Variant report

Variant	rs10511171
Chromosome Location	chr3:98713265-98713266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:98536035..98537025-chr3:98712684..98713619,5	K562	blood:
2	chr3:98535012..98536001-chr3:98712960..98713772,2	MCF-7	breast:
3	chr3:98536449..98537173-chr3:98712702..98713434,3	MCF-7	breast:
4	chr3:98543087..98543918-chr3:98712722..98713277,2	MCF-7	breast:
5	chr3:98536046..98537400-chr3:98712632..98713675,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000057019	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10433438	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10511169	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10935518	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.86[ASN][1000 genomes]
rs10935542	0.84[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10935564	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10935610	0.93[AMR][1000 genomes]
rs11708475	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11716000	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11716007	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11716281	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11716579	0.86[ASN][1000 genomes]
rs11719660	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11914591	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11916285	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap]
rs11918243	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11918944	0.94[ASN][1000 genomes]
rs11920205	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11920327	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11922078	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923486	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11923805	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11928233	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12203	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs13069458	0.94[ASN][1000 genomes]
rs1440154	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs1471588	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16840260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17212369	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17213336	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];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17278047	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17278278	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17852693	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1822017	1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs1827158	0.84[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55650073	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55662129	0.86[ASN][1000 genomes]
rs55730510	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55764252	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55988144	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56290036	0.86[ASN][1000 genomes]
rs56322058	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62276861	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62276862	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62276864	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276869	0.94[ASN][1000 genomes]
rs62276879	0.88[ASN][1000 genomes]
rs62276883	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276884	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276885	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276888	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62276909	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62276944	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62279661	0.84[AMR][1000 genomes]
rs6440159	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6440253	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66517942	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6805605	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73138027	0.86[ASN][1000 genomes]
rs73138030	0.86[ASN][1000 genomes]
rs73138048	0.86[ASN][1000 genomes]
rs73138053	0.86[ASN][1000 genomes]
rs73138055	0.86[ASN][1000 genomes]
rs73138058	0.81[ASN][1000 genomes]
rs73138063	0.86[ASN][1000 genomes]
rs73138082	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73140009	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73140027	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73140032	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7432439	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7614892	0.86[ASN][1000 genomes]
rs7629550	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7638009	0.94[ASN][1000 genomes]
rs7642785	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs982291	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1007486	chr3:98597738-99249081	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10511171	OR5K2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98705600-98716400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:98711000-98721200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:98712400-98713600	Enhancers	A549	lung
4	chr3:98712400-98713800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:98712800-98723000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:98713200-98721000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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