Variant report

Variant	rs9867661
Chromosome Location	chr3:68102361-68102362
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11706410	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs11920538	0.80[CEU][hapmap]
rs12486136	0.92[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs12486933	0.88[CEU][hapmap]
rs12638261	0.84[CEU][hapmap]
rs13076275	0.87[CEU][hapmap]
rs13085443	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13314479	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs13316249	0.81[EUR][1000 genomes]
rs13316279	0.81[EUR][1000 genomes]
rs13317047	0.81[EUR][1000 genomes]
rs13326766	0.81[EUR][1000 genomes]
rs3924581	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4129248	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]
rs4130988	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4130989	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4130990	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6419759	0.88[CEU][hapmap];0.98[GIH][hapmap];0.82[TSI][hapmap]
rs6548948	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6548962	0.92[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs6548980	0.81[EUR][1000 genomes]
rs6548981	0.81[EUR][1000 genomes]
rs6548984	0.92[CEU][hapmap];0.98[GIH][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6548985	0.92[CEU][hapmap];0.98[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs6548986	0.81[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs6548999	0.88[CEU][hapmap]
rs6768632	0.90[GIH][hapmap]
rs6770795	0.84[EUR][1000 genomes]
rs6782017	0.84[EUR][1000 genomes]
rs6800369	0.84[CEU][hapmap]
rs7374608	0.81[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs7428056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7429303	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7430568	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7433022	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7433028	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7610023	0.84[CEU][hapmap];0.84[GIH][hapmap];0.89[TSI][hapmap]
rs7622220	0.81[CHB][hapmap]
rs7650405	0.84[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap]
rs9812284	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815465	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9822658	0.83[GIH][hapmap]
rs9843452	0.81[CEU][hapmap]
rs9855500	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs9868432	0.90[GIH][hapmap]
rs9870065	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9873459	0.81[CEU][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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9867661	MAGI1	cis	cerebellum	SCAN
rs9867661	LRIG1	cis	cerebellum	SCAN
rs9867661	FAM19A1	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:68098000-68105000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr3:68099600-68105800	Weak transcription	Small Intestine	intestine
3	chr3:68099800-68103600	Weak transcription	Fetal Intestine Large	intestine
4	chr3:68099800-68105000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:68101800-68103800	Weak transcription	Fetal Intestine Small	intestine

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