Variant report

Variant	rs3762859
Chromosome Location	chr4:47953087-47953088
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10002498	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020447	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10025104	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs10030927	0.81[CEU][hapmap]
rs1036681	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10461075	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10805158	0.89[EUR][1000 genomes]
rs10938498	0.80[EUR][1000 genomes]
rs10938508	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11732840	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11946535	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12506026	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12647189	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13143926	0.87[ASN][1000 genomes]
rs1348023	0.89[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap]
rs1371728	1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1440220	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1440222	1.00[ASN][1000 genomes]
rs1440227	0.81[CEU][hapmap]
rs1507922	0.90[GIH][hapmap];0.82[TSI][hapmap]
rs1545200	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1550444	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167692	0.89[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs1808853	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1812964	0.95[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188900	1.00[ASN][1000 genomes]
rs1968542	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972883	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972884	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2014934	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2033894	0.92[EUR][1000 genomes]
rs2033895	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053404	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs2119204	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119205	0.85[EUR][1000 genomes]
rs2119207	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119208	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs224801	0.87[ASN][1000 genomes]
rs2289433	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs2352456	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352457	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2352466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2581496	1.00[ASN][1000 genomes]
rs28464733	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2882950	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3113877	1.00[ASN][1000 genomes]
rs3113879	1.00[ASN][1000 genomes]
rs3113880	0.87[ASN][1000 genomes]
rs321625	1.00[ASN][1000 genomes]
rs321639	0.89[ASN][1000 genomes]
rs321640	1.00[ASN][1000 genomes]
rs321641	0.87[ASN][1000 genomes]
rs321647	0.87[ASN][1000 genomes]
rs321649	0.87[ASN][1000 genomes]
rs3762858	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3811761	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845160	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4308343	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365692	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507330	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529019	0.81[CEU][hapmap]
rs4694868	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694871	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694872	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs4694875	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4694878	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695287	1.00[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695294	0.87[EUR][1000 genomes]
rs4695296	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4695302	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695303	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs4695306	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs4695309	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695312	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695316	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6414687	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs6447586	0.81[CEU][hapmap]
rs6447593	0.85[CEU][hapmap]
rs6447596	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447599	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6447602	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6815975	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6818556	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs6819506	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823572	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826909	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6827508	0.88[CEU][hapmap]
rs6829073	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap]
rs6832334	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6833320	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841271	0.89[CEU][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6844286	0.81[CEU][hapmap]
rs6845451	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6850142	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs707723	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7668778	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670219	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7672090	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690406	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690522	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7690562	0.83[CEU][hapmap]
rs893861	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893863	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893864	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920463	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291317	0.81[CEU][hapmap];0.97[GIH][hapmap]
rs9291318	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291319	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995022	0.96[AMR][1000 genomes];1.00[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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription 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 lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3762859	CNGA1	cis	Heart Left Ventricle	GTEx
rs3762859	CNGA1	cis	Thyroid	GTEx
rs3762859	CNGA1	cis	Esophagus Muscularis	GTEx
rs3762859	NFXL1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47950600-47953600	Strong transcription	Liver	Liver
2	chr4:47953000-47953600	Enhancers	Primary neutrophils fromperipheralblood	blood

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