Variant report

Variant	rs12294962
Chromosome Location	chr11:26610137-26610138
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10835008	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10835031	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11029622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11029624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11029633	0.80[MKK][hapmap]
rs11029634	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11029635	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11029653	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs11029655	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12269966	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[ASN][1000 genomes]
rs12270321	0.83[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12282129	1.00[ASN][1000 genomes]
rs12288077	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12293283	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12293598	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12295638	0.93[TSI][hapmap]
rs12295913	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12417786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12418283	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12418403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12421216	1.00[ASN][1000 genomes]
rs12421673	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1353142	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1389454	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17243601	0.93[ASN][1000 genomes]
rs17243608	0.93[ASN][1000 genomes]
rs17243615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs61877276	0.93[ASN][1000 genomes]
rs61877282	0.93[ASN][1000 genomes]
rs66495309	1.00[ASN][1000 genomes]
rs66527152	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66591292	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs68030591	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125967	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7127915	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72881705	0.93[ASN][1000 genomes]
rs72881737	0.93[ASN][1000 genomes]
rs72881740	0.93[ASN][1000 genomes]
rs72881742	0.93[ASN][1000 genomes]
rs72881752	0.93[ASN][1000 genomes]
rs72881763	0.93[ASN][1000 genomes]
rs72881790	0.93[ASN][1000 genomes]
rs72881791	0.93[ASN][1000 genomes]
rs72881793	0.93[ASN][1000 genomes]
rs72883216	0.93[ASN][1000 genomes]
rs72883218	0.93[ASN][1000 genomes]
rs72883221	0.93[ASN][1000 genomes]
rs72883224	0.93[ASN][1000 genomes]
rs72883225	0.93[ASN][1000 genomes]
rs72883226	0.93[ASN][1000 genomes]
rs72883230	0.93[ASN][1000 genomes]
rs72883231	0.93[ASN][1000 genomes]
rs72883237	0.93[ASN][1000 genomes]
rs72883242	0.93[ASN][1000 genomes]
rs72883245	0.93[ASN][1000 genomes]
rs72883247	0.93[ASN][1000 genomes]
rs73434383	1.00[ASN][1000 genomes]
rs7935600	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935694	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938517	1.00[MEX][hapmap]
rs7945396	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044544	chr11:26506962-26967285	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1050121	chr11:26532655-26675303	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv540974	chr11:26532655-26675303	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv916187	chr11:26576875-27328603	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	esv10740	chr11:26607958-26610913	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
6	nsv522526	chr11:26608497-26610518	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
7	nsv553900	chr11:26608497-26610759	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
8	nsv553901	chr11:26608497-26611796	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
9	nsv553902	chr11:26608602-26610759	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
10	nsv553903	chr11:26608661-26610759	Enhancers Weak transcription	n/a	n/a	inside rSNPs	diseases
11	nsv553904	chr11:26608776-26610759	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
12	nsv553905	chr11:26608839-26610518	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
13	nsv553906	chr11:26608839-26610759	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
14	nsv975163	chr11:26609968-26620267	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12294962	GNAI2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:26600400-26643000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr11:26603800-26623200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr11:26604000-26623600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:26606800-26614600	Weak transcription	Placenta	Placenta
5	chr11:26607600-26635400	Weak transcription	Adipose Nuclei	Adipose
6	chr11:26609200-26613800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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