Variant report

Variant	rs12497400
Chromosome Location	chr3:59986922-59986923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10510826	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12152244	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12487051	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12495052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12495662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs13314734	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17061683	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17061684	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17061708	0.93[MEX][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs17061716	0.93[MEX][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs17254065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17254231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17254574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17255191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17310854	1.00[ASN][1000 genomes]
rs17311592	1.00[ASN][1000 genomes]
rs17312006	1.00[ASN][1000 genomes]
rs17319929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17320006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17375746	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17376950	1.00[ASN][1000 genomes]
rs17377293	1.00[ASN][1000 genomes]
rs17394135	1.00[CHB][hapmap]
rs213292	1.00[CHB][hapmap]
rs213293	1.00[CHB][hapmap]
rs213424	1.00[CHB][hapmap]
rs3772504	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3772506	0.84[GIH][hapmap]
rs3772507	0.84[GIH][hapmap]
rs4411839	1.00[CHB][hapmap]
rs5007870	1.00[ASN][1000 genomes]
rs57249968	1.00[ASN][1000 genomes]
rs57561694	1.00[ASN][1000 genomes]
rs58024458	0.86[EUR][1000 genomes]
rs58526463	1.00[ASN][1000 genomes]
rs59871933	1.00[ASN][1000 genomes]
rs60287158	1.00[ASN][1000 genomes]
rs62238355	1.00[ASN][1000 genomes]
rs62238356	1.00[ASN][1000 genomes]
rs62238357	1.00[ASN][1000 genomes]
rs62238368	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62238369	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62238370	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62238371	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62240079	1.00[ASN][1000 genomes]
rs62240080	1.00[ASN][1000 genomes]
rs62240081	1.00[ASN][1000 genomes]
rs62240082	1.00[ASN][1000 genomes]
rs62240083	1.00[ASN][1000 genomes]
rs62240086	1.00[ASN][1000 genomes]
rs62240087	1.00[ASN][1000 genomes]
rs62240088	1.00[ASN][1000 genomes]
rs62240089	1.00[ASN][1000 genomes]
rs62240090	1.00[ASN][1000 genomes]
rs62240091	1.00[ASN][1000 genomes]
rs62240113	1.00[ASN][1000 genomes]
rs62240115	1.00[ASN][1000 genomes]
rs62240117	1.00[ASN][1000 genomes]
rs62240119	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6767115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6797938	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6798364	1.00[ASN][1000 genomes]
rs6800973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[ASN][1000 genomes]
rs72877063	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612646	1.00[ASW][hapmap];0.86[MEX][hapmap];1.00[AFR][1000 genomes]
rs802773	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv876838	chr3:59952152-59999690	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590388	chr3:59957252-60018326	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv590389	chr3:59981525-59998389	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59967400-59993000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:59980600-59992800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:59983000-59993200	Weak transcription	Dnd41	blood
4	chr3:59983400-59987200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:59985000-59988600	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr3:59985600-59989200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:59985800-59988600	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:59985800-59993000	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr3:59986000-59987600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:59986200-59987000	Enhancers	Fetal Thymus	thymus
11	chr3:59986200-59988200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:59986600-59987000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:59986600-59987200	Enhancers	Thymus	Thymus
14	chr3:59986800-59987600	Enhancers	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links