Variant report

Variant	rs4869631
Chromosome Location	chr5:35777067-35777068
allele	A/G
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	FOS	chr5:35776998-35777164	MCF10A-Er-Src	breast:	n/a	chr5:35777064-35777073 chr5:35777061-35777072 chr5:35777064-35777074 chr5:35777066-35777073 chr5:35777063-35777074
2	CTCF	chr5:35777051-35777097	Pancreas_OC	pancreas:	n/a	n/a
3	FOS	chr5:35776949-35777108	MCF10A-Er-Src	breast:	n/a	chr5:35777064-35777073 chr5:35777061-35777072 chr5:35777064-35777074 chr5:35777066-35777073 chr5:35777063-35777074
4	GATA3	chr5:35776966-35777279	T-47D	breast:	n/a	chr5:35777063-35777072

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:35775517..35778648-chr5:35922425..35925646,3	MCF-7	breast:

Variant related genes	Relation type
SPEF2	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10042959	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10043875	0.90[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12519864	0.82[TSI][hapmap]
rs16902391	0.82[TSI][hapmap]
rs16902406	0.82[TSI][hapmap]
rs2361391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2361392	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs4128903	0.87[AMR][1000 genomes]
rs4129892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4130605	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4130606	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131256	0.90[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes]
rs4242258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4869466	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4869619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57588520	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62353696	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451212	0.90[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6451214	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451215	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6451216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6876874	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6888367	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6888729	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6893048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6895801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6896356	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6897787	0.87[YRI][hapmap]
rs7380557	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7380587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7443019	0.80[EUR][1000 genomes]
rs7443130	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs7447258	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7448303	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs7710187	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7736028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9292602	1.00[GIH][hapmap]
rs931554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525477	chr5:35530905-35792990	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35771000-35781800	Weak transcription	Brain Anterior Caudate	brain
2	chr5:35772200-35777400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:35772400-35780600	Weak transcription	HSMM	muscle
4	chr5:35772800-35778000	Weak transcription	Fetal Thymus	thymus
5	chr5:35772800-35778000	Weak transcription	Thymus	Thymus
6	chr5:35774200-35777200	Weak transcription	Primary T cells from cord blood	blood
7	chr5:35774400-35777200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:35774600-35780800	Weak transcription	NHDF-Ad	bronchial
9	chr5:35774600-35781000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:35775000-35779600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr5:35775400-35777400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr5:35776400-35777600	Enhancers	Hela-S3	cervix
13	chr5:35776800-35777600	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:35776800-35780400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr5:35777000-35777200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr5:35777000-35777200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr5:35777000-35777200	Enhancers	HMEC	breast
18	chr5:35777000-35777400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr5:35777000-35777400	Enhancers	NHLF	lung
20	chr5:35777000-35777600	Enhancers	Osteobl	bone
21	chr5:35777000-35778000	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr5:35777000-35778000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr5:35777000-35778000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr5:35777000-35778200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:35777000-35780400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr5:35777000-35780600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:35777000-35780800	Weak transcription	HUVEC	blood vessel

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