Variant report

Variant	rs4851171
Chromosome Location	chr2:99510817-99510818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99509338..99511041-chr2:99519600..99521247,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10169003	0.94[EUR][1000 genomes]
rs10172158	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178956	0.98[ASN][1000 genomes]
rs10181972	0.94[EUR][1000 genomes]
rs10188156	0.87[EUR][1000 genomes]
rs11123755	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887536	0.91[EUR][1000 genomes]
rs11893888	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12468024	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12474283	0.84[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12712033	0.84[JPT][hapmap]
rs12712035	0.83[JPT][hapmap];0.86[EUR][1000 genomes]
rs12712036	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs12712038	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712039	0.89[EUR][1000 genomes]
rs12712041	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12712043	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13004700	0.84[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13004923	0.94[EUR][1000 genomes]
rs13005124	0.85[CHB][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13011428	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13025076	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13025913	0.92[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13028500	0.90[CHB][hapmap];0.80[JPT][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1581250	0.94[EUR][1000 genomes]
rs1581251	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1607256	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17758170	0.81[CEU][hapmap]
rs1878585	0.94[EUR][1000 genomes]
rs1878589	0.81[CEU][hapmap]
rs1976766	0.90[AMR][1000 genomes]
rs1983352	0.86[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs2280256	0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs4263159	0.80[CEU][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs4311103	0.82[CHB][hapmap]
rs4850888	0.86[EUR][1000 genomes]
rs4850889	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851162	0.87[EUR][1000 genomes]
rs4851163	0.87[EUR][1000 genomes]
rs4851167	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851170	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851173	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851174	0.80[AMR][1000 genomes]
rs4851175	0.80[AMR][1000 genomes]
rs4851177	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56125264	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6419564	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6542838	0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs6542839	0.84[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs6542841	0.84[CEU][hapmap]
rs6542843	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6711022	0.82[EUR][1000 genomes]
rs6713991	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs6714243	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6717372	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719634	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6724477	0.81[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap]
rs6726156	0.83[EUR][1000 genomes]
rs6739176	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6739503	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6742047	0.80[AMR][1000 genomes]
rs6757098	0.84[CEU][hapmap]
rs6760065	0.84[CEU][hapmap]
rs7423519	0.81[CEU][hapmap]
rs7579189	0.80[CEU][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs7608889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs883773	0.84[CEU][hapmap]
rs925887	0.84[ASW][hapmap];0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.89[TSI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs981601	0.80[CEU][hapmap];0.84[JPT][hapmap];0.87[EUR][1000 genomes]
rs981602	0.80[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582518	chr2:99498774-99546355	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4851171	FAHD2B	cis	parietal	SCAN
rs4851171	MAL	cis	parietal	SCAN
rs4851171	LIPT1	cis	parietal	SCAN
rs4851171	C2orf15	cis	parietal	SCAN
rs4851171	TSGA10	cis	Lymphoblastoid	GTEx
rs4851171	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99500000-99517000	Weak transcription	Gastric	stomach
2	chr2:99509400-99511200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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