Variant report

Variant	rs4927961
Chromosome Location	chr3:51110195-51110196
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs11130280	0.84[CHD][hapmap]
rs12485331	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485754	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12487496	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12488700	0.93[JPT][hapmap];0.91[YRI][hapmap]
rs12488831	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs12488948	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs12489219	0.89[EUR][1000 genomes]
rs12490026	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12491206	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12491836	1.00[EUR][1000 genomes]
rs12492615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12492690	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12492850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs12493034	0.89[EUR][1000 genomes]
rs12493323	0.89[EUR][1000 genomes]
rs12493359	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12495561	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs12496621	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12496830	0.89[EUR][1000 genomes]
rs13061003	0.82[CHD][hapmap]
rs13080170	0.82[CHD][hapmap]
rs1480364	0.81[CHD][hapmap]
rs1809388	0.89[EUR][1000 genomes]
rs2061949	0.94[MEX][hapmap]
rs2086395	0.89[EUR][1000 genomes]
rs2101056	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2127654	1.00[EUR][1000 genomes]
rs2170177	0.84[EUR][1000 genomes]
rs2170178	0.81[CHD][hapmap]
rs2355943	0.81[CHD][hapmap]
rs2355946	0.84[EUR][1000 genomes]
rs2883809	0.81[CHD][hapmap]
rs3762711	1.00[EUR][1000 genomes]
rs4078296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap]
rs4130473	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4323036	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4346580	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4356848	0.82[CHD][hapmap]
rs4367100	0.81[CHD][hapmap]
rs4443210	0.82[CHD][hapmap]
rs4560329	0.84[CHD][hapmap]
rs4927975	1.00[YRI][hapmap]
rs4974092	0.81[CHD][hapmap]
rs4974094	0.81[CHD][hapmap]
rs4974099	0.81[CHD][hapmap]
rs4974100	0.89[EUR][1000 genomes]
rs4974112	0.89[EUR][1000 genomes]
rs56052360	0.89[EUR][1000 genomes]
rs57406588	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58720544	0.89[EUR][1000 genomes]
rs58911602	0.89[EUR][1000 genomes]
rs59682667	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59834534	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59957657	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60128296	0.84[EUR][1000 genomes]
rs60461297	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60567238	0.89[EUR][1000 genomes]
rs60740654	0.89[EUR][1000 genomes]
rs60882641	0.89[EUR][1000 genomes]
rs6445549	0.81[CHD][hapmap]
rs6446239	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6772197	0.82[CHD][hapmap]
rs6784455	0.81[CHD][hapmap]
rs6787805	0.83[CHD][hapmap]
rs6792254	0.89[EUR][1000 genomes]
rs6795573	0.82[CHD][hapmap]
rs6796847	0.81[CHD][hapmap]
rs72936442	0.89[EUR][1000 genomes]
rs72936462	0.84[EUR][1000 genomes]
rs72941919	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941940	0.84[AFR][1000 genomes]
rs72943130	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72943137	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72943166	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72948197	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72948200	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72953143	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72953162	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72953175	1.00[EUR][1000 genomes]
rs7372342	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs7427526	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7427615	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs7433217	0.81[CHD][hapmap]
rs7614482	0.82[CHD][hapmap]
rs7627266	0.82[CHD][hapmap]
rs899750	0.81[CHD][hapmap]
rs9860403	0.81[CHD][hapmap]
rs9865532	0.82[CHD][hapmap]
rs9878592	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs995543	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4927961	HEMK1	cis	multi-tissue	Pritchard
rs4927961	MAPKAPK3	cis	lymphoblastoid	seeQTL
rs4927961	HEMK	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51103400-51119600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:51105800-51112800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:51108000-51120400	Weak transcription	Fetal Brain Male	brain
4	chr3:51109600-51120000	Weak transcription	Left Ventricle	heart

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