Variant report

Variant	rs6548958
Chromosome Location	chr3:68112468-68112469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10865603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127865	0.81[ASW][hapmap];0.87[GIH][hapmap]
rs11921557	0.84[ASN][1000 genomes]
rs13078759	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1595489	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs4302389	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4419383	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4508789	1.00[CEU][hapmap]
rs4602395	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs56831191	0.80[ASN][1000 genomes]
rs57701717	0.82[ASN][1000 genomes]
rs60993082	0.84[ASN][1000 genomes]
rs6548943	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6548957	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6548964	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6548970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6548977	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6548978	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6548979	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6548998	0.87[GIH][hapmap]
rs6549003	0.81[ASW][hapmap];0.87[GIH][hapmap]
rs6549006	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs6549018	0.84[ASN][1000 genomes]
rs6771439	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6777162	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6781199	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6785163	0.84[ASN][1000 genomes]
rs6786795	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792628	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6809593	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7626911	0.84[ASN][1000 genomes]
rs7630992	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7634100	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs961915	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9821459	0.87[GIH][hapmap]
rs9860971	0.81[ASN][1000 genomes]
rs9867112	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874375	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990002	0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002010	chr3:67785913-68312064	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1009871	chr3:67862617-68312064	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv536583	chr3:67862617-68312064	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1010231	chr3:67894825-68117879	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv999747	chr3:68066423-68188180	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv536584	chr3:68066423-68188180	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv2752014	chr3:68091879-68416989	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv1007450	chr3:68094416-68346546	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:68108200-68112600	Enhancers	Primary T helper cells PMA-I stimulated	--
2	chr3:68110800-68124000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:68111600-68113200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:68111600-68119800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr3:68112000-68113600	Enhancers	Fetal Brain Female	brain
6	chr3:68112400-68112800	Weak transcription	Fetal Brain Male	brain

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