Variant report

Variant	rs12375254
Chromosome Location	chr8:125054365-125054366
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr8:125054164-125054658	SK-N-SH	brain:	n/a	n/a
2	EP300	chr8:125051759-125055472	SK-N-SH	brain:	n/a	chr8:125054259-125054267 chr8:125054847-125054861
3	POLR2A	chr8:125054252-125054607	SK-N-SH	brain:	n/a	n/a
4	MXI1	chr8:125052934-125054972	SK-N-SH	brain:	n/a	n/a
5	EP300	chr8:125054211-125054780	SK-N-SH_RA	brain:	n/a	chr8:125054259-125054267
6	RAD21	chr8:125054229-125054490	SK-N-SH_RA	brain:	n/a	n/a
7	TCF12	chr8:125053235-125054858	SK-N-SH	brain:	n/a	n/a
8	TCF12	chr8:125054168-125054713	SK-N-SH	brain:	n/a	n/a
9	GATA2	chr8:125053424-125054949	SH-SY5Y	brain:	n/a	n/a
10	GATA3	chr8:125054227-125054819	SH-SY5Y	brain:	n/a	n/a
11	GATA3	chr8:125054109-125054822	SK-N-SH	brain:	n/a	n/a
12	EP300	chr8:125054172-125054756	SK-N-SH_RA	brain:	n/a	chr8:125054259-125054267

No.	Distal block	Cell Line	Cell type
1	chr8:125052912..125056665-chr8:125383684..125385533,3	MCF-7	breast:
2	chr8:125048985..125052591-chr8:125053625..125056640,3	MCF-7	breast:
3	chr8:125053217..125056265-chr8:125057070..125060007,3	MCF-7	breast:
4	chr8:125050340..125052770-chr8:125053493..125055124,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254249	TF binding region
FER1L6-AS1	TF binding region
ENSG00000164983	Chromatin interaction
ENSG00000254249	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10094266	0.84[EUR][1000 genomes]
rs10094533	0.80[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs10102566	0.80[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs10106600	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs10113772	0.80[EUR][1000 genomes]
rs1073178	0.80[CEU][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs1075051	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs10808530	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs10808531	0.84[EUR][1000 genomes]
rs10956163	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs10956164	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs11984962	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12541155	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs12545670	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs13251412	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs13254252	0.83[EUR][1000 genomes]
rs13254498	0.80[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs13258808	0.80[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13258930	0.80[EUR][1000 genomes]
rs13261097	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs13263969	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs13269044	0.80[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs2069078	0.80[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs3886123	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4242353	0.89[CEU][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4294164	0.80[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs4311644	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4330676	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs4345538	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs4389914	1.00[CEU][hapmap];0.89[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4392878	1.00[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4404895	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs4410885	0.84[EUR][1000 genomes]
rs4412351	0.80[CEU][hapmap];0.82[EUR][1000 genomes]
rs4430074	0.80[CEU][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs4446721	0.86[TSI][hapmap]
rs4460351	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs4483140	0.80[CEU][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4484683	0.84[EUR][1000 genomes]
rs4510842	0.81[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4576412	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4870886	0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4871451	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4871452	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4871453	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4871454	1.00[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4871457	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4871458	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4871459	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4871460	0.80[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs4871461	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs4871462	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs59583746	0.83[EUR][1000 genomes]
rs6470214	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6470216	0.80[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs6470217	0.84[EUR][1000 genomes]
rs6470218	0.83[EUR][1000 genomes]
rs6470219	0.80[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs6470220	0.82[EUR][1000 genomes]
rs6470221	0.80[CEU][hapmap]
rs6983060	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6984093	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6987082	0.84[EUR][1000 genomes]
rs6991629	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs6995745	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7001300	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7003992	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7005123	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs7007739	0.80[CEU][hapmap];0.81[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs7009406	0.80[CEU][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs7010375	0.80[CEU][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs7012186	0.80[CEU][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs7013226	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs7815620	0.80[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs7815768	0.80[EUR][1000 genomes]
rs7816075	0.84[EUR][1000 genomes]
rs7822018	0.80[CEU][hapmap]
rs7825506	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7826405	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs7831422	1.00[CEU][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7832499	0.80[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs7836974	0.83[EUR][1000 genomes]
rs7840702	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7841692	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7842213	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9297683	0.84[EUR][1000 genomes]
rs9297684	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs9297685	0.80[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs9643188	0.80[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:125050600-125054800	Enhancers	Fetal Intestine Small	intestine
2	chr8:125051200-125054800	Enhancers	Fetal Intestine Large	intestine
3	chr8:125051400-125054400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr8:125051400-125054400	Enhancers	Fetal Muscle Leg	muscle
5	chr8:125051600-125054400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr8:125052000-125054400	Enhancers	Primary hematopoietic stem cells	blood
7	chr8:125052000-125054400	Enhancers	Placenta Amnion	Placenta Amnion
8	chr8:125052200-125054400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:125052200-125054600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr8:125052600-125083600	Weak transcription	Gastric	stomach
11	chr8:125053000-125060400	Weak transcription	Left Ventricle	heart
12	chr8:125053600-125054600	Enhancers	Brain Germinal Matrix	brain
13	chr8:125053600-125058600	Enhancers	Fetal Heart	heart
14	chr8:125053800-125056200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr8:125053800-125059800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr8:125053800-125062400	Weak transcription	Stomach Mucosa	stomach
17	chr8:125054000-125054400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr8:125054000-125055400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:125054200-125056400	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr8:125054200-125056400	Weak transcription	A549	lung
21	chr8:125054200-125061000	Weak transcription	Fetal Stomach	stomach

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