Variant report

Variant	rs3113878
Chromosome Location	chr4:48001125-48001126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10002498	0.90[GIH][hapmap]
rs10020447	0.90[GIH][hapmap]
rs10025104	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs10030927	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs10938515	0.88[ASN][1000 genomes]
rs10938516	0.84[CHB][hapmap]
rs11733284	0.88[JPT][hapmap]
rs11736427	0.88[JPT][hapmap]
rs11944982	0.93[ASN][1000 genomes]
rs13116684	0.87[GIH][hapmap]
rs13120847	0.88[JPT][hapmap]
rs13146880	0.88[JPT][hapmap]
rs1348023	0.97[GIH][hapmap]
rs1440227	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs1507920	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1507922	0.89[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];0.86[YRI][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1550444	0.90[GIH][hapmap]
rs1583808	0.88[CHB][hapmap]
rs167692	0.97[GIH][hapmap]
rs16860723	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs16860815	0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1961011	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972883	0.90[GIH][hapmap]
rs2033895	0.90[GIH][hapmap]
rs2033897	0.88[CHB][hapmap];0.90[CHD][hapmap]
rs2053404	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs2053408	0.88[ASN][1000 genomes]
rs2289433	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap]
rs2581494	0.91[AFR][1000 genomes]
rs321620	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs321622	0.88[JPT][hapmap]
rs321630	0.88[JPT][hapmap]
rs321631	0.88[JPT][hapmap]
rs321632	0.87[GIH][hapmap]
rs321636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321638	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321643	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321645	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3762858	0.90[GIH][hapmap]
rs3762859	0.90[GIH][hapmap]
rs4365692	0.90[GIH][hapmap]
rs4518215	0.82[ASN][1000 genomes]
rs4529019	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs4694867	0.87[CHB][hapmap]
rs4694868	0.90[GIH][hapmap]
rs4694871	0.90[GIH][hapmap]
rs4694872	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs4695285	0.88[CHB][hapmap]
rs4695286	0.88[CHB][hapmap]
rs4695287	0.86[GIH][hapmap]
rs4695300	0.88[CHB][hapmap]
rs4695303	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs4695306	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs4695307	0.94[CHB][hapmap]
rs4695309	0.90[GIH][hapmap]
rs4695321	0.90[ASN][1000 genomes]
rs59936075	0.92[ASN][1000 genomes]
rs6414687	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs6447586	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs6447593	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs6447601	0.82[ASN][1000 genomes]
rs6447605	0.93[ASN][1000 genomes]
rs6447606	0.90[ASN][1000 genomes]
rs6447608	0.88[ASN][1000 genomes]
rs6811385	0.88[CHB][hapmap]
rs6816153	0.88[ASN][1000 genomes]
rs6818556	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs6827508	0.88[CEU][hapmap];0.87[JPT][hapmap]
rs6829073	0.87[GIH][hapmap]
rs6829804	0.93[ASN][1000 genomes]
rs6832334	0.90[GIH][hapmap]
rs6832503	0.88[JPT][hapmap]
rs6833320	0.90[GIH][hapmap]
rs6838837	0.88[ASN][1000 genomes]
rs6839185	0.89[ASN][1000 genomes]
rs6841271	0.97[GIH][hapmap]
rs6844286	0.85[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs6854375	0.84[CHB][hapmap];0.88[JPT][hapmap]
rs73244450	0.82[ASN][1000 genomes]
rs73244455	0.87[ASN][1000 genomes]
rs73244464	0.93[ASN][1000 genomes]
rs73244465	0.91[ASN][1000 genomes]
rs73244466	0.92[ASN][1000 genomes]
rs73244467	0.93[ASN][1000 genomes]
rs7667811	0.90[ASN][1000 genomes]
rs7690103	0.93[ASN][1000 genomes]
rs7690562	0.88[CEU][hapmap]
rs893864	0.90[GIH][hapmap]
rs9291317	0.85[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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
6	nsv1013163	chr4:47977844-48022511	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv537084	chr4:47977844-48022511	Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3113878	CNGA1	cis	Heart Left Ventricle	GTEx
rs3113878	CNGA1	cis	Adipose Subcutaneous	GTEx
rs3113878	CNGA1	cis	Muscle Skeletal	GTEx
rs3113878	CNGA1	cis	Esophagus Muscularis	GTEx
rs3113878	CNGA1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48000000-48001800	ZNF genes & repeats	Liver	Liver

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