Variant report

Variant	rs4241479
Chromosome Location	chr3:94588217-94588218
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11718955	0.83[CEU][hapmap];0.88[JPT][hapmap]
rs11719000	0.84[CEU][hapmap];0.81[GIH][hapmap];0.83[JPT][hapmap]
rs11919926	0.88[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap]
rs13082015	0.99[ASN][1000 genomes]
rs13314320	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13324772	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13324801	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1368194	0.84[ASN][1000 genomes]
rs1368195	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1368196	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1368197	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1368198	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1368199	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1432468	0.83[JPT][hapmap]
rs1432472	0.87[ASN][1000 genomes]
rs1991752	0.84[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs1991753	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2053009	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2116612	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2163680	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2163681	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2163682	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300066	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs300090	0.88[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap]
rs380053	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap]
rs4461422	0.99[ASN][1000 genomes]
rs4462967	0.88[ASN][1000 genomes]
rs4493433	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4583664	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4593024	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4857495	0.87[ASN][1000 genomes]
rs6437515	0.83[JPT][hapmap]
rs6777772	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6780216	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6801609	0.99[ASN][1000 genomes]
rs7427844	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7626749	0.84[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs7627012	0.94[JPT][hapmap]
rs7642399	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646332	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7649609	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7652148	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653317	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7653599	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9637418	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9714169	0.84[CEU][hapmap];0.81[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.83[MEX][hapmap]
rs9832016	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9832891	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9841084	0.81[AMR][1000 genomes]
rs9842192	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9842195	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9842368	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847887	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848372	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9854077	0.84[CEU][hapmap];0.81[CHB][hapmap];0.83[JPT][hapmap]
rs9857434	0.94[JPT][hapmap]
rs9867704	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9871980	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9872890	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879048	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4241479	ARL13B	cis	parietal	SCAN
rs4241479	OR5H6	cis	cerebellum	SCAN
rs4241479	DHFRL1	cis	cerebellum	SCAN

Chromatin state (count:2 , 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
2	chr3:94588200-94588400	Enhancers	Adipose Nuclei	Adipose

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