Variant report

Variant	rs10490808
Chromosome Location	chr3:59964699-59964700
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11130742	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11130743	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12630463	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061330	0.88[ASN][1000 genomes]
rs13061337	0.83[EUR][1000 genomes]
rs13063413	0.91[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13070349	0.94[ASN][1000 genomes]
rs13070475	0.99[ASN][1000 genomes]
rs13073897	0.85[EUR][1000 genomes]
rs13077692	0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]
rs13081936	1.00[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13081972	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13088505	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13088669	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13092173	0.94[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13092997	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13094437	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096138	0.95[CEU][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs212014	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2687899	0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs2736791	0.91[EUR][1000 genomes]
rs3772458	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3772464	0.81[ASN][1000 genomes]
rs3772468	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772473	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3772484	0.83[CHB][hapmap];1.00[ASN][1000 genomes]
rs3772491	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772492	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3772499	1.00[CEU][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772500	1.00[CEU][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772502	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3772505	0.91[CEU][hapmap];0.83[CHB][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs3821478	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3821479	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821480	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3821481	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821482	0.93[ASN][1000 genomes]
rs4679625	0.81[EUR][1000 genomes]
rs6446101	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs6771484	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771698	1.00[ASN][1000 genomes]
rs6784057	0.87[CEU][hapmap];0.86[GIH][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs6805337	0.99[ASN][1000 genomes]
rs7615116	0.86[ASN][1000 genomes]
rs7640107	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs802772	0.91[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs802774	0.94[ASN][1000 genomes]
rs812445	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];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	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

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59961600-59969000	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:59963000-59969400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:59963800-59964800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr3:59964000-59967800	Enhancers	Primary T cells from cord blood	blood
5	chr3:59964200-59967400	Enhancers	Fetal Thymus	thymus
6	chr3:59964400-59965000	Enhancers	Primary T cells fromperipheralblood	blood
7	chr3:59964400-59967400	Enhancers	Thymus	Thymus
8	chr3:59964400-59968400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr3:59964400-59970600	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr3:59964600-59965000	Flanking Active TSS	GM12878-XiMat	blood
11	chr3:59964600-59966200	Genic enhancers	Dnd41	blood
12	chr3:59964600-59969000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:59964600-59969600	Enhancers	Primary T helper cells fromperipheralblood	blood

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