chr9:2,283,300–2,283,939

chr9 : 2,283,300 – 2,283,939

639 bp 77 TFs 5 linked genes

This 639 bp open chromatin element is linked to 5 target genes and is bound by 77 transcription factors.

Linked Genes

5 genes

Gene	Expression	Dist. to TSS	Distance	Link type
SMARCA2		125.2 kb	Distal	Multiome
VLDLR-AS1		337.8 kb	Distal	Multiome+HiCAR
VLDLR		337.9 kb	Distal	Multiome+HiCAR
KCNV2		433.9 kb	Distal	Multiome+HiCAR
PUM3		560.5 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

77 transcription factors

ChIP WTC11 ENCFF556XTF 445 bp overlap

Motif DE_24h DE_24h-ATF2_MA1632.2 10 bp overlap

ChIP H-1_DE GSE126661.BRD3.H-1_DE 109 bp overlap

ChIP H1 ENCFF126NLU 558 bp overlap

CREB1 1 dataset

Motif DE_24h DE_24h-CREB1_MA0018.5 8 bp overlap

FIGLA 1 dataset

Motif DE_24h DE_24h-FIGLA_MA0820.2 6 bp overlap

FOXA2 2 datasets

ChIP DE DE-FOXA2-1 307 bp overlap

ChIP DE DE-FOXA2-2 476 bp overlap

FOXN3 2 datasets

Motif DE_12h DE_12h-FOXN3_MA1489.1 8 bp overlap

Motif DE_24h DE_24h-FOXN3_MA1489.1 8 bp overlap

GATA4 2 datasets

ChIP DE DE-GATA4-1 639 bp overlap

ChIP DE DE-GATA4-2 632 bp overlap

GATA6 9 datasets

ChIP DE DE-GATA6-1 635 bp overlap

ChIP DE DE-GATA6-2 639 bp overlap

ChIP DE_D1 S09-DE-d1-GATA6-exp1 639 bp overlap

ChIP DE_D1 S14-DE-d1-GATA6-exp1 639 bp overlap

ChIP DE_D1 S41-DE-d1-GATA6-exp2 639 bp overlap

ChIP DE_D2 S55-DE-d2-GATA6-exp2 639 bp overlap

ChIP HUES-8_DE_JNKi GSE109524.GATA6.HUES-8_DE_JNKi 461 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.GATA6.HUES-8_DE_ctrl 465 bp overlap

ChIP endoderm_KO GSE117136.GATA6.endoderm_KO 244 bp overlap

GTF3C2 1 dataset

ChIP H9 GSE94418.GTF3C2.H9 205 bp overlap

HAND2 2 datasets

Motif DE_12h DE_12h-HAND2_MA1638.2 6 bp overlap

Motif DE_24h DE_24h-HAND2_MA1638.2 6 bp overlap

Hand1 5 datasets

Motif DE_12h DE_12h-Hand1_MA2123.1 9 bp overlap

Motif DE_24h DE_24h-Hand1_MA2123.1 9 bp overlap

Motif DE_36h DE_36h-Hand1_MA2123.1 9 bp overlap

Motif DE_48h DE_48h-Hand1_MA2123.1 9 bp overlap

Motif DE_60h DE_60h-Hand1_MA2123.1 9 bp overlap

IKZF1 5 datasets

Motif DE_12h DE_12h-IKZF1_MA1508.2 8 bp overlap

Motif DE_24h DE_24h-IKZF1_MA1508.2 8 bp overlap

Motif DE_36h DE_36h-IKZF1_MA1508.2 8 bp overlap

Motif DE_48h DE_48h-IKZF1_MA1508.2 8 bp overlap

Motif DE_60h DE_60h-IKZF1_MA1508.2 8 bp overlap

IRF3 5 datasets

Motif DE_12h DE_12h-IRF3_MA1418.2 17 bp overlap

Motif DE_24h DE_24h-IRF3_MA1418.2 17 bp overlap

Motif DE_36h DE_36h-IRF3_MA1418.2 17 bp overlap

Motif DE_48h DE_48h-IRF3_MA1418.2 17 bp overlap

Motif DE_60h DE_60h-IRF3_MA1418.2 17 bp overlap

IRF8 5 datasets

Motif DE_12h DE_12h-IRF8_MA0652.2 13 bp overlap

Motif DE_24h DE_24h-IRF8_MA0652.2 13 bp overlap

Motif DE_36h DE_36h-IRF8_MA0652.2 13 bp overlap

Motif DE_48h DE_48h-IRF8_MA0652.2 13 bp overlap

Motif DE_60h DE_60h-IRF8_MA0652.2 13 bp overlap

Irf1 8 datasets

Motif DE_12h DE_12h-Irf1_MA0050.4 11 bp overlap

Motif DE_12h DE_12h-Irf1_MA0050.4 11 bp overlap

Motif DE_24h DE_24h-Irf1_MA0050.4 11 bp overlap

Motif DE_24h DE_24h-Irf1_MA0050.4 11 bp overlap

Motif DE_36h DE_36h-Irf1_MA0050.4 11 bp overlap

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

ChIP DE_D1 S08-DE-d1-JUN-exp1 512 bp overlap

ChIP DE_D1 S13-DE-d1-JUN-exp1 420 bp overlap

ChIP DE_D1 S40-DE-d1-JUN-exp2 628 bp overlap

ChIP DE_D2 S02-DE-d2-JUN-exp1 636 bp overlap

ChIP DE_D2 S54-DE-d2-JUN-exp2 633 bp overlap

ChIP ESC S24-ESC-d0-JUN-exp1 541 bp overlap

ChIP ESC S34-ESC-d0-JUN-exp2 505 bp overlap

ChIP HUES-8 GSE109524.JUN.HUES-8 466 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.JUN.HUES-8_DE_ctrl 639 bp overlap

ChIP H1 ENCFF010YXS 311 bp overlap

MAF::NFE2 1 dataset

Motif DE_24h DE_24h-MAFNFE2_MA0501.2 11 bp overlap

MEIS1 5 datasets

Motif DE_12h DE_12h-MEIS1_MA0498.3 5 bp overlap

Motif DE_24h DE_24h-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_60h DE_60h-MEIS1_MA0498.3 5 bp overlap

MYBL2 2 datasets

ChIP WTC11 ENCFF166TKT 339 bp overlap

ChIP WTC11 ENCFF166TKT 497 bp overlap

MYF6 5 datasets

Motif DE_12h DE_12h-MYF6_MA0667.1 10 bp overlap

Motif DE_24h DE_24h-MYF6_MA0667.1 10 bp overlap

Motif DE_36h DE_36h-MYF6_MA0667.1 10 bp overlap

Motif DE_48h DE_48h-MYF6_MA0667.1 10 bp overlap

Motif DE_60h DE_60h-MYF6_MA0667.1 10 bp overlap

Msgn1 5 datasets

Motif DE_12h DE_12h-Msgn1_MA1524.3 10 bp overlap

Motif DE_24h DE_24h-Msgn1_MA1524.3 10 bp overlap

Motif DE_36h DE_36h-Msgn1_MA1524.3 10 bp overlap

Motif DE_48h DE_48h-Msgn1_MA1524.3 10 bp overlap

Motif DE_60h DE_60h-Msgn1_MA1524.3 10 bp overlap

NANOG 10 datasets

ChIP GM23338 ENCFF065NZG 311 bp overlap

ChIP GM23338 ENCSR061DGF.NANOG.GM23338 126 bp overlap

ChIP H1 ENCFF747ZPQ 241 bp overlap

ChIP HUES-8 GSE109524.NANOG.HUES-8 449 bp overlap

ChIP WA01 ERP004238.NANOG.WA01 332 bp overlap

ChIP WA01 ENCSR000BMT.NANOG.WA01 196 bp overlap

ChIP WA01_3IL ERP004238.NANOG.WA01_3IL 639 bp overlap

ChIP WA09 GSE105028.NANOG.WA09 399 bp overlap

ChIP WA09_heat-shock GSE105028.NANOG.WA09_heat-shock 268 bp overlap

ChIP hESC GSE18292.NANOG.hESC 99 bp overlap

NEUROD1 2 datasets

Motif DE_12h DE_12h-NEUROD1_MA1109.2 8 bp overlap

Motif DE_24h DE_24h-NEUROD1_MA1109.2 8 bp overlap

Motif DE_24h DE_24h-NFIA_MA0670.2 6 bp overlap

Motif DE_24h DE_24h-NFIC_MA0161.3 7 bp overlap

Motif DE_24h DE_24h-NFIX_MA0671.2 6 bp overlap

NR2C1 1 dataset

Motif DE_24h DE_24h-NR2C1_MA1535.2 6 bp overlap

NR2C2 1 dataset

Motif DE_24h DE_24h-NR2C2_MA1536.2 6 bp overlap

Neurod2 2 datasets

Motif DE_12h DE_12h-Neurod2_MA0668.3 8 bp overlap

Motif DE_24h DE_24h-Neurod2_MA0668.3 8 bp overlap

Nfatc2 5 datasets

Motif DE_12h DE_12h-Nfatc2_MA0152.3 8 bp overlap

Motif DE_24h DE_24h-Nfatc2_MA0152.3 8 bp overlap

Motif DE_36h DE_36h-Nfatc2_MA0152.3 8 bp overlap

Motif DE_48h DE_48h-Nfatc2_MA0152.3 8 bp overlap

Motif DE_60h DE_60h-Nfatc2_MA0152.3 8 bp overlap

Nfe2l2 1 dataset

Motif DE_24h DE_24h-Nfe2l2_MA0150.3 11 bp overlap

Nr1H2 1 dataset

Motif DE_24h DE_24h-Nr1H2_MA1996.2 6 bp overlap

Nr1H4 1 dataset

Motif DE_24h DE_24h-Nr1H4_MA1110.3 6 bp overlap

Nr1h3 1 dataset

Motif DE_24h DE_24h-Nr1h3_MA2337.1 6 bp overlap

Nr1h3::Rxra 1 dataset

Motif DE_24h DE_24h-Nr1h3Rxra_MA0494.2 16 bp overlap

ChIP WTC11 ENCFF634NAO 71 bp overlap

POU2F1 2 datasets

Motif DE_12h DE_12h-POU2F1_MA0785.2 9 bp overlap

Motif DE_24h DE_24h-POU2F1_MA0785.2 9 bp overlap

POU2F2 2 datasets

Motif DE_12h DE_12h-POU2F2_MA0507.3 13 bp overlap

Motif DE_24h DE_24h-POU2F2_MA0507.3 13 bp overlap

POU2F3 2 datasets

Motif DE_12h DE_12h-POU2F3_MA0627.3 9 bp overlap

Motif DE_24h DE_24h-POU2F3_MA0627.3 9 bp overlap

POU3F1 2 datasets

Motif DE_12h DE_12h-POU3F1_MA0786.2 10 bp overlap

Motif DE_24h DE_24h-POU3F1_MA0786.2 10 bp overlap

POU3F2 2 datasets

Motif DE_12h DE_12h-POU3F2_MA0787.1 12 bp overlap

Motif DE_24h DE_24h-POU3F2_MA0787.1 12 bp overlap

POU3F4 2 datasets

Motif DE_12h DE_12h-POU3F4_MA0789.1 9 bp overlap

Motif DE_24h DE_24h-POU3F4_MA0789.1 9 bp overlap

POU5F1 2 datasets

ChIP DE_D1 DED1-OCT4_Batch_II 446 bp overlap

ChIP hESC_PRIMED GSE69646.POU5F1.hESC_PRIMED 254 bp overlap

POU5F1B 2 datasets

Motif DE_12h DE_12h-POU5F1B_MA0792.1 9 bp overlap

Motif DE_24h DE_24h-POU5F1B_MA0792.1 9 bp overlap

Pou5f1::Sox2 2 datasets

Motif DE_12h DE_12h-Pou5f1Sox2_MA0142.1 15 bp overlap

Motif DE_24h DE_24h-Pou5f1Sox2_MA0142.1 15 bp overlap

Prdm14 5 datasets

Motif DE_12h DE_12h-Prdm14_MA1998.2 8 bp overlap

Motif DE_24h DE_24h-Prdm14_MA1998.2 8 bp overlap

Motif DE_36h DE_36h-Prdm14_MA1998.2 8 bp overlap

Motif DE_48h DE_48h-Prdm14_MA1998.2 8 bp overlap

Motif DE_60h DE_60h-Prdm14_MA1998.2 8 bp overlap

Ptf1A 2 datasets

Motif DE_12h DE_12h-Ptf1A_MA1618.2 9 bp overlap

Motif DE_24h DE_24h-Ptf1A_MA1618.2 9 bp overlap

Motif DE_24h DE_24h-Rarg_MA0860.1 17 bp overlap

SMAD2 1 dataset

ChIP hESC_YAP-_activinA_15h GSE99202.SMAD2.hESC_YAP-_activinA_15h 407 bp overlap

SMAD2-3 3 datasets

ChIP HUES-8_DE GSE109524.SMAD2-3.HUES-8_DE 639 bp overlap

ChIP HUES-8_DE_JNKi GSE109524.SMAD2-3.HUES-8_DE_JNKi 464 bp overlap

ChIP HUES-8_DE_ctrl GSE109524.SMAD2-3.HUES-8_DE_ctrl 639 bp overlap

SMAD2_3 5 datasets

ChIP DE_D1 S07-DE-d1-SMAD2_3-exp1 639 bp overlap

ChIP DE_D1 S12-DE-d1-SMAD2_3-exp1 639 bp overlap

ChIP DE_D1 S39-DE-d1-SMAD2_3-exp2 639 bp overlap

ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 639 bp overlap

ChIP DE_D2 S53-DE-d2-SMAD2_3-exp2 639 bp overlap

SMARCA4 1 dataset

ChIP hiPSC GSE124903.SMARCA4.hiPSC 199 bp overlap

SOX15 5 datasets

Motif DE_12h DE_12h-SOX15_MA1152.2 7 bp overlap

Motif DE_24h DE_24h-SOX15_MA1152.2 7 bp overlap

Motif DE_36h DE_36h-SOX15_MA1152.2 7 bp overlap

Motif DE_48h DE_48h-SOX15_MA1152.2 7 bp overlap

Motif DE_60h DE_60h-SOX15_MA1152.2 7 bp overlap

SOX17 1 dataset

ChIP DE_D2 DED2-SOX17_Batch_II 304 bp overlap

SOX17_M 1 dataset

ChIP DE_D2 DED2-SOX17-M_Batch_II 427 bp overlap

Motif DE_12h DE_12h-SP5_MA1965.2 6 bp overlap

Motif DE_24h DE_24h-SP5_MA1965.2 6 bp overlap

Motif DE_36h DE_36h-SP5_MA1965.2 6 bp overlap

SREBF1 1 dataset

Motif DE_24h DE_24h-SREBF1_MA0829.3 10 bp overlap

SREBF2 1 dataset

Motif DE_24h DE_24h-SREBF2_MA0828.3 10 bp overlap

STAT1::STAT2 5 datasets

Motif DE_12h DE_12h-STAT1STAT2_MA0517.2 13 bp overlap

Motif DE_24h DE_24h-STAT1STAT2_MA0517.2 13 bp overlap

Motif DE_36h DE_36h-STAT1STAT2_MA0517.2 13 bp overlap

Motif DE_48h DE_48h-STAT1STAT2_MA0517.2 13 bp overlap

Motif DE_60h DE_60h-STAT1STAT2_MA0517.2 13 bp overlap

Sox6 5 datasets

Motif DE_12h DE_12h-Sox6_MA0515.1 10 bp overlap

Motif DE_24h DE_24h-Sox6_MA0515.1 10 bp overlap

Motif DE_36h DE_36h-Sox6_MA0515.1 10 bp overlap

Motif DE_48h DE_48h-Sox6_MA0515.1 10 bp overlap

Motif DE_60h DE_60h-Sox6_MA0515.1 10 bp overlap

TEAD4 1 dataset

ChIP ESC S26-ESC-d0-TEAD4-exp1 372 bp overlap

Motif DE_24h DE_24h-THRA_MA1969.2 18 bp overlap

THRB 6 datasets

Motif DE_12h DE_12h-THRB_MA1576.2 18 bp overlap

Motif DE_24h DE_24h-THRB_MA1576.2 18 bp overlap

Motif DE_24h DE_24h-THRB_MA1576.2 18 bp overlap

Motif DE_36h DE_36h-THRB_MA1576.2 18 bp overlap

Motif DE_48h DE_48h-THRB_MA1576.2 18 bp overlap

Motif DE_60h DE_60h-THRB_MA1576.2 18 bp overlap

ChIP H9_ectoderm GSE142050.TP53.H9_ectoderm 340 bp overlap

TRERF1 1 dataset

ChIP WTC11 ENCFF113BUM 245 bp overlap

ChIP WTC11 ENCFF699QGS 358 bp overlap

ChIP WTC11 ENCFF139JAW 417 bp overlap

Motif DE_24h DE_24h-ZEB1_MA0103.4 6 bp overlap

ZFP14 3 datasets

Motif DE_12h DE_12h-ZFP14_MA1972.1 15 bp overlap

Motif DE_24h DE_24h-ZFP14_MA1972.1 15 bp overlap

Motif DE_36h DE_36h-ZFP14_MA1972.1 15 bp overlap

ZNF121 1 dataset

ChIP WTC11 ENCFF291API 297 bp overlap

ZNF460 1 dataset

Motif DE_24h DE_24h-ZNF460_MA1596.1 16 bp overlap

ZNF582 3 datasets

Motif DE_12h DE_12h-ZNF582_MA1983.2 19 bp overlap

Motif DE_24h DE_24h-ZNF582_MA1983.2 19 bp overlap

Motif DE_36h DE_36h-ZNF582_MA1983.2 19 bp overlap

ZNF671 1 dataset

ChIP WTC11 ENCFF053HBV 265 bp overlap

Zfp335 1 dataset

Motif DE_24h DE_24h-Zfp335_MA2002.2 7 bp overlap