Variant report

Variant	rs7641185
Chromosome Location	chr3:105169118-105169119
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105166673..105169567-chr3:105177342..105179589,2	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1036581	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12488994	0.88[CHD][hapmap]
rs13100098	0.88[CHD][hapmap]
rs13100997	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1438538	0.88[CHD][hapmap]
rs2033802	0.94[ASW][hapmap];0.96[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2053307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178407	0.81[CHD][hapmap]
rs4894924	0.82[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6767277	0.88[CHD][hapmap]
rs6769302	0.88[CHD][hapmap]
rs6779807	0.88[CHD][hapmap]
rs6790159	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7428824	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7431531	0.88[CHD][hapmap]
rs7644273	0.82[CHD][hapmap]
rs9288803	0.94[ASW][hapmap];0.94[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs9827147	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9827196	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9864062	0.96[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9870921	0.96[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105137400-105178600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:105144400-105185000	Weak transcription	Aorta	Aorta
3	chr3:105150800-105177800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:105155800-105177600	Weak transcription	HSMM	muscle
5	chr3:105163400-105177200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:105163600-105177400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr3:105167400-105170800	Enhancers	Brain Angular Gyrus	brain
8	chr3:105167600-105174400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:105167800-105174800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:105167800-105176600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:105167800-105177400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:105167800-105177400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr3:105167800-105185000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:105168000-105177800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr3:105168000-105178600	Weak transcription	A549	lung
16	chr3:105168200-105171000	Enhancers	Brain Substantia Nigra	brain
17	chr3:105168200-105179400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:105168400-105169400	Enhancers	Brain Cingulate Gyrus	brain
19	chr3:105169000-105169200	Enhancers	Brain Anterior Caudate	brain
20	chr3:105169000-105169400	Flanking Active TSS	Brain Hippocampus Middle	brain

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