chr3 : 98,532,271 – 98,533,110
839 bp 85 TFs 2 linked genes
This 839 bp open chromatin element is linked to CLDND1 and ENSG00000248839 and is bound by 85 transcription factors.
Linked Genes
2 genes
Gene↕ Expression Dist. to TSS↑ Distance↕ Link type↕
CLDND1 9.4 kb Proximal Proximity
ENSG00000248839 9.7 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.
chr3:98,527,271 – 98,538,110
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
85 transcription factors
Source
Cell type
APC 1 dataset
ChIP HCT-116 GSE103894.APC.HCT-116 277 bp overlap
AR 12 datasets
ChIP LNCaP GSE80256.AR.LNCaP 146 bp overlap
ChIP LNCaP GSE80256.AR.LNCaP 61 bp overlap
ChIP LNCaP_1F5_SIFOXA1 GSE30623.AR.LNCaP_1F5_SIFOXA1 245 bp overlap
ChIP LNCaP_FOXA1 ERP003503.AR.LNCaP_FOXA1 153 bp overlap
ChIP LNCaP_GFP_Ethanol GSE128883.AR.LNCaP_GFP_Ethanol 69 bp overlap
ChIP LNCaP_R1881 GSE69043.AR.LNCaP_R1881 161 bp overlap
ChIP LNCaP_SHFOXA1_R1881 GSE37345.AR.LNCaP_SHFOXA1_R1881 350 bp overlap
ChIP LNCaP_SHFOXP1_DHT GSE62492.AR.LNCaP_SHFOXP1_DHT 161 bp overlap
ChIP VCaP_DHT24H GSE58428.AR.VCaP_DHT24H 398 bp overlap
ChIP VCaP_DHT24H_SHFOXA1 GSE58428.AR.VCaP_DHT24H_SHFOXA1 604 bp overlap
ChIP VCaP_DHT24H_SHRUNX1 GSE58428.AR.VCaP_DHT24H_SHRUNX1 371 bp overlap
ChIP VCaP_R1881_30M GSE84432.AR.VCaP_R1881_30M 137 bp overlap
ARID1A 1 dataset
ChIP NGP GSE134626.ARID1A.NGP 484 bp overlap
ARID3A 1 dataset
ChIP GM12878 ENCFF006WWZ 351 bp overlap
ARNTL 2 datasets
ChIP U2OS GSE44236.ARNTL.U2OS 263 bp overlap
ChIP U2OS_DMSO GSE85096.ARNTL.U2OS_DMSO 60 bp overlap
ATF2 2 datasets
ChIP GM12878 ENCSR000BQK.ATF2.GM12878 449 bp overlap
ChIP GM12878 ENCSR000BQK.ATF2.GM12878 284 bp overlap
BACH1 2 datasets
ChIP GM12878 ENCFF576UEQ 328 bp overlap
ChIP GM12878 ENCSR636MKU.BACH1.GM12878 289 bp overlap
BCL11A 2 datasets
ChIP GM12878 ENCSR000BHA.BCL11A.GM12878 202 bp overlap
ChIP GM12878 ENCSR000BHA.BCL11A.GM12878 197 bp overlap
BCL3 3 datasets
ChIP GM12878 ENCFF854PAY 351 bp overlap
ChIP GM12878 ENCFF854PAY 351 bp overlap
ChIP GM12878 ENCSR000BNQ.BCL3.GM12878 506 bp overlap
BRD4 13 datasets
ChIP CD4_JG1 GSE33281.BRD4.CD4_JG1 683 bp overlap
ChIP CD4_JG1 GSE33281.BRD4.CD4_JG1 106 bp overlap
ChIP HCT-116 GSE73319.BRD4.HCT-116 336 bp overlap
ChIP HEK293_sgNT GSE129407.BRD4.HEK293_sgNT 463 bp overlap
ChIP KK-1_DMSO GSE94732.BRD4.KK-1_DMSO 463 bp overlap
ChIP Kelly_sensitive GSE103030.BRD4.Kelly_sensitive 152 bp overlap
ChIP MPNST_PDJQ GSE62499.BRD4.MPNST_PDJQ 286 bp overlap
ChIP MPNST_PDJQ GSE62499.BRD4.MPNST_PDJQ 495 bp overlap
ChIP MV4-11-B_BI00894999_100nM_4h GSE101821.BRD4.MV4-11-B_BI00894999_100nM_4h 178 bp overlap
ChIP MV4-11_SGC GSE71776.BRD4.MV4-11_SGC 135 bp overlap
ChIP P493-6_MYC_0H GSE42262.BRD4.P493-6_MYC_0H 122 bp overlap
ChIP P493-6_MYC_24H GSE42262.BRD4.P493-6_MYC_24H 87 bp overlap
ChIP retina_AB1-RB GSE86981.BRD4.retina_AB1-RB 275 bp overlap
CBFB 2 datasets
ChIP GM12878 ENCSR860UHK.CBFB.GM12878 581 bp overlap
ChIP GM12878 ENCSR860UHK.CBFB.GM12878 113 bp overlap
CBX5 1 dataset
ChIP GM12878 ENCFF542UDC 465 bp overlap
CDK9 1 dataset
ChIP P493-6 GSE36354.CDK9.P493-6 174 bp overlap
CHD1 1 dataset
ChIP GM12878 ENCFF566UBH 405 bp overlap
CREB1 3 datasets
ChIP GM12878 ENCFF870CVH 145 bp overlap
ChIP GM12878 ENCSR000BUF.CREB1.GM12878 222 bp overlap
ChIP GM12878 ENCSR000BUF.CREB1.GM12878 142 bp overlap
CREM 3 datasets
ChIP GM12878 ENCFF391UGE 354 bp overlap
ChIP GM12878 ENCSR839XZU.CREM.GM12878 308 bp overlap
ChIP GM12878 ENCSR839XZU.CREM.GM12878 456 bp overlap
CTBP1 1 dataset
ChIP K-562 ENCSR201NQZ.CTBP1.K-562 278 bp overlap
Cebpa 1 dataset
ChIP BLaER1 ENCFF031ISE 255 bp overlap
EED 1 dataset
ChIP ProEs GSE59087.EED.ProEs 146 bp overlap
EOMES 1 dataset
ChIP hESC GSE26097.EOMES.hESC 223 bp overlap
ERG 1 dataset
ChIP VCaP_DHAT_18H GSE28950.ERG.VCaP_DHAT_18H 143 bp overlap
ETS1 2 datasets
ChIP CTV-1_DSG GSE128835.ETS1.CTV-1_DSG 113 bp overlap
ChIP CTV-1_DSG_SPI1-mut GSE128835.ETS1.CTV-1_DSG_SPI1-mut 240 bp overlap
ETV6 1 dataset
ChIP GM12878 ENCFF105ZMI 157 bp overlap
EZH2 2 datasets
ChIP DND41 ENCSR000ASW.EZH2.DND41 177 bp overlap
ChIP SU-DHL-5 GSE45982.EZH2.SU-DHL-5 124 bp overlap
FOXA2 3 datasets
ChIP DE DE-FOXA2-1 277 bp overlap
ChIP DE DE-FOXA2-1 326 bp overlap
ChIP DE DE-FOXA2-2 549 bp overlap
FOXM1 4 datasets
ChIP GM12878 ENCFF264DJE 93 bp overlap
ChIP GM12878 ENCFF264DJE 292 bp overlap
ChIP GM12878 ENCSR000BRU.FOXM1.GM12878 246 bp overlap
ChIP GM12878 ENCSR000BRU.FOXM1.GM12878 139 bp overlap
FOXP1 1 dataset
ChIP LNCaP GSE62492.FOXP1.LNCaP 239 bp overlap
GATA2 4 datasets
ChIP LNCaP GSE38391.GATA2.LNCaP 137 bp overlap
ChIP LNCaP GSE52725.GATA2.LNCaP 137 bp overlap
ChIP LNCaP_CSFCS GSE69043.GATA2.LNCaP_CSFCS 492 bp overlap
ChIP SH-SY5Y ENCSR000EYB.GATA2.SH-SY5Y 220 bp overlap
GATA3 1 dataset
ChIP Kelly GSE65664.GATA3.Kelly 203 bp overlap
GATA4 3 datasets
ChIP DE DE-GATA4-1 388 bp overlap
ChIP DE DE-GATA4-2 612 bp overlap
ChIP foregut GSE117136.GATA4.foregut 286 bp overlap
GATA6 4 datasets
ChIP DE DE-GATA6-1 272 bp overlap
ChIP DE DE-GATA6-2 707 bp overlap
ChIP DE_D2 S55-DE-d2-GATA6-exp2 597 bp overlap
ChIP endoderm_KO GSE117136.GATA6.endoderm_KO 382 bp overlap
HAND2 3 datasets
ChIP CLB-Ga GSE90683.HAND2.CLB-Ga 551 bp overlap
ChIP Kelly GSE94822.HAND2.Kelly 254 bp overlap
ChIP SK-N-BE2-C GSE94822.HAND2.SK-N-BE2-C 281 bp overlap
HDAC6 1 dataset
ChIP GM12878 ENCSR933EYC.HDAC6.GM12878 335 bp overlap
IKZF1 1 dataset
ChIP GM12878 ENCFF824TGK 187 bp overlap
IRF4 3 datasets
ChIP NCI-H929 GSE142493.IRF4.NCI-H929 117 bp overlap
ChIP NCI-H929 GSE56857.IRF4.NCI-H929 117 bp overlap
ChIP T-cell GSE136853.IRF4.T-cell 544 bp overlap
KDM1A 1 dataset
ChIP SH-SY5Y_B3 GSE58258.KDM1A.SH-SY5Y_B3 164 bp overlap
LARP7 2 datasets
ChIP GM12878 ENCFF513CEX 441 bp overlap
ChIP GM12878 ENCFF513CEX 365 bp overlap
MAX 2 datasets
ChIP GM12878 ENCFF849VCQ 413 bp overlap
ChIP P493-6_CMYC_1H GSE36354.MAX.P493-6_CMYC_1H 83 bp overlap
MED1 1 dataset
ChIP P493-6 GSE36354.MED1.P493-6 183 bp overlap
MEIS2 1 dataset
ChIP K-562 ENCSR851BNE.MEIS2.K-562 429 bp overlap
MLLT1 1 dataset
ChIP GM12878 ENCFF995GXC 839 bp overlap
MTA3 3 datasets
ChIP GM12878 ENCFF681QPL 645 bp overlap
ChIP GM12878 ENCFF681QPL 557 bp overlap
ChIP GM12878 ENCFF681QPL 340 bp overlap
MYC 1 dataset
ChIP P493-6_MST-312 GSE77061.MYC.P493-6_MST-312 207 bp overlap
MYCN 1 dataset
ChIP Kelly_sensitive GSE115249.MYCN.Kelly_sensitive 213 bp overlap
NCOA2 1 dataset
ChIP MCF-7 ERP000901.NCOA2.MCF-7 56 bp overlap
NFATC1 1 dataset
ChIP GM12878 ENCFF023CAZ 318 bp overlap
NFATC3 1 dataset
ChIP GM12878 ENCSR437GBJ.NFATC3.GM12878 121 bp overlap
NFIC 2 datasets
ChIP GM12878 ENCFF259FWL 375 bp overlap
ChIP GM12878 ENCSR000BRN.NFIC.GM12878 603 bp overlap
NIPBL 2 datasets
ChIP GM12878 GSE93080.NIPBL.GM12878 225 bp overlap
ChIP GM12878 GSE93080.NIPBL.GM12878 499 bp overlap
NR3C1 1 dataset
ChIP LNCaP_1F5_SIFOXA1 GSE30623.NR3C1.LNCaP_1F5_SIFOXA1 199 bp overlap
PAX3-FOXO1 1 dataset
ChIP RH4 GSE140115.PAX3-FOXO1.RH4 109 bp overlap
PAX5 2 datasets
ChIP GM12878 ENCSR000BHJ.PAX5.GM12878 218 bp overlap
ChIP GM12878 ENCSR000BHD.PAX5.GM12878 130 bp overlap
PBX2 2 datasets
ChIP K-562 ENCSR263DFP.PBX2.K-562 338 bp overlap
ChIP K562 ENCFF286KMN 261 bp overlap
PBX3 1 dataset
ChIP GM12878 ENCSR000BGR.PBX3.GM12878 124 bp overlap
PKNOX1 5 datasets
ChIP GM12878 ENCFF589FCY 413 bp overlap
ChIP GM12878 ENCFF589FCY 69 bp overlap
ChIP GM12878 ENCSR711XNY.PKNOX1.GM12878 391 bp overlap
ChIP GM12878 ENCSR711XNY.PKNOX1.GM12878 127 bp overlap
ChIP K-562 ENCSR115SMW.PKNOX1.K-562 294 bp overlap
PML 3 datasets
ChIP GM12878 ENCFF160JQZ 334 bp overlap
ChIP GM12878 ENCFF160JQZ 194 bp overlap
ChIP GM12878 ENCFF160JQZ 287 bp overlap
POLR2A 29 datasets
ChIP GM12878 ENCFF263VRI 445 bp overlap
ChIP GM12878 ENCFF412KAE 839 bp overlap
ChIP GM12878 ENCFF521FXC 839 bp overlap
ChIP GM12878 ENCFF631ERR 491 bp overlap
ChIP GM12878 ENCFF631ERR 340 bp overlap
ChIP GM12878 ENCFF631ERR 78 bp overlap
ChIP GM12878 ENCFF899QYP 470 bp overlap
ChIP GM12878 ENCFF899QYP 334 bp overlap
ChIP GM12891 ENCFF012SUT 600 bp overlap
ChIP GM12891 ENCFF127ICP 839 bp overlap
ChIP GM12891 ENCFF379FCI 701 bp overlap
ChIP GM12892 ENCFF245LYF 456 bp overlap
ChIP GM12892 ENCFF506PGQ 123 bp overlap
ChIP GM12892 ENCFF542ZFO 839 bp overlap
ChIP GM15510 ENCFF880HVJ 98 bp overlap
ChIP GM15510 ENCFF880HVJ 384 bp overlap
ChIP GM15510 ENCFF880HVJ 437 bp overlap
ChIP GM18505 ENCFF311CYB 55 bp overlap
ChIP GM18505 ENCFF311CYB 402 bp overlap
ChIP GM18505 ENCFF311CYB 347 bp overlap
ChIP GM18505 ENCFF311CYB 71 bp overlap
ChIP GM18526 ENCFF599EPS 431 bp overlap
ChIP GM18526 ENCFF599EPS 109 bp overlap
ChIP GM18951 ENCFF079KKO 255 bp overlap
ChIP GM19099 ENCFF726IBN 406 bp overlap
ChIP GM19099 ENCFF726IBN 291 bp overlap
ChIP GM19099 ENCFF726IBN 60 bp overlap
ChIP GM19193 ENCFF599VTO 367 bp overlap
ChIP transverse colon ENCFF098HBD 154 bp overlap
POU2F2 4 datasets
ChIP GM12878 ENCFF207RKY 199 bp overlap
ChIP GM12891 ENCFF166YPP 182 bp overlap
ChIP GM12891 ENCFF166YPP 311 bp overlap
ChIP GM12891 ENCSR000BII.POU2F2.GM12891 193 bp overlap
RELA 1 dataset
ChIP GM12878 ENCSR664POU.RELA.GM12878 291 bp overlap
RELB 2 datasets
ChIP GM12878 ENCFF217ADF 141 bp overlap
ChIP GM12878 ENCSR387QUV.RELB.GM12878 228 bp overlap
REST 3 datasets
ChIP GM12878 ENCFF943QPB 56 bp overlap
ChIP GM12878 ENCSR000BQS.REST.GM12878 155 bp overlap
ChIP GM12878 ENCSR000BQS.REST.GM12878 196 bp overlap
SMAD1 3 datasets
ChIP GM12878 ENCFF130NRZ 58 bp overlap
ChIP GM12878 ENCSR813DCK.SMAD1.GM12878 511 bp overlap
ChIP GM12878 ENCSR813DCK.SMAD1.GM12878 53 bp overlap
SMAD2_3 1 dataset
ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 341 bp overlap
SMAD5 3 datasets
ChIP GM12878 ENCFF178LKN 124 bp overlap
ChIP GM12878 ENCFF178LKN 423 bp overlap
ChIP GM12878 ENCFF178LKN 465 bp overlap
SMARCA4 5 datasets
ChIP A-549_AG15723 GSE132290.SMARCA4.A-549_AG15723 63 bp overlap
ChIP CTV-1_DSG GSE128835.SMARCA4.CTV-1_DSG 148 bp overlap
ChIP CTV-1_DSG_SPI1-mut GSE128835.SMARCA4.CTV-1_DSG_SPI1-mut 257 bp overlap
ChIP CTV-1_FLAG GSE128835.SMARCA4.CTV-1_FLAG 89 bp overlap
ChIP CTV-1_delQ GSE128835.SMARCA4.CTV-1_delQ 110 bp overlap
SNAI2 2 datasets
ChIP SMS-CTR_T48 GSE137168.SNAI2.SMS-CTR_T48 170 bp overlap
ChIP SMS-CTR_T48 GSE137168.SNAI2.SMS-CTR_T48 220 bp overlap
SOX17 1 dataset
ChIP DE_D2 DED2-SOX17_Batch_II 434 bp overlap
SOX17_M 1 dataset
ChIP DE_D2 DED2-SOX17-M_Batch_II 600 bp overlap
SOX2 2 datasets
ChIP LK2 GSE137459.SOX2.LK2 339 bp overlap
ChIP LK2_GFP GSE137459.SOX2.LK2_GFP 626 bp overlap
SPI1 13 datasets
ChIP CD34_FETAL GSE70660.SPI1.CD34_FETAL 50 bp overlap
ChIP CTV-1_FLAG_15perc GSE128835.SPI1.CTV-1_FLAG_15perc 147 bp overlap
ChIP CTV-1_delA GSE128835.SPI1.CTV-1_delA 91 bp overlap
ChIP CTV-1_delQ GSE128835.SPI1.CTV-1_delQ 170 bp overlap
ChIP CTV-1_delQA GSE128835.SPI1.CTV-1_delQA 82 bp overlap
ChIP GM12891 ENCSR000BIJ.SPI1.GM12891 63 bp overlap
ChIP HL-60 ENCFF645GBT 105 bp overlap
ChIP K-562 GSE70482.SPI1.K-562 57 bp overlap
ChIP Kasumi-1_SICTR GSE60130.SPI1.Kasumi-1_SICTR 113 bp overlap
ChIP NCI-H929 GSE56857.SPI1.NCI-H929 267 bp overlap
ChIP NCI-H929 GSE56857.SPI1.NCI-H929 285 bp overlap
ChIP dendrite GSE58864.SPI1.dendrite 81 bp overlap
ChIP monocyte_MACROPHAGE GSE31621.SPI1.monocyte_MACROPHAGE 50 bp overlap
STAT1 2 datasets
ChIP GM12878 ENCFF655XMZ 354 bp overlap
ChIP GM12878 ENCSR332EYT.STAT1.GM12878 314 bp overlap
STAT5A 1 dataset
ChIP GM12878 ENCFF267JUM 233 bp overlap
SUPT6H 1 dataset
ChIP HCT-116_Inhibitor GSE130509.SUPT6H.HCT-116_Inhibitor 261 bp overlap
TAF1 4 datasets
ChIP GM12878 ENCSR000BGS.TAF1.GM12878 151 bp overlap
ChIP GM12878 ENCSR000BGS.TAF1.GM12878 180 bp overlap
ChIP GM12878 ENCSR000BGS.TAF1.GM12878 192 bp overlap
ChIP GM12891 ENCSR000BIM.TAF1.GM12891 105 bp overlap
TCF3 2 datasets
ChIP GM12878 ENCSR000BQT.TCF3.GM12878 230 bp overlap
ChIP GM12878 ENCSR000BQT.TCF3.GM12878 159 bp overlap
TCF7 1 dataset
ChIP GM12878 ENCFF749DPM 59 bp overlap
TEAD4 1 dataset
ChIP hMSC-TERT4 GSE140782.TEAD4.hMSC-TERT4 61 bp overlap
VDR 1 dataset
ChIP LCLGM10861_CALCITRIOL GSE22484.VDR.LCLGM10861_CALCITRIOL 245 bp overlap
YY1 4 datasets
ChIP GM12878 ENCFF908JTL 333 bp overlap
ChIP GM12891 ENCSR000BKJ.YY1.GM12891 140 bp overlap
ChIP GM12892 ENCSR000BLT.YY1.GM12892 147 bp overlap
ChIP GM12892 ENCSR000BLT.YY1.GM12892 160 bp overlap
ZBED1 2 datasets
ChIP GM12878 ENCFF007OSW 190 bp overlap
ChIP GM12878 ENCFF007OSW 417 bp overlap
ZFX 2 datasets
ChIP HCT-116 GSE102616.ZFX.HCT-116 194 bp overlap
ChIP HCT-116 ENCSR503GVO.ZFX.HCT-116 195 bp overlap
ZNF687 1 dataset
ChIP GM12878 ENCSR859FDL.ZNF687.GM12878 722 bp overlap
ZNF707 1 dataset
ChIP HEK293T GSE78099.ZNF707.HEK293T 171 bp overlap
ZNF83 2 datasets
ChIP K-562 ENCSR257XVY.ZNF83.K-562 251 bp overlap
ChIP K562 ENCFF340RTV 669 bp overlap
ZXDB 1 dataset
ChIP HEK293 ENCSR559IOZ.ZXDB.HEK293 266 bp overlap
Huangfu Lab · Publications · Resources · Contact