Variant report

Variant	rs2053009
Chromosome Location	chr3:94591213-94591214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1017370	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10804440	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1120672	0.82[EUR][1000 genomes]
rs11706789	0.81[EUR][1000 genomes]
rs11710300	0.81[EUR][1000 genomes]
rs11718955	0.87[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11719000	0.92[CEU][hapmap];0.80[GIH][hapmap];0.83[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs11918258	0.81[EUR][1000 genomes]
rs11919926	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes]
rs13082015	0.92[ASN][1000 genomes]
rs13314320	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13324772	0.80[ASN][1000 genomes]
rs13324801	0.80[ASN][1000 genomes]
rs1368193	0.81[EUR][1000 genomes]
rs1368194	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1368195	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1368196	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1368197	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1368198	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1368199	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1432468	0.83[JPT][hapmap]
rs1432472	0.92[ASN][1000 genomes]
rs1529652	0.81[EUR][1000 genomes]
rs1529654	0.81[EUR][1000 genomes]
rs1549860	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1897461	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1991752	0.92[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs1991753	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2116611	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2116612	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2163680	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2163681	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2163682	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2370168	0.82[EUR][1000 genomes]
rs300066	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs300090	0.96[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs300301	0.80[AMR][1000 genomes]
rs380053	0.96[CEU][hapmap];0.81[CHB][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4241479	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4461422	0.92[ASN][1000 genomes]
rs4462967	0.81[ASN][1000 genomes]
rs4493433	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4583664	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4593024	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4857128	0.83[EUR][1000 genomes]
rs4857129	0.80[EUR][1000 genomes]
rs4857495	0.92[ASN][1000 genomes]
rs6437515	0.82[JPT][hapmap]
rs6777772	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6780216	0.80[ASN][1000 genomes]
rs6801609	0.92[ASN][1000 genomes]
rs7427844	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7625912	0.83[EUR][1000 genomes]
rs7626615	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7626749	0.92[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7627012	0.94[JPT][hapmap]
rs7642399	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7646332	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7649609	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7652148	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7653317	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7653599	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9637418	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9714169	0.92[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs9809325	0.81[EUR][1000 genomes]
rs9822600	0.81[EUR][1000 genomes]
rs9832016	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9832891	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9842192	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9842195	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9842368	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9847887	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9848372	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854077	0.92[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs9857434	0.94[JPT][hapmap]
rs9861234	0.81[EUR][1000 genomes]
rs9867704	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9871980	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9872890	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9879048	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9880324	0.81[EUR][1000 genomes]
rs991552	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460763	chr3:94384332-94596072	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv590988	chr3:94384332-94596072	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv877168	chr3:94430430-94614333	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv460764	chr3:94479849-94654181	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv590989	chr3:94479849-94654181	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2053009	OR5H6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:94584000-94592800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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