Variant report

Variant	rs9865905
Chromosome Location	chr3:156649594-156649595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10212230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10936040	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10936043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11709901	0.91[ASN][1000 genomes]
rs11712111	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12629380	0.95[ASN][1000 genomes]
rs12634915	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12638253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13068223	0.84[JPT][hapmap]
rs13070271	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs13088978	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1320011	0.94[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs13322318	0.83[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1384538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1574980	0.94[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs17382070	0.94[ASN][1000 genomes]
rs1995425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2060015	0.89[ASN][1000 genomes]
rs2321290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2321292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2321293	0.83[ASN][1000 genomes]
rs2321455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2874488	0.84[JPT][hapmap]
rs2874494	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2874495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs344073	0.84[JPT][hapmap]
rs344079	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs344080	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs344082	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs344084	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs344087	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs34667021	0.91[ASN][1000 genomes]
rs3910072	0.86[ASN][1000 genomes]
rs4315647	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs453219	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs4589888	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680311	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs4680312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680314	0.81[ASN][1000 genomes]
rs4680317	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62275765	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6762708	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs6765353	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs6780427	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6784421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6803064	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7615304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7622309	0.81[ASN][1000 genomes]
rs7637701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638330	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs7638625	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9812895	0.93[ASN][1000 genomes]
rs9814813	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9818684	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs9820830	0.83[CEU][hapmap]
rs9837038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9844054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9847187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9858158	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9866373	0.97[ASN][1000 genomes]
rs9867621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9870137	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs9871817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9875585	0.90[ASN][1000 genomes]
rs9875688	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9876010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9876148	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs987724	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9878585	1.00[CHB][hapmap];1.00[JPT][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	nsv592120	chr3:156626091-156691604	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9865905	LINC00886	cis	Stomach	GTEx
rs9865905	LINC00886	cis	Artery Tibial	GTEx
rs9865905	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs9865905	LINC00886	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156646600-156652600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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