FIP 521 bp overlap
DLX1 1 dataset
Motif ES_0h ES_0h-DLX1_MA0879.3 6 bp overlap
DLX6 1 dataset
Motif ES_0h ES_0h-DLX6_MA0882.2 6 bp overlap
DMRT3 1 dataset
Motif ES_0h ES_0h-DMRT3_MA0610.2 7 bp overlap
Dlx2 1 dataset
Motif ES_0h ES_0h-Dlx2_MA0885.3 8 bp overlap
Dlx3 1 dataset
Motif ES_0h ES_0h-Dlx3_MA0880.2 6 bp overlap
Dlx4 1 dataset
Motif ES_0h ES_0h-Dlx4_MA0881.2 6 bp overlap
Dlx5 1 dataset
Motif ES_0h ES_0h-Dlx5_MA1476.3 8 bp overlap
EBF1 1 dataset
Motif ES_0h ES_0h-EBF1_MA0154.5 11 bp overlap
ELF1 2 datasets
ChIP GM12878 ENCFF692SMY 423 bp overlap
ChIP GM12878 ENCSR841NDX.ELF1.GM12878 164 bp overlap
EP300 3 datasets
ChIP H1 ENCFF927IYK 297 bp overlap
ChIP WA01 ENCSR000BKK.EP300.WA01 265 bp overlap
ChIP hESC GSE17917.EP300.hESC 301 bp overlap
Ebf4 1 dataset
Motif ES_0h ES_0h-Ebf4_MA2122.1 11 bp overlap
FOXS1 1 dataset
Motif DE_12h DE_12h-FOXS1_MA2118.1 8 bp overlap
GATA3 2 datasets
ChIP Jurkat GSE76181.GATA3.Jurkat 243 bp overlap
ChIP thymocyte GSE71751.GATA3.thymocyte 129 bp overlap
GBX2 1 dataset
Motif ES_0h ES_0h-GBX2_MA0890.2 6 bp overlap
HAND2 1 dataset
Motif ES_0h ES_0h-HAND2_MA1638.2 6 bp overlap
HDAC2 1 dataset
ChIP WA01 ENCSR000BNR.HDAC2.WA01 234 bp overlap
HESX1 1 dataset
Motif ES_0h ES_0h-HESX1_MA0894.2 6 bp overlap
HOXA6 1 dataset
Motif ES_0h ES_0h-HOXA6_MA1497.2 7 bp overlap
HOXA7 1 dataset
Motif ES_0h ES_0h-HOXA7_MA1498.3 6 bp overlap
HOXB6 1 dataset
Motif ES_0h ES_0h-HOXB6_MA1500.2 7 bp overlap
HOXB7 1 dataset
Motif ES_0h ES_0h-HOXB7_MA1501.2 7 bp overlap
HOXB8 1 dataset
Motif ES_0h ES_0h-HOXB8_MA1502.2 7 bp overlap
HOXD8 1 dataset
Motif ES_0h ES_0h-HOXD8_MA0910.3 7 bp overlap
Hmx1 1 dataset
Motif ES_0h ES_0h-Hmx1_MA0896.2 9 bp overlap
Hmx3 1 dataset
Motif ES_0h ES_0h-Hmx3_MA0898.2 9 bp overlap
IKZF2 2 datasets
ChIP GM12878 ENCFF238LYK 390 bp overlap
ChIP GM12878 ENCSR822AHX.IKZF2.GM12878 269 bp overlap
ISL2 1 dataset
Motif ES_0h ES_0h-ISL2_MA0914.2 6 bp overlap
KMT2A 2 datasets
ChIP L826 GSE83671.KMT2A.L826 192 bp overlap
ChIP blood_cord GSE83671.KMT2A.blood_cord 168 bp overlap
LBX2 1 dataset
Motif ES_0h ES_0h-LBX2_MA0699.2 6 bp overlap
LHX2 1 dataset
Motif ES_0h ES_0h-LHX2_MA0700.3 6 bp overlap
MAF 1 dataset
ChIP CD4_Th1 GSE72266.MAF.CD4_Th1 310 bp overlap
MLLT1 1 dataset
ChIP GM12878 ENCSR552XSN.MLLT1.GM12878 255 bp overlap
MORC2 1 dataset
ChIP H9 GSE95374.MORC2.H9 378 bp overlap
MSX1 1 dataset
Motif ES_0h ES_0h-MSX1_MA0666.3 6 bp overlap
MSX2 1 dataset
Motif ES_0h ES_0h-MSX2_MA0708.3 6 bp overlap
MTA2 2 datasets
ChIP GM12878 ENCFF615CWQ 362 bp overlap
ChIP GM12878 ENCSR293QAR.MTA2.GM12878 486 bp overlap
MYB 6 datasets
ChIP CD4_TH2 GSE72266.MYB.CD4_TH2 242 bp overlap
ChIP CD4_Th1 GSE72266.MYB.CD4_Th1 443 bp overlap
Motif ES_0h ES_0h-MYB_MA0100.4 6 bp overlap
ChIP Jurkat GSE59657.MYB.Jurkat 556 bp overlap
ChIP MOLT-3 GSE59657.MYB.MOLT-3 521 bp overlap
ChIP PF-382 GSE94000.MYB.PF-382 319 bp overlap
MYBL2 1 dataset
Motif ES_0h ES_0h-MYBL2_MA0777.1 15 bp overlap
MYOG 1 dataset
Motif ES_0h ES_0h-MYOG_MA0500.3 8 bp overlap
MZF1 1 dataset
Motif ES_0h ES_0h-MZF1_MA0056.3 8 bp overlap
Msx3 1 dataset
Motif ES_0h ES_0h-Msx3_MA0709.2 6 bp overlap
NANOG 11 datasets
ChIP GM23338 ENCFF065NZG 311 bp overlap
ChIP GM23338 ENCSR061DGF.NANOG.GM23338 282 bp overlap
ChIP H1 ENCFF747ZPQ 241 bp overlap
ChIP HUES-8 GSE109524.NANOG.HUES-8 556 bp overlap
ChIP WA01 ERP004238.NANOG.WA01 502 bp overlap
ChIP WA01 ENCSR000BMT.NANOG.WA01 390 bp overlap
ChIP WA01_3IL ERP004238.NANOG.WA01_3IL 556 bp overlap
ChIP WA09 GSE105028.NANOG.WA09 333 bp overlap
ChIP hESC GSE18292.NANOG.hESC 210 bp overlap
ChIP hESC GSE20650.NANOG.hESC 157 bp overlap
ChIP hESC GSE18292.NANOG.hESC 93 bp overlap
NFATC2 4 datasets
ChIP CD4 GSE116695.NFATC2.CD4 184 bp overlap
ChIP CD4_CD28-ab GSE116695.NFATC2.CD4_CD28-ab 177 bp overlap
ChIP CD4_fly-DNA GSE116695.NFATC2.CD4_fly-DNA 260 bp overlap
ChIP CD4_fly-DNA_no-CD28 GSE116695.NFATC2.CD4_fly-DNA_no-CD28 116 bp overlap
NFIA 1 dataset
Motif ES_0h ES_0h-NFIA_MA0670.2 6 bp overlap
NFIX 1 dataset
Motif ES_0h ES_0h-NFIX_MA0671.2 6 bp overlap
NHLH1 1 dataset
Motif ES_0h ES_0h-NHLH1_MA0048.3 9 bp overlap
NIPBL 2 datasets
ChIP hESC GSE64758.NIPBL.hESC 268 bp overlap
ChIP hESC_WNT3A GSE64758.NIPBL.hESC_WNT3A 253 bp overlap
NOTCH1 2 datasets
ChIP CUTLL1 GSE29600.NOTCH1.CUTLL1 216 bp overlap
ChIP HPBALL GSE39263.NOTCH1.HPBALL 556 bp overlap
Neurod2 2 datasets
Motif ES_0h ES_0h-Neurod2_MA0668.3 8 bp overlap
Motif ES_0h ES_0h-Neurod2_MA1993.2 6 bp overlap
Nkx3-2 1 dataset
Motif ES_0h ES_0h-Nkx3-2_MA0122.4 10 bp overlap
Nobox 1 dataset
Motif ES_0h ES_0h-Nobox_MA0125.2 6 bp overlap
Nr2e3 1 dataset
Motif ES_0h ES_0h-Nr2e3_MA0164.2 6 bp overlap
OLIG2 1 dataset
ChIP brain-prefrontal-cortex_2017039 GSE129039.OLIG2.brain-prefrontal-cortex_2017039 297 bp overlap
Olig2 1 dataset
Motif ES_0h ES_0h-Olig2_MA1997.2 6 bp overlap
PAX5 1 dataset
ChIP GM12878 ENCSR000BHD.PAX5.GM12878 107 bp overlap
PBX1 1 dataset
ChIP RCH-ACV GSE85988.PBX1.RCH-ACV 313 bp overlap
POLR2A 4 datasets
ChIP GM12878 ENCFF412KAE 203 bp overlap
ChIP GM12878 ENCFF899QYP 310 bp overlap
ChIP GM12892 ENCFF542ZFO 333 bp overlap
ChIP GM12892 ENCFF542ZFO 132 bp overlap
POU5F1 5 datasets
ChIP HUES-8 GSE109524.POU5F1.HUES-8 505 bp overlap
ChIP NCCIT_SNF5 GSE36134.POU5F1.NCCIT_SNF5 487 bp overlap
ChIP hESC ENCSR264RJX.POU5F1.hESC 254 bp overlap
ChIP hESC_PRIMED GSE69646.POU5F1.hESC_PRIMED 331 bp overlap
ChIP hiPSC_3s2 GSE81899.POU5F1.hiPSC_3s2 146 bp overlap
Ptf1A 1 dataset
Motif ES_0h ES_0h-Ptf1A_MA1618.2 9 bp overlap
RAX 1 dataset
Motif ES_0h ES_0h-RAX_MA0718.2 6 bp overlap
RBPJ 4 datasets
ChIP CUTLL1 GSE29600.RBPJ.CUTLL1 120 bp overlap
ChIP GSC8-11_12d-das GSE74557.RBPJ.GSC8-11_12d-das 437 bp overlap
ChIP GSC8-11_dasatinib GSE74557.RBPJ.GSC8-11_dasatinib 320 bp overlap
ChIP NHEK GSE29498.RBPJ.NHEK 150 bp overlap
RUNX1 3 datasets
ChIP Jurkat GSE68976.RUNX1.Jurkat 395 bp overlap
ChIP Jurkat GSE76181.RUNX1.Jurkat 173 bp overlap
ChIP NALM-6 GSE126300.RUNX1.NALM-6 325 bp overlap
RUNX2 1 dataset
ChIP Karpas-45 GSE151819.RUNX2.Karpas-45 216 bp overlap
Runx1 1 dataset
Motif ES_0h ES_0h-Runx1_MA0002.3 9 bp overlap
SALL3 1 dataset
ChIP hiPSC GSE104863.SALL3.hiPSC 76 bp overlap
SIN3A 4 datasets
ChIP H1 ENCFF042ZSL 449 bp overlap
ChIP H1 ENCFF896IJG 301 bp overlap
ChIP WA01 ENCSR000EBO.SIN3A.WA01 190 bp overlap
ChIP WA01 ENCSR000BIS.SIN3A.WA01 266 bp overlap
SMAD2-3 1 dataset
ChIP HUVEC-C_TGFB1 GSE134556.SMAD2-3.HUVEC-C_TGFB1 246 bp overlap
SMARCA4 4 datasets
ChIP CTV-1_FLAG GSE128835.SMARCA4.CTV-1_FLAG 244 bp overlap
ChIP CTV-1_FLAG_SPI1-mut GSE128835.SMARCA4.CTV-1_FLAG_SPI1-mut 393 bp overlap
ChIP CTV-1_delA GSE128835.SMARCA4.CTV-1_delA 339 bp overlap
ChIP hiPSC_WT GSE124903.SMARCA4.hiPSC_WT 239 bp overlap
SMARCB1 1 dataset
ChIP hiPSC_WT GSE124903.SMARCB1.hiPSC_WT 207 bp overlap
SMARCC1 1 dataset
ChIP hiPSC_WT GSE124903.SMARCC1.hiPSC_WT 282 bp overlap
SOX14 1 dataset
Motif DE_12h DE_12h-SOX14_MA1562.2 9 bp overlap
SOX2 3 datasets
ChIP LK2_GFP GSE137459.SOX2.LK2_GFP 327 bp overlap
ChIP hESC GSE69479.SOX2.hESC 185 bp overlap
ChIP hiPSC GSE56567.SOX2.hiPSC 373 bp overlap
SOX8 1 dataset
Motif DE_12h DE_12h-SOX8_MA0868.3 7 bp overlap
SP1 2 datasets
ChIP H1 ENCFF263FUH 321 bp overlap
ChIP WA01 ENCSR000BIR.SP1.WA01 335 bp overlap
SRY 1 dataset
Motif DE_12h DE_12h-SRY_MA0084.2 7 bp overlap
Six3 1 dataset
Motif ES_0h ES_0h-Six3_MA0631.2 11 bp overlap
Sox11 1 dataset
Motif ES_0h ES_0h-Sox11_MA0869.3 8 bp overlap
Stat2 1 dataset
Motif ES_0h ES_0h-Stat2_MA1623.2 10 bp overlap
TAL1 1 dataset
ChIP MOLT-3 GSE59657.TAL1.MOLT-3 440 bp overlap
TBX21 1 dataset
ChIP Th1_CD3-CD28_donor2 GSE81881.TBX21.Th1_CD3-CD28_donor2 103 bp overlap
TCF12 4 datasets
ChIP GM12878 ENCFF433DMU 341 bp overlap
ChIP H1 ENCFF203EBH 251 bp overlap
ChIP Jurkat GSE29180.TCF12.Jurkat 281 bp overlap
ChIP WA01 ENCSR000BIT.TCF12.WA01 309 bp overlap
TCF3 3 datasets
ChIP 697_HF GSE138031.TCF3.697_HF 261 bp overlap
ChIP NPC GSE154479.TCF3.NPC 556 bp overlap
ChIP RCH-ACV GSE85988.TCF3.RCH-ACV 549 bp overlap
TCF4 2 datasets
ChIP CAL-1 GSE76147.TCF4.CAL-1 264 bp overlap
ChIP GEN2-2 GSE76147.TCF4.GEN2-2 435 bp overlap
Tcf12 1 dataset
Motif ES_0h ES_0h-Tcf12_MA0521.3 6 bp overlap
Twist2 1 dataset
Motif ES_0h ES_0h-Twist2_MA0633.3 6 bp overlap
ZIM3 1 dataset
Motif ES_0h ES_0h-ZIM3_MA1709.2 11 bp overlap
ZMAT4 1 dataset
ChIP WTC11 ENCFF608UXZ 241 bp overlap
ZNF143 1 dataset
ChIP MCF-7_E2 GSE76454.ZNF143.MCF-7_E2 101 bp overlap
ZNF24 3 datasets
Motif ES_0h ES_0h-ZNF24_MA1124.1 13 bp overlap
ChIP GM12878 ENCFF688STO 341 bp overlap
ChIP GM12878 ENCSR072PWP.ZNF24.GM12878 170 bp overlap
ZNF582 1 dataset
Motif DE_12h DE_12h-ZNF582_MA1983.2 19 bp overlap
ZNF652 1 dataset
Motif ES_0h ES_0h-ZNF652_MA1657.2 9 bp overlap
ZNF677 1 dataset
Motif ES_0h ES_0h-ZNF677_MA2101.1 12 bp overlap
ZNF687 1 dataset
ChIP GM12878 ENCFF233SGE 386 bp overlap