Variant report

Variant	rs2957679
Chromosome Location	chr11:10407462-10407463
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10770108	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042762	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042769	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042770	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11042772	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11042773	0.82[AFR][1000 genomes]
rs12365418	0.83[AFR][1000 genomes]
rs1597448	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1597449	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16907747	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198008	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198009	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2198010	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2403305	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2403306	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923085	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2923086	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2923087	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2923088	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2923115	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923117	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923120	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923121	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2923122	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2923124	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2923125	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957658	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2957664	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2957665	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957666	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957667	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957668	0.89[ASN][1000 genomes]
rs2957669	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957670	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957675	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957677	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957678	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5015228	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6416051	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7112833	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7117816	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7117951	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7934497	0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430319	chr11:10027543-10711224	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv1037131	chr11:10401998-10429998	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv553477	chr11:10403539-10429998	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2957679	SYT9	cis	cerebellum	SCAN
rs2957679	SNORA23	cis	cerebellum	SCAN
rs2957679	OLFML1	cis	cerebellum	SCAN
rs2957679	RPL27A	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:10402800-10408400	Weak transcription	Esophagus	oesophagus
2	chr11:10403400-10408400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:10407200-10407600	Enhancers	Lung	lung
4	chr11:10407200-10407600	Enhancers	NHDF-Ad	bronchial
5	chr11:10407200-10407800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:10407200-10407800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
7	chr11:10407200-10408200	Enhancers	Duodenum Smooth Muscle	Duodenum
8	chr11:10407200-10408200	Enhancers	Stomach Smooth Muscle	stomach
9	chr11:10407200-10408400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr11:10407200-10408400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:10407200-10408600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr11:10407200-10408800	Enhancers	Fetal Muscle Leg	muscle
13	chr11:10407200-10410000	Enhancers	HSMM	muscle
14	chr11:10407200-10410400	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr11:10407200-10410600	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr11:10407200-10410800	Enhancers	Colon Smooth Muscle	Colon
17	chr11:10407200-10411000	Enhancers	Ovary	ovary
18	chr11:10407200-10411000	Enhancers	NHLF	lung
19	chr11:10407200-10412800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:10407200-10412800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:10407200-10412800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:10407200-10412800	Enhancers	Adipose Nuclei	Adipose
23	chr11:10407400-10407600	Enhancers	Right Atrium	heart
24	chr11:10407400-10407600	Enhancers	Osteobl	bone
25	chr11:10407400-10410400	Enhancers	Rectal Smooth Muscle	rectum
26	chr11:10407400-10411000	Enhancers	Fetal Stomach	stomach

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