Variant report

Variant	rs4851170
Chromosome Location	chr2:99504323-99504324
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10169003	0.94[EUR][1000 genomes]
rs10172158	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10178956	0.98[ASN][1000 genomes]
rs10181972	0.94[EUR][1000 genomes]
rs10188156	0.88[EUR][1000 genomes]
rs10192266	0.80[AMR][1000 genomes]
rs11123755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11887536	0.91[EUR][1000 genomes]
rs11893888	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12468024	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12474283	0.84[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12712033	0.84[JPT][hapmap]
rs12712035	0.83[JPT][hapmap];0.87[EUR][1000 genomes]
rs12712036	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs12712038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712039	0.89[EUR][1000 genomes]
rs12712041	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12712043	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13004700	0.84[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13004923	0.94[EUR][1000 genomes]
rs13005124	0.85[CHB][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13011428	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13025076	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13025913	0.93[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13028500	0.90[CHB][hapmap];0.80[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1356424	0.80[EUR][1000 genomes]
rs1581250	0.94[EUR][1000 genomes]
rs1581251	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1607256	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17758170	0.81[CEU][hapmap]
rs1878585	0.94[EUR][1000 genomes]
rs1878589	0.81[CEU][hapmap]
rs1976766	0.91[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];0.83[EUR][1000 genomes]
rs4263159	0.80[CEU][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs4311103	0.82[CHB][hapmap]
rs4850888	0.87[EUR][1000 genomes]
rs4850889	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851162	0.88[EUR][1000 genomes]
rs4851163	0.88[EUR][1000 genomes]
rs4851167	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851171	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];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851174	0.81[AMR][1000 genomes]
rs4851175	0.81[AMR][1000 genomes]
rs4851177	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56125264	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6419564	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6542838	0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs6542839	0.84[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs6542841	0.84[CEU][hapmap]
rs6542843	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6711022	0.83[EUR][1000 genomes]
rs6713991	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs6714243	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6717372	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719634	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs6724477	0.81[CEU][hapmap];0.86[GIH][hapmap];0.83[MEX][hapmap]
rs6726156	0.83[EUR][1000 genomes]
rs6739176	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6739503	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6742047	0.81[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];0.88[EUR][1000 genomes]
rs7608889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[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];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs981601	0.80[CEU][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes]
rs981602	0.80[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.87[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
rs4851170	C2orf15	cis	parietal	SCAN
rs4851170	TSGA10	cis	multi-tissue	Pritchard
rs4851170	LIPT1	cis	parietal	SCAN
rs4851170	FAHD2B	cis	parietal	SCAN
rs4851170	MAL	cis	parietal	SCAN
rs4851170	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99497800-99505600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:99500000-99517000	Weak transcription	Gastric	stomach
3	chr2:99502600-99504400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain

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