Variant report

Variant	rs9822658
Chromosome Location	chr3:68106746-68106747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12486136	0.82[GIH][hapmap]
rs4129248	0.86[GIH][hapmap]
rs6419759	0.86[GIH][hapmap]
rs6548962	0.86[GIH][hapmap]
rs6548984	0.86[GIH][hapmap]
rs6548985	0.86[GIH][hapmap]
rs6548986	0.95[GIH][hapmap]
rs6770795	0.81[EUR][1000 genomes]
rs6782017	0.81[EUR][1000 genomes]
rs6798030	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7374608	0.95[GIH][hapmap]
rs7428056	0.81[GIH][hapmap]
rs7430568	0.83[GIH][hapmap]
rs7433087	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610023	0.95[GIH][hapmap];0.81[MEX][hapmap]
rs7650405	0.95[GIH][hapmap]
rs9855500	0.95[GIH][hapmap]
rs9867661	0.83[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9822658	LRIG1	cis	cerebellum	SCAN
rs9822658	FAM19A1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:68105000-68109000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr3:68105200-68107000	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr3:68105400-68106800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr3:68105400-68107000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:68105400-68108400	Weak transcription	Fetal Intestine Large	intestine
6	chr3:68105800-68106800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr3:68106000-68106800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr3:68106000-68108200	Weak transcription	Small Intestine	intestine
9	chr3:68106200-68106800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
10	chr3:68106200-68106800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:68106200-68108000	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr3:68106200-68108200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr3:68106200-68108600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr3:68106200-68108600	Weak transcription	Fetal Intestine Small	intestine
15	chr3:68106600-68106800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:68106600-68107000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:68106600-68107800	Active TSS	Primary T cells fromperipheralblood	blood
18	chr3:68106600-68107800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
19	chr3:68106600-68108400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr3:68106600-68108600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links