chr3 : 127,209,659 – 127,210,613
954 bp 89 TFs 1 linked gene
This 954 bp open chromatin element is linked to PLXNA1 and is bound by 89 transcription factors.
Linked Genes
1 gene
Gene↕ Expression Dist. to TSS↑ Distance↕ Link type↕
PLXNA1 227.4 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.
chr3:127,204,659 – 127,215,613
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
89 transcription factors
Source
Cell type
AFF4 1 dataset
ChIP MCF-7 GSE144036.AFF4.MCF-7 246 bp overlap
AR 2 datasets
ChIP LNCaP-abl GSE39459.AR.LNCaP-abl 159 bp overlap
ChIP MDA-MB-453 ERP003503.AR.MDA-MB-453 199 bp overlap
BRD4 6 datasets
ChIP Kelly_resistant GSE103030.BRD4.Kelly_resistant 289 bp overlap
ChIP Kelly_sensitive GSE103030.BRD4.Kelly_sensitive 954 bp overlap
ChIP retina_AB1-FW15 GSE86981.BRD4.retina_AB1-FW15 293 bp overlap
ChIP retina_AB1-FW20 GSE86981.BRD4.retina_AB1-FW20 205 bp overlap
ChIP retina_AB1-RB GSE86981.BRD4.retina_AB1-RB 281 bp overlap
ChIP retina_AB1-RB GSE86981.BRD4.retina_AB1-RB 264 bp overlap
CHD1 1 dataset
ChIP hMSC-TERT_osteoblast GSE89179.CHD1.hMSC-TERT_osteoblast 284 bp overlap
CTCF 10 datasets
ChIP 786-O_NORMOXIA GSE78113.CTCF.786-O_NORMOXIA 236 bp overlap
ChIP Kelly_resistant GSE103030.CTCF.Kelly_resistant 115 bp overlap
ChIP Loucy ENCSR464DKE.CTCF.Loucy 176 bp overlap
ChIP OCI-Ly3 ENCSR756ZKG.CTCF.OCI-Ly3 312 bp overlap
ChIP WERI-Rb-1 ENCFF349QKF 231 bp overlap
ChIP WERI-Rb-1 ENCSR000DXW.CTCF.WERI-Rb-1 136 bp overlap
ChIP endodermal cell ENCFF471YCZ 446 bp overlap
ChIP leukemia GSE142161.CTCF.leukemia 300 bp overlap
ChIP leukemia_CEBPA-24h GSE142161.CTCF.leukemia_CEBPA-24h 307 bp overlap
ChIP leukemia_CEBPA-96h GSE142161.CTCF.leukemia_CEBPA-96h 205 bp overlap
CTCFL 2 datasets
ChIP Kelly_resistant GSE103030.CTCFL.Kelly_resistant 183 bp overlap
ChIP Kelly_shLUC-res GSE115248.CTCFL.Kelly_shLUC-res 325 bp overlap
Cebpa 2 datasets
ChIP BLaER1 ENCFF274GAT 251 bp overlap
ChIP BLaER1 ENCFF335XTP 257 bp overlap
Crx 1 dataset
Motif DE_24h DE_24h-Crx_MA0467.3 6 bp overlap
DNMT3B 1 dataset
ChIP HUES-8_TripleKO-TET1-2-3 GSE99346.DNMT3B.HUES-8_TripleKO-TET1-2-3 449 bp overlap
DPF2 2 datasets
ChIP GM12878 ENCSR509FWH.DPF2.GM12878 472 bp overlap
ChIP GM12878 ENCSR509FWH.DPF2.GM12878 286 bp overlap
E2F6 3 datasets
ChIP K-562 ENCSR000BLI.E2F6.K-562 95 bp overlap
ChIP WA01 ENCSR000BSI.E2F6.WA01 56 bp overlap
ChIP WA01 ENCSR000BSI.E2F6.WA01 138 bp overlap
ELF1 1 dataset
ChIP GM12878 ENCSR000BMB.ELF1.GM12878 366 bp overlap
EOMES 1 dataset
ChIP hESC GSE26097.EOMES.hESC 250 bp overlap
EP300 2 datasets
ChIP SK-N-SH ENCFF829RWA 373 bp overlap
ChIP SK-N-SH ENCSR000EHV.EP300.SK-N-SH 134 bp overlap
ERG 1 dataset
ChIP ME-1 GSE46044.ERG.ME-1 200 bp overlap
ESR1 9 datasets
ChIP Ishikawa_DMSO_D538G_clone3 GSE132426.ESR1.Ishikawa_DMSO_D538G_clone3 280 bp overlap
ChIP MCF-7_PaPE-1_OA GSE93510.ESR1.MCF-7_PaPE-1_OA 470 bp overlap
ChIP MCF-7_PaPE-1_OA GSE93510.ESR1.MCF-7_PaPE-1_OA 325 bp overlap
ChIP T-47D GSE148277.ESR1.T-47D 587 bp overlap
ChIP T-47D_Y537S GSE148277.ESR1.T-47D_Y537S 358 bp overlap
ChIP T-47D_Y537S GSE148277.ESR1.T-47D_Y537S 362 bp overlap
ChIP T-47D_Y537S_E2 GSE148277.ESR1.T-47D_Y537S_E2 238 bp overlap
ChIP U2OS_E2 GSE26110.ESR1.U2OS_E2 54 bp overlap
ChIP U2OS_E2 GSE26110.ESR1.U2OS_E2 173 bp overlap
EWSR1-FLI1 1 dataset
Motif DE_24h DE_24h-EWSR1-FLI1_MA0149.1 18 bp overlap
EZH2 4 datasets
ChIP Hep-3B2-1-7 GSE128137.EZH2.Hep-3B2-1-7 318 bp overlap
ChIP Karpas-422_CPI360-D4 GSE134136.EZH2.Karpas-422_CPI360-D4 272 bp overlap
ChIP SK-N-MC ENCFF674XUJ 132 bp overlap
ChIP SU-DHL-6 GSE134136.EZH2.SU-DHL-6 443 bp overlap
FEZF2 1 dataset
Motif DE_24h DE_24h-FEZF2_MA2341.1 8 bp overlap
FOXA2 1 dataset
ChIP DE DE-FOXA2-1 310 bp overlap
FOXH1 1 dataset
Motif DE_24h DE_24h-FOXH1_MA0479.2 8 bp overlap
GABPA 1 dataset
ChIP RWPE-1 GSE29808.GABPA.RWPE-1 184 bp overlap
GATA4 2 datasets
ChIP DE DE-GATA4-1 639 bp overlap
ChIP DE DE-GATA4-2 531 bp overlap
GATA6 10 datasets
ChIP DE DE-GATA6-1 636 bp overlap
ChIP DE DE-GATA6-2 721 bp overlap
ChIP DE_D1 S09-DE-d1-GATA6-exp1 774 bp overlap
ChIP DE_D1 S14-DE-d1-GATA6-exp1 214 bp overlap
ChIP DE_D1 S14-DE-d1-GATA6-exp1 376 bp overlap
ChIP DE_D1 S41-DE-d1-GATA6-exp2 713 bp overlap
ChIP DE_D2 S55-DE-d2-GATA6-exp2 726 bp overlap
ChIP HUES-8_DE_JNKi GSE109524.GATA6.HUES-8_DE_JNKi 954 bp overlap
ChIP HUES-8_DE_ctrl GSE109524.GATA6.HUES-8_DE_ctrl 774 bp overlap
ChIP endoderm_KO GSE117136.GATA6.endoderm_KO 462 bp overlap
GATAD2B 1 dataset
ChIP GM12878 ENCSR828NCB.GATAD2B.GM12878 124 bp overlap
GFI1 1 dataset
Motif DE_24h DE_24h-GFI1_MA0038.3 11 bp overlap
GLIS3 1 dataset
ChIP H9_plus GSE109562.GLIS3.H9_plus 476 bp overlap
GSC 1 dataset
Motif DE_24h DE_24h-GSC_MA0648.2 6 bp overlap
GSC2 1 dataset
Motif DE_24h DE_24h-GSC2_MA0891.2 6 bp overlap
Gfi1B 1 dataset
Motif DE_24h DE_24h-Gfi1B_MA0483.2 10 bp overlap
HAND2 1 dataset
ChIP SK-N-BE2-C GSE94822.HAND2.SK-N-BE2-C 196 bp overlap
HCFC1R1 1 dataset
ChIP cartilage GSE100311.HCFC1R1.cartilage 224 bp overlap
HDAC2 1 dataset
ChIP WA01 ENCSR000AVB.HDAC2.WA01 139 bp overlap
ISL2 1 dataset
Motif DE_24h DE_24h-ISL2_MA0914.2 6 bp overlap
JARID2 2 datasets
ChIP MRC-5_IPS25_CTR GSE48515.JARID2.MRC-5_IPS25_CTR 327 bp overlap
ChIP UTEIPS6 GSE48516.JARID2.UTEIPS6 100 bp overlap
JUN 5 datasets
ChIP DE_D1 S08-DE-d1-JUN-exp1 488 bp overlap
ChIP DE_D1 S13-DE-d1-JUN-exp1 461 bp overlap
ChIP DE_D1 S40-DE-d1-JUN-exp2 583 bp overlap
ChIP DE_D2 S02-DE-d2-JUN-exp1 727 bp overlap
ChIP HUES-8_DE_ctrl GSE109524.JUN.HUES-8_DE_ctrl 619 bp overlap
KMT2A 2 datasets
ChIP OCI-AML-3_DMSO GSE129636.KMT2A.OCI-AML-3_DMSO 201 bp overlap
ChIP RCH-ACV GSE83671.KMT2A.RCH-ACV 432 bp overlap
MAX 5 datasets
ChIP H1 ENCFF914VQY 357 bp overlap
ChIP MCF-7 ENCSR000BUL.MAX.MCF-7 129 bp overlap
ChIP NCI-H128 GSE41105.MAX.NCI-H128 165 bp overlap
ChIP NCI-H2171 GSE36354.MAX.NCI-H2171 400 bp overlap
ChIP NCI-H2171 GSE41105.MAX.NCI-H2171 292 bp overlap
MEIS1 1 dataset
Motif DE_24h DE_24h-MEIS1_MA0498.3 5 bp overlap
MXI1 1 dataset
ChIP SK-N-SH ENCSR000EIA.MXI1.SK-N-SH 151 bp overlap
MYB 2 datasets
ChIP DU528 GSE94000.MYB.DU528 211 bp overlap
ChIP MOLT-3 GSE59657.MYB.MOLT-3 159 bp overlap
MYC 2 datasets
ChIP MCF-7 ENCSR000DMQ.MYC.MCF-7 129 bp overlap
ChIP NCI-H2171 GSE36354.MYC.NCI-H2171 334 bp overlap
MYCN 8 datasets
ChIP BE2C GSE80151.MYCN.BE2C 306 bp overlap
ChIP COG-N-415 GSE138295.MYCN.COG-N-415 490 bp overlap
ChIP Kelly GSE94782.MYCN.Kelly 319 bp overlap
ChIP Kelly GSE94822.MYCN.Kelly 313 bp overlap
ChIP Kelly_sensitive GSE115249.MYCN.Kelly_sensitive 288 bp overlap
ChIP LA-N-5 GSE138295.MYCN.LA-N-5 416 bp overlap
ChIP SK-N-BE2-C GSE80151.MYCN.SK-N-BE2-C 306 bp overlap
ChIP SK-N-BE2-C GSE94822.MYCN.SK-N-BE2-C 187 bp overlap
NFKB1 2 datasets
ChIP HEK293T GSE129618.NFKB1.HEK293T 325 bp overlap
ChIP L1236 GSE63736.NFKB1.L1236 106 bp overlap
NFKB2 1 dataset
ChIP L1236 GSE63736.NFKB2.L1236 94 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
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
OTX1 1 dataset
Motif DE_24h DE_24h-OTX1_MA0711.2 6 bp overlap
PITX1 1 dataset
Motif DE_24h DE_24h-PITX1_MA0682.3 6 bp overlap
PITX3 1 dataset
Motif DE_24h DE_24h-PITX3_MA0714.2 6 bp overlap
POU5F1 1 dataset
ChIP DE_D1 DED1-OCT4_Batch_II 719 bp overlap
POU5F1_M 1 dataset
ChIP DE_D1 DED1-OCT4-M_Batch_II 919 bp overlap
PRDM9 1 dataset
Motif DE_24h DE_24h-PRDM9_MA1723.2 20 bp overlap
PTBP1 2 datasets
ChIP Hep-G2 ENCSR156APP.PTBP1.Hep-G2 320 bp overlap
ChIP Hep-G2 GSE120104.PTBP1.Hep-G2 320 bp overlap
RCOR1 1 dataset
ChIP SK-N-SH ENCSR009TKN.RCOR1.SK-N-SH 157 bp overlap
RELB 1 dataset
ChIP GM12878 ENCSR387QUV.RELB.GM12878 140 bp overlap
RHOXF1 1 dataset
Motif DE_24h DE_24h-RHOXF1_MA0719.2 6 bp overlap
RUNX1 1 dataset
ChIP AML_age-50-70 GSE111821.RUNX1.AML_age-50-70 398 bp overlap
RUNX1T1 1 dataset
ChIP Kasumi-1 GSE115115.RUNX1T1.Kasumi-1 182 bp overlap
SMAD2 4 datasets
ChIP endoderm GSE29422.SMAD2.endoderm 248 bp overlap
ChIP hESC GSE29422.SMAD2.hESC 227 bp overlap
ChIP hESC_YAP-_activinA_15h GSE99202.SMAD2.hESC_YAP-_activinA_15h 719 bp overlap
ChIP hESC_activinA_15h GSE99202.SMAD2.hESC_activinA_15h 448 bp overlap
SMAD2_3 5 datasets
ChIP DE_D1 S07-DE-d1-SMAD2_3-exp1 924 bp overlap
ChIP DE_D1 S12-DE-d1-SMAD2_3-exp1 954 bp overlap
ChIP DE_D1 S39-DE-d1-SMAD2_3-exp2 954 bp overlap
ChIP DE_D2 S01-DE-d2-SMAD2_3-exp1 954 bp overlap
ChIP DE_D2 S53-DE-d2-SMAD2_3-exp2 954 bp overlap
SMAD3 5 datasets
ChIP BG03_DIFF_2H GSE36578.SMAD3.BG03_DIFF_2H 264 bp overlap
ChIP BG03_DIFF_48H GSE36578.SMAD3.BG03_DIFF_48H 145 bp overlap
ChIP BG03_DIFF_48H GSE36578.SMAD3.BG03_DIFF_48H 284 bp overlap
ChIP endoderm GSE29422.SMAD3.endoderm 215 bp overlap
ChIP hESC GSE29422.SMAD3.hESC 168 bp overlap
SMAD4 2 datasets
ChIP endoderm GSE29422.SMAD4.endoderm 250 bp overlap
ChIP hESC GSE29422.SMAD4.hESC 172 bp overlap
SMARCA4 2 datasets
ChIP J-Lat_GFP-Clone-A72_DMSO GSE100266.SMARCA4.J-Lat_GFP-Clone-A72_DMSO 395 bp overlap
ChIP hiPSC GSE124903.SMARCA4.hiPSC 159 bp overlap
SMARCC1 2 datasets
ChIP DE_D1 S10-DE-d1-BAF155-exp1 385 bp overlap
ChIP DE_D1 S15-DE-d1-BAF155-exp1 455 bp overlap
SMC3 1 dataset
ChIP neural ENCSR404BPV.SMC3.neural 287 bp overlap
SOX10 1 dataset
Motif DE_24h DE_24h-SOX10_MA0442.3 6 bp overlap
SOX17_M 1 dataset
ChIP DE_D2 DED2-SOX17-M_Batch_II 398 bp overlap
SP5 1 dataset
Motif DE_24h DE_24h-SP5_MA1965.2 6 bp overlap
SUZ12 4 datasets
ChIP CRL-7250_shSS18-SSX GSE108025.SUZ12.CRL-7250_shSS18-SSX 117 bp overlap
ChIP CRL-7250_shSS18-SSX GSE108025.SUZ12.CRL-7250_shSS18-SSX 352 bp overlap
ChIP CRL-7250_shSS18-SSX GSE108025.SUZ12.CRL-7250_shSS18-SSX 216 bp overlap
ChIP Karpas-422_CPI360-D8 GSE134136.SUZ12.Karpas-422_CPI360-D8 375 bp overlap
T 2 datasets
ChIP H9_ENDODERM GSE60606.T.H9_ENDODERM 214 bp overlap
ChIP H9_MESODERM GSE60606.T.H9_MESODERM 280 bp overlap
TAL1 1 dataset
ChIP MOLT-3 GSE59657.TAL1.MOLT-3 168 bp overlap
TFAP2B 1 dataset
ChIP SK-N-SH ENCFF869XXQ 216 bp overlap
TRIM28 1 dataset
ChIP AF22 GSE84259.TRIM28.AF22 283 bp overlap
TWIST1 2 datasets
ChIP BE2C GSE80151.TWIST1.BE2C 287 bp overlap
ChIP SK-N-BE2-C GSE80151.TWIST1.SK-N-BE2-C 287 bp overlap
YY1 1 dataset
ChIP Huh-7 GSE97411.YY1.Huh-7 438 bp overlap
ZBTB48 1 dataset
ChIP U2OS_ZBTB48-KO GSE96776.ZBTB48.U2OS_ZBTB48-KO 298 bp overlap
ZEB1 1 dataset
ChIP GM12878 ENCSR000BND.ZEB1.GM12878 137 bp overlap
ZIC2 1 dataset
ChIP HEK293 ENCFF033NQQ 684 bp overlap
ZNF16 1 dataset
Motif DE_24h DE_24h-ZNF16_MA1654.2 21 bp overlap
ZNF257 1 dataset
Motif DE_24h DE_24h-ZNF257_MA1710.2 10 bp overlap
ZNF354C 1 dataset
Motif DE_24h DE_24h-ZNF354C_MA0130.1 6 bp overlap
ZNF449 1 dataset
Motif DE_24h DE_24h-ZNF449_MA1656.2 10 bp overlap
Zic1::Zic2 1 dataset
Motif DE_24h DE_24h-Zic1Zic2_MA1628.2 7 bp overlap
Zic2 1 dataset
Motif DE_24h DE_24h-Zic2_MA1629.2 9 bp overlap
Zic3 1 dataset
Motif DE_24h DE_24h-Zic3_MA0697.3 7 bp overlap
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