Variant report

Variant	rs4858793
Chromosome Location	chr3:48415007-48415008
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1037773	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs10470686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1109227	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs11130170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130171	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs11712561	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11797	0.82[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs12487542	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13069724	1.00[CEU][hapmap];0.97[GIH][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs13071337	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13072012	0.86[EUR][1000 genomes]
rs13076076	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs13091785	0.89[EUR][1000 genomes]
rs13314659	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13324374	0.89[EUR][1000 genomes]
rs1459242	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459249	0.91[EUR][1000 genomes]
rs1459250	0.85[EUR][1000 genomes]
rs1563736	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1870444	0.87[EUR][1000 genomes]
rs1975844	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2045554	0.89[EUR][1000 genomes]
rs2242150	1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs2279077	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2290822	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs2362450	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs2362452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28824259	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2885509	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2885510	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3214041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34761139	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35215722	0.86[EUR][1000 genomes]
rs3774808	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs4490383	0.87[EUR][1000 genomes]
rs4858795	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs4858817	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858819	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs56298324	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60512868	0.91[EUR][1000 genomes]
rs6442116	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442117	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442118	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6442120	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs6442123	0.88[EUR][1000 genomes]
rs6770470	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6776700	1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs6779262	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784322	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6784541	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794875	1.00[CEU][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs6796491	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6800475	0.89[EUR][1000 genomes]
rs6804774	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6810060	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7126	0.90[EUR][1000 genomes]
rs725309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs730566	0.82[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs73074358	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs734071	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs7618883	0.85[EUR][1000 genomes]
rs7630741	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7634377	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7635522	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7636044	0.96[CEU][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes]
rs7636782	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7639743	0.85[EUR][1000 genomes]
rs7651407	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs7653691	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs898225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs922075	1.00[CEU][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs9311423	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311424	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311428	0.87[CHD][hapmap];0.90[JPT][hapmap]
rs9809843	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812647	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9815103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826195	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826247	0.88[EUR][1000 genomes]
rs9838618	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs9849509	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs9862575	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9864371	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9864815	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875280	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9876781	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs9876891	0.92[EUR][1000 genomes]
rs9881491	0.89[EUR][1000 genomes]
rs9883759	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs9883927	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs4858793	ALAS1	cis	parietal	SCAN
rs4858793	NME6	cis	cerebellum	SCAN
rs4858793	TMA7	cis	Muscle Skeletal	GTEx
rs4858793	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs4858793	ZNF589	cis	cerebellum	SCAN
rs4858793	C3orf18	cis	cerebellum	SCAN
rs4858793	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs4858793	SBK1	trans	cerebellum	SCAN
rs4858793	ZNF589	cis	parietal	SCAN
rs4858793	SCOTIN	cis	multi-tissue	Pritchard
rs4858793	AMT	cis	parietal	SCAN
rs4858793	CXCR6	cis	parietal	SCAN
rs4858793	AMT	cis	cerebellum	SCAN
rs4858793	PLXNB1	cis	lymphoblastoid	seeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48413000-48415400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:48414000-48415200	Enhancers	Fetal Heart	heart
3	chr3:48414400-48415200	Enhancers	HepG2	liver
4	chr3:48414800-48415200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:48415000-48415200	Active TSS	Pancreas	Pancrea
6	chr3:48415000-48415400	Enhancers	iPS-15b Cell Line	embryonic stem cell

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