Variant report

Variant	rs11120694
Chromosome Location	chr1:216077764-216077765
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10495012	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs10864214	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10864215	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11120697	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs11120698	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11120699	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12034100	0.84[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap]
rs12046356	0.94[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12091359	0.89[YRI][hapmap]
rs12562080	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347629	0.81[CHB][hapmap]
rs1836937	0.81[ASN][1000 genomes]
rs1934423	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365632	0.88[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845529	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs3908469	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4100655	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs4655288	0.92[YRI][hapmap]
rs4655433	0.89[YRI][hapmap]
rs4655437	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs492474	0.93[CHB][hapmap]
rs498911	0.93[CHB][hapmap]
rs513746	0.93[CHB][hapmap]
rs517577	0.93[CHB][hapmap]
rs633846	0.88[CHB][hapmap];0.85[CHD][hapmap]
rs646576	0.93[CHB][hapmap]
rs647908	0.93[CHB][hapmap]
rs662355	0.93[CHB][hapmap]
rs6661521	0.94[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.89[YRI][hapmap]
rs6665202	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs6675583	0.99[ASN][1000 genomes]
rs772713	0.93[CHB][hapmap];0.80[CHD][hapmap]
rs942837	0.93[CHB][hapmap]
rs942838	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv949671	chr1:215942740-216120815	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv832548	chr1:215987089-216175724	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv520724	chr1:216077764-216080155	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11120694	USH2A	cis	parietal	SCAN
rs11120694	NEK2	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216076200-216079600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:216076800-216077800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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