chr3 : 3,266,443 – 3,267,740
1,297 bp 96 TFs 2 linked genes
This 1.3 kb open chromatin element is linked to CRBN and TRNT1 and is bound by 96 transcription factors.
Linked Genes
2 genes
Gene↕ Expression Dist. to TSS↑ Distance↕ Link type↕
CRBN 87.6 kb Distal Multiome
TRNT1 140.4 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.
chr3:3,261,443 – 3,272,740
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
96 transcription factors
Source
Cell type
Ascl2 3 datasets
Motif DE_36h DE_36h-Ascl2_MA0816.1 10 bp overlap
Motif DE_48h DE_48h-Ascl2_MA0816.1 10 bp overlap
Motif DE_60h DE_60h-Ascl2_MA0816.1 10 bp overlap
BHLHE22 3 datasets
Motif DE_36h DE_36h-BHLHE22_MA1635.2 6 bp overlap
Motif DE_48h DE_48h-BHLHE22_MA1635.2 6 bp overlap
Motif DE_60h DE_60h-BHLHE22_MA1635.2 6 bp overlap
CDK6 1 dataset
ChIP KB_IL GSE52469.CDK6.KB_IL 101 bp overlap
Cebpa 1 dataset
ChIP BLaER1 ENCFF896HSY 362 bp overlap
DMRT3 2 datasets
Motif DE_48h DE_48h-DMRT3_MA0610.2 7 bp overlap
Motif DE_60h DE_60h-DMRT3_MA0610.2 7 bp overlap
DMRTC2 3 datasets
Motif DE_36h DE_36h-DMRTC2_MA1479.2 11 bp overlap
Motif DE_48h DE_48h-DMRTC2_MA1479.2 11 bp overlap
Motif DE_60h DE_60h-DMRTC2_MA1479.2 11 bp overlap
DUX4 1 dataset
Motif DE_48h DE_48h-DUX4_MA0468.1 11 bp overlap
EOMES 1 dataset
ChIP hESC GSE26097.EOMES.hESC 271 bp overlap
ESR1 1 dataset
ChIP MDA-MB-134-VI_ESTROGEN GSE51022.ESR1.MDA-MB-134-VI_ESTROGEN 270 bp overlap
FOXA2 2 datasets
ChIP DE DE-FOXA2-1 600 bp overlap
ChIP DE DE-FOXA2-2 460 bp overlap
GATA1::TAL1 3 datasets
Motif DE_36h DE_36h-GATA1TAL1_MA0140.3 17 bp overlap
Motif DE_48h DE_48h-GATA1TAL1_MA0140.3 17 bp overlap
Motif DE_60h DE_60h-GATA1TAL1_MA0140.3 17 bp overlap
GATA4 3 datasets
ChIP DE DE-GATA4-1 294 bp overlap
ChIP DE DE-GATA4-1 563 bp overlap
ChIP DE DE-GATA4-2 580 bp overlap
GATA6 6 datasets
ChIP DE DE-GATA6-1 280 bp overlap
ChIP DE DE-GATA6-1 549 bp overlap
ChIP DE DE-GATA6-2 681 bp overlap
ChIP DE_D1 S14-DE-d1-GATA6-exp1 367 bp overlap
ChIP HUES-8_DE_JNKi GSE109524.GATA6.HUES-8_DE_JNKi 450 bp overlap
ChIP endoderm_KO GSE117136.GATA6.endoderm_KO 481 bp overlap
GRHL2 1 dataset
Motif DE_48h DE_48h-GRHL2_MA1105.3 8 bp overlap
HDAC3 1 dataset
ChIP RH4_DMSO-6H GSE116344.HDAC3.RH4_DMSO-6H 199 bp overlap
HOXA3 3 datasets
Motif DE_36h DE_36h-HOXA3_MA2119.1 7 bp overlap
Motif DE_48h DE_48h-HOXA3_MA2119.1 7 bp overlap
Motif DE_60h DE_60h-HOXA3_MA2119.1 7 bp overlap
HOXA4 3 datasets
Motif DE_36h DE_36h-HOXA4_MA1496.2 7 bp overlap
Motif DE_48h DE_48h-HOXA4_MA1496.2 7 bp overlap
Motif DE_60h DE_60h-HOXA4_MA1496.2 7 bp overlap
HOXB4 4 datasets
Motif DE_36h DE_36h-HOXB4_MA1499.2 6 bp overlap
Motif DE_48h DE_48h-HOXB4_MA1499.2 6 bp overlap
Motif DE_48h DE_48h-HOXB4_MA1499.2 6 bp overlap
Motif DE_60h DE_60h-HOXB4_MA1499.2 6 bp overlap
HOXB9 3 datasets
Motif DE_36h DE_36h-HOXB9_MA1503.2 9 bp overlap
Motif DE_48h DE_48h-HOXB9_MA1503.2 9 bp overlap
Motif DE_60h DE_60h-HOXB9_MA1503.2 9 bp overlap
HOXC10 3 datasets
Motif DE_36h DE_36h-HOXC10_MA0905.2 9 bp overlap
Motif DE_48h DE_48h-HOXC10_MA0905.2 9 bp overlap
Motif DE_60h DE_60h-HOXC10_MA0905.2 9 bp overlap
HOXC4 4 datasets
Motif DE_36h DE_36h-HOXC4_MA1504.2 6 bp overlap
Motif DE_48h DE_48h-HOXC4_MA1504.2 6 bp overlap
Motif DE_48h DE_48h-HOXC4_MA1504.2 6 bp overlap
Motif DE_60h DE_60h-HOXC4_MA1504.2 6 bp overlap
HOXC9 3 datasets
Motif DE_36h DE_36h-HOXC9_MA0485.3 9 bp overlap
Motif DE_48h DE_48h-HOXC9_MA0485.3 9 bp overlap
Motif DE_60h DE_60h-HOXC9_MA0485.3 9 bp overlap
HOXD4 4 datasets
Motif DE_36h DE_36h-HOXD4_MA1507.2 6 bp overlap
Motif DE_48h DE_48h-HOXD4_MA1507.2 6 bp overlap
Motif DE_48h DE_48h-HOXD4_MA1507.2 6 bp overlap
Motif DE_60h DE_60h-HOXD4_MA1507.2 6 bp overlap
Hoxa11 3 datasets
Motif DE_36h DE_36h-Hoxa11_MA0911.2 9 bp overlap
Motif DE_48h DE_48h-Hoxa11_MA0911.2 9 bp overlap
Motif DE_60h DE_60h-Hoxa11_MA0911.2 9 bp overlap
IRF7 3 datasets
Motif DE_36h DE_36h-IRF7_MA0772.2 13 bp overlap
Motif DE_48h DE_48h-IRF7_MA0772.2 13 bp overlap
Motif DE_60h DE_60h-IRF7_MA0772.2 13 bp overlap
Irf1 3 datasets
Motif DE_36h DE_36h-Irf1_MA0050.4 11 bp overlap
Motif DE_48h DE_48h-Irf1_MA0050.4 11 bp overlap
Motif DE_60h DE_60h-Irf1_MA0050.4 11 bp overlap
KDM1A 1 dataset
ChIP SH-SY5Y_B3 GSE58258.KDM1A.SH-SY5Y_B3 197 bp overlap
LIN54 3 datasets
Motif DE_36h DE_36h-LIN54_MA0619.2 7 bp overlap
Motif DE_48h DE_48h-LIN54_MA0619.2 7 bp overlap
Motif DE_60h DE_60h-LIN54_MA0619.2 7 bp overlap
Lef1 3 datasets
Motif DE_36h DE_36h-Lef1_MA0768.3 8 bp overlap
Motif DE_48h DE_48h-Lef1_MA0768.3 8 bp overlap
Motif DE_60h DE_60h-Lef1_MA0768.3 8 bp overlap
MAF::NFE2 2 datasets
Motif DE_48h DE_48h-MAFNFE2_MA0501.2 11 bp overlap
Motif DE_60h DE_60h-MAFNFE2_MA0501.2 11 bp overlap
MAFG::NFE2L1 2 datasets
Motif DE_48h DE_48h-MAFGNFE2L1_MA0089.3 11 bp overlap
Motif DE_60h DE_60h-MAFGNFE2L1_MA0089.3 11 bp overlap
MEIS1 6 datasets
Motif DE_36h DE_36h-MEIS1_MA0498.3 5 bp overlap
Motif DE_36h DE_36h-MEIS1_MA0498.3 5 bp overlap
Motif DE_48h DE_48h-MEIS1_MA0498.3 5 bp overlap
Motif DE_48h DE_48h-MEIS1_MA0498.3 5 bp overlap
Motif DE_60h DE_60h-MEIS1_MA0498.3 5 bp overlap
Motif DE_60h DE_60h-MEIS1_MA0498.3 5 bp overlap
MEIS2 3 datasets
Motif DE_36h DE_36h-MEIS2_MA0774.1 8 bp overlap
Motif DE_48h DE_48h-MEIS2_MA0774.1 8 bp overlap
Motif DE_60h DE_60h-MEIS2_MA0774.1 8 bp overlap
MEIS3 3 datasets
Motif DE_36h DE_36h-MEIS3_MA0775.2 7 bp overlap
Motif DE_48h DE_48h-MEIS3_MA0775.2 7 bp overlap
Motif DE_60h DE_60h-MEIS3_MA0775.2 7 bp overlap
MGA::EVX1 7 datasets
Motif DE_36h DE_36h-MGAEVX1_MA1960.2 11 bp overlap
Motif DE_36h DE_36h-MGAEVX1_MA1960.2 11 bp overlap
Motif DE_48h DE_48h-MGAEVX1_MA1960.2 11 bp overlap
Motif DE_48h DE_48h-MGAEVX1_MA1960.2 11 bp overlap
Motif DE_48h DE_48h-MGAEVX1_MA1960.2 11 bp overlap
Motif DE_60h DE_60h-MGAEVX1_MA1960.2 11 bp overlap
Motif DE_60h DE_60h-MGAEVX1_MA1960.2 11 bp overlap
MXI1 3 datasets
Motif DE_36h DE_36h-MXI1_MA1108.3 6 bp overlap
Motif DE_48h DE_48h-MXI1_MA1108.3 6 bp overlap
Motif DE_60h DE_60h-MXI1_MA1108.3 6 bp overlap
MYB 1 dataset
Motif DE_48h DE_48h-MYB_MA0100.4 6 bp overlap
MYF6 1 dataset
Motif DE_48h DE_48h-MYF6_MA0667.1 10 bp overlap
MZF1 3 datasets
Motif DE_36h DE_36h-MZF1_MA0056.3 8 bp overlap
Motif DE_48h DE_48h-MZF1_MA0056.3 8 bp overlap
Motif DE_60h DE_60h-MZF1_MA0056.3 8 bp overlap
Mecom 2 datasets
Motif DE_36h DE_36h-Mecom_MA0029.2 11 bp overlap
Motif DE_48h DE_48h-Mecom_MA0029.2 11 bp overlap
Msgn1 1 dataset
Motif DE_48h DE_48h-Msgn1_MA1524.3 10 bp overlap
NHLH1 3 datasets
Motif DE_36h DE_36h-NHLH1_MA0048.3 9 bp overlap
Motif DE_48h DE_48h-NHLH1_MA0048.3 9 bp overlap
Motif DE_60h DE_60h-NHLH1_MA0048.3 9 bp overlap
NKX6-1 3 datasets
Motif DE_36h DE_36h-NKX6-1_MA0674.2 7 bp overlap
Motif DE_48h DE_48h-NKX6-1_MA0674.2 7 bp overlap
Motif DE_60h DE_60h-NKX6-1_MA0674.2 7 bp overlap
NKX6-3 4 datasets
Motif DE_36h DE_36h-NKX6-3_MA1530.2 8 bp overlap
Motif DE_48h DE_48h-NKX6-3_MA1530.2 8 bp overlap
Motif DE_48h DE_48h-NKX6-3_MA1530.2 8 bp overlap
Motif DE_60h DE_60h-NKX6-3_MA1530.2 8 bp overlap
NR1H2::RXRA 2 datasets
Motif DE_48h DE_48h-NR1H2RXRA_MA0115.1 17 bp overlap
Motif DE_60h DE_60h-NR1H2RXRA_MA0115.1 17 bp overlap
NR1I2 2 datasets
Motif DE_48h DE_48h-NR1I2_MA1533.2 15 bp overlap
Motif DE_60h DE_60h-NR1I2_MA1533.2 15 bp overlap
NR2C1 2 datasets
Motif DE_48h DE_48h-NR2C1_MA1535.2 6 bp overlap
Motif DE_60h DE_60h-NR2C1_MA1535.2 6 bp overlap
NR2C2 2 datasets
Motif DE_48h DE_48h-NR2C2_MA1536.2 6 bp overlap
Motif DE_60h DE_60h-NR2C2_MA1536.2 6 bp overlap
NR2F1 2 datasets
Motif DE_48h DE_48h-NR2F1_MA0017.3 12 bp overlap
Motif DE_60h DE_60h-NR2F1_MA0017.3 12 bp overlap
Neurod2 3 datasets
Motif DE_36h DE_36h-Neurod2_MA1993.2 6 bp overlap
Motif DE_48h DE_48h-Neurod2_MA1993.2 6 bp overlap
Motif DE_60h DE_60h-Neurod2_MA1993.2 6 bp overlap
Nfe2l2 2 datasets
Motif DE_48h DE_48h-Nfe2l2_MA0150.3 11 bp overlap
Motif DE_60h DE_60h-Nfe2l2_MA0150.3 11 bp overlap
Nr1H2 2 datasets
Motif DE_48h DE_48h-Nr1H2_MA1996.2 6 bp overlap
Motif DE_60h DE_60h-Nr1H2_MA1996.2 6 bp overlap
Nr1H4 2 datasets
Motif DE_48h DE_48h-Nr1H4_MA1110.3 6 bp overlap
Motif DE_60h DE_60h-Nr1H4_MA1110.3 6 bp overlap
Nr1h3 2 datasets
Motif DE_48h DE_48h-Nr1h3_MA2337.1 6 bp overlap
Motif DE_60h DE_60h-Nr1h3_MA2337.1 6 bp overlap
Nr2F6 3 datasets
Motif DE_36h DE_36h-Nr2F6_MA0728.1 15 bp overlap
Motif DE_48h DE_48h-Nr2F6_MA0728.1 15 bp overlap
Motif DE_60h DE_60h-Nr2F6_MA0728.1 15 bp overlap
Olig2 3 datasets
Motif DE_36h DE_36h-Olig2_MA1997.2 6 bp overlap
Motif DE_48h DE_48h-Olig2_MA1997.2 6 bp overlap
Motif DE_60h DE_60h-Olig2_MA1997.2 6 bp overlap
PAX3-FOXO1 1 dataset
ChIP RH4 GSE140115.PAX3-FOXO1.RH4 236 bp overlap
PHOX2A 1 dataset
Motif DE_48h DE_48h-PHOX2A_MA0713.1 11 bp overlap
PHOX2B 1 dataset
Motif DE_48h DE_48h-PHOX2B_MA0681.3 12 bp overlap
POU1F1 3 datasets
Motif DE_36h DE_36h-POU1F1_MA0784.3 14 bp overlap
Motif DE_48h DE_48h-POU1F1_MA0784.3 14 bp overlap
Motif DE_60h DE_60h-POU1F1_MA0784.3 14 bp overlap
POU2F1::SOX2 3 datasets
Motif DE_36h DE_36h-POU2F1SOX2_MA1962.1 17 bp overlap
Motif DE_48h DE_48h-POU2F1SOX2_MA1962.1 17 bp overlap
Motif DE_60h DE_60h-POU2F1SOX2_MA1962.1 17 bp overlap
POU2F2 3 datasets
Motif DE_36h DE_36h-POU2F2_MA0507.3 13 bp overlap
Motif DE_48h DE_48h-POU2F2_MA0507.3 13 bp overlap
Motif DE_60h DE_60h-POU2F2_MA0507.3 13 bp overlap
POU3F2 3 datasets
Motif DE_36h DE_36h-POU3F2_MA0787.1 12 bp overlap
Motif DE_48h DE_48h-POU3F2_MA0787.1 12 bp overlap
Motif DE_60h DE_60h-POU3F2_MA0787.1 12 bp overlap
POU5F1 1 dataset
ChIP BJ_INDUCED GSE36570.POU5F1.BJ_INDUCED 109 bp overlap
POU6F1 4 datasets
Motif DE_36h DE_36h-POU6F1_MA1549.2 7 bp overlap
Motif DE_48h DE_48h-POU6F1_MA1549.2 7 bp overlap
Motif DE_48h DE_48h-POU6F1_MA1549.2 7 bp overlap
Motif DE_60h DE_60h-POU6F1_MA1549.2 7 bp overlap
POU6F2 1 dataset
Motif DE_48h DE_48h-POU6F2_MA0793.2 9 bp overlap
PROP1 1 dataset
Motif DE_48h DE_48h-PROP1_MA0715.1 11 bp overlap
Pou5f1::Sox2 3 datasets
Motif DE_36h DE_36h-Pou5f1Sox2_MA0142.1 15 bp overlap
Motif DE_48h DE_48h-Pou5f1Sox2_MA0142.1 15 bp overlap
Motif DE_60h DE_60h-Pou5f1Sox2_MA0142.1 15 bp overlap
Pparg::Rxra 3 datasets
Motif DE_36h DE_36h-PpargRxra_MA0065.3 13 bp overlap
Motif DE_48h DE_48h-PpargRxra_MA0065.3 13 bp overlap
Motif DE_60h DE_60h-PpargRxra_MA0065.3 13 bp overlap
RARA 3 datasets
Motif DE_36h DE_36h-RARA_MA0729.1 18 bp overlap
Motif DE_48h DE_48h-RARA_MA0729.1 18 bp overlap
Motif DE_60h DE_60h-RARA_MA0729.1 18 bp overlap
Rarb 3 datasets
Motif DE_36h DE_36h-Rarb_MA0857.1 16 bp overlap
Motif DE_48h DE_48h-Rarb_MA0857.1 16 bp overlap
Motif DE_60h DE_60h-Rarb_MA0857.1 16 bp overlap
Rarg 4 datasets
Motif DE_36h DE_36h-Rarg_MA0859.2 15 bp overlap
Motif DE_48h DE_48h-Rarg_MA0859.2 15 bp overlap
Motif DE_48h DE_48h-Rarg_MA0860.1 17 bp overlap
Motif DE_60h DE_60h-Rarg_MA0859.2 15 bp overlap
SMAD2 1 dataset
ChIP endoderm GSE29422.SMAD2.endoderm 219 bp overlap
SMAD2-3 1 dataset
ChIP HUES-8_DE GSE109524.SMAD2-3.HUES-8_DE 505 bp overlap
SMAD2_3 2 datasets
ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 454 bp overlap
ChIP DE_D2 S53-DE-d2-SMAD2_3-exp2 411 bp overlap
SMAD3 1 dataset
ChIP endoderm GSE29422.SMAD3.endoderm 156 bp overlap
SMARCB1 1 dataset
ChIP MCF-7 GSE123284.SMARCB1.MCF-7 173 bp overlap
SOX17 1 dataset
ChIP DE_D2 DED2-SOX17_Batch_II 460 bp overlap
SOX17_M 1 dataset
ChIP DE_D2 DED2-SOX17-M_Batch_II 401 bp overlap
SOX2 1 dataset
ChIP HNSC GSE69479.SOX2.HNSC 335 bp overlap
SOX9 3 datasets
Motif DE_36h DE_36h-SOX9_MA0077.2 8 bp overlap
Motif DE_48h DE_48h-SOX9_MA0077.2 8 bp overlap
Motif DE_60h DE_60h-SOX9_MA0077.2 8 bp overlap
TCF7L1 5 datasets
Motif DE_36h DE_36h-TCF7L1_MA1421.1 12 bp overlap
Motif DE_48h DE_48h-TCF7L1_MA1421.1 12 bp overlap
Motif DE_48h DE_48h-TCF7L1_MA1421.1 12 bp overlap
Motif DE_60h DE_60h-TCF7L1_MA1421.1 12 bp overlap
Motif DE_60h DE_60h-TCF7L1_MA1421.1 12 bp overlap
TFAP4 3 datasets
Motif DE_36h DE_36h-TFAP4_MA0691.1 10 bp overlap
Motif DE_48h DE_48h-TFAP4_MA0691.1 10 bp overlap
Motif DE_60h DE_60h-TFAP4_MA0691.1 10 bp overlap
TFCP2 1 dataset
Motif DE_48h DE_48h-TFCP2_MA1968.2 9 bp overlap
THRA 2 datasets
Motif DE_48h DE_48h-THRA_MA1969.2 18 bp overlap
Motif DE_60h DE_60h-THRA_MA1969.2 18 bp overlap
THRB 2 datasets
Motif DE_48h DE_48h-THRB_MA1575.2 17 bp overlap
Motif DE_48h DE_48h-THRB_MA1576.2 18 bp overlap
Tcf12 3 datasets
Motif DE_36h DE_36h-Tcf12_MA0521.3 6 bp overlap
Motif DE_48h DE_48h-Tcf12_MA0521.3 6 bp overlap
Motif DE_60h DE_60h-Tcf12_MA0521.3 6 bp overlap
Tcf21 1 dataset
Motif DE_48h DE_48h-Tcf21_MA0832.2 10 bp overlap
Twist2 3 datasets
Motif DE_36h DE_36h-Twist2_MA0633.3 6 bp overlap
Motif DE_48h DE_48h-Twist2_MA0633.3 6 bp overlap
Motif DE_60h DE_60h-Twist2_MA0633.3 6 bp overlap
USF1 2 datasets
Motif DE_48h DE_48h-USF1_MA0093.4 10 bp overlap
Motif DE_60h DE_60h-USF1_MA0093.4 10 bp overlap
YY1 1 dataset
ChIP RH4_DMSO-6H GSE116344.YY1.RH4_DMSO-6H 176 bp overlap
ZBTB18 1 dataset
Motif DE_48h DE_48h-ZBTB18_MA0698.2 11 bp overlap
ZKSCAN2 1 dataset
ChIP HEK293T GSE78099.ZKSCAN2.HEK293T 203 bp overlap
ZNF274 3 datasets
Motif DE_36h DE_36h-ZNF274_MA1592.2 12 bp overlap
Motif DE_48h DE_48h-ZNF274_MA1592.2 12 bp overlap
Motif DE_60h DE_60h-ZNF274_MA1592.2 12 bp overlap
ZNF768 2 datasets
Motif DE_48h DE_48h-ZNF768_MA1731.2 9 bp overlap
Motif DE_60h DE_60h-ZNF768_MA1731.2 9 bp overlap
ZNF784 1 dataset
Motif DE_48h DE_48h-ZNF784_MA1717.2 8 bp overlap
Huangfu Lab · Publications · Resources · Contact