Variant report

Variant	rs4129248
Chromosome Location	chr3:68105359-68105360
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11706410	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11708116	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11709861	0.87[ASN][1000 genomes]
rs12486136	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12486933	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs13076275	0.96[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap]
rs13085443	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085628	0.95[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4130988	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4130989	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4130990	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6419759	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6548948	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6548962	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6548980	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6548981	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6548984	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6548985	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6548986	0.82[GIH][hapmap]
rs6548999	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6549020	0.95[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs6768632	0.94[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs6774687	0.95[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs6798030	0.84[EUR][1000 genomes]
rs7374608	0.82[GIH][hapmap]
rs7428056	0.94[ASW][hapmap];0.89[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7428837	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7429303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430480	0.85[ASN][1000 genomes]
rs7430568	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433022	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7433028	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433087	0.84[EUR][1000 genomes]
rs7610023	0.82[GIH][hapmap]
rs7617661	0.84[CHB][hapmap]
rs7638117	0.86[ASN][1000 genomes]
rs7650405	0.82[GIH][hapmap]
rs9812284	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9815465	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9819989	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9820035	0.87[ASN][1000 genomes]
rs9822658	0.86[GIH][hapmap]
rs9855500	0.82[GIH][hapmap]
rs9867661	0.92[CEU][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9868432	0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9870065	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4129248	FAM19A1	cis	cerebellum	SCAN
rs4129248	LRIG1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:68099600-68105800	Weak transcription	Small Intestine	intestine
2	chr3:68103600-68105400	Enhancers	Fetal Intestine Large	intestine
3	chr3:68103800-68106200	Enhancers	Fetal Intestine Small	intestine
4	chr3:68104200-68106600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:68104800-68106200	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:68105000-68106200	Enhancers	Primary T cells from cord blood	blood
7	chr3:68105000-68106200	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr3:68105000-68106200	Enhancers	Duodenum Mucosa	Duodenum
9	chr3:68105000-68106600	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:68105000-68106600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr3:68105000-68106600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:68105000-68109000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:68105200-68107000	Enhancers	Primary T killer memory cells from peripheral blood	blood

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