Variant report

Variant	rs12634915
Chromosome Location	chr3:156692235-156692236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156689383..156692274-chr3:156693134..156695144,2	MCF-7	breast:

Extended variants
information (count: 88 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10212230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10936040	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs10936043	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.99[ASN][1000 genomes]
rs11707041	0.89[ASN][1000 genomes]
rs11707914	0.81[AFR][1000 genomes]
rs11709901	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712111	0.86[ASN][1000 genomes]
rs11927500	0.81[YRI][hapmap]
rs12629380	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12638253	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.89[ASN][1000 genomes]
rs13070271	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs13088978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1320011	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs13321802	0.81[YRI][hapmap]
rs13322318	0.92[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1384538	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1574980	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs16826858	0.81[YRI][hapmap]
rs16826899	0.81[YRI][hapmap]
rs17382070	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1995425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2060015	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2321290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2321292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2321455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2633815	0.81[YRI][hapmap]
rs2874488	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs2874494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2874495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs344073	0.83[JPT][hapmap]
rs344076	0.81[YRI][hapmap]
rs344078	0.81[YRI][hapmap]
rs344079	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344080	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344082	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs344083	0.81[YRI][hapmap]
rs344084	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344087	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344092	0.81[YRI][hapmap]
rs34667021	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3910072	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4315647	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs453219	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs4589888	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680311	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs4680312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4680317	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs491423	0.81[YRI][hapmap]
rs62275765	0.82[ASN][1000 genomes]
rs6441099	0.81[YRI][hapmap]
rs6441103	0.81[YRI][hapmap]
rs6762708	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs6763644	0.81[YRI][hapmap]
rs6765353	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs6780427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6784421	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6786167	0.81[YRI][hapmap]
rs6787535	0.81[YRI][hapmap]
rs6792917	0.81[YRI][hapmap]
rs6803064	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7615304	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7630909	0.81[YRI][hapmap]
rs7635521	0.81[YRI][hapmap]
rs7637701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7638330	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7638625	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812895	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9814813	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap]
rs9818684	0.89[CEU][hapmap];0.80[JPT][hapmap];0.86[TSI][hapmap]
rs9820830	0.85[CEU][hapmap]
rs9837038	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs9844054	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9861359	0.81[YRI][hapmap]
rs9865905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9866373	0.93[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9870137	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9871817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9875585	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875688	0.87[ASN][1000 genomes]
rs9876010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9876148	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs987724	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap]
rs9878585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9878709	0.81[YRI][hapmap]

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	nsv829765	chr3:156568263-156718496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12634915	LINC00886	cis	Stomach	GTEx
rs12634915	LINC00886	cis	lung	GTEx
rs12634915	LINC00886	cis	Esophagus Muscularis	GTEx
rs12634915	LINC00886	cis	Artery Aorta	GTEx
rs12634915	LINC00886	cis	Artery Tibial	GTEx
rs12634915	LINC00886	cis	Adipose Subcutaneous	GTEx
rs12634915	LINC00886	cis	Nerve Tibial	GTEx
rs12634915	LINC00886	cis	Muscle Skeletal	GTEx
rs12634915	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156691400-156692400	Enhancers	HMEC	breast
2	chr3:156691400-156692400	Enhancers	NHEK	skin
3	chr3:156691400-156692800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:156691800-156693000	Enhancers	GM12878-XiMat	blood
5	chr3:156692200-156692400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:156692200-156694000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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