Variant report

Variant	rs1251587
Chromosome Location	chr1:76422097-76422098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1021462	0.83[JPT][hapmap]
rs10732724	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs10873738	0.83[JPT][hapmap]
rs10873804	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11161852	0.83[JPT][hapmap]
rs11161887	0.86[JPT][hapmap]
rs11162053	0.81[ASN][1000 genomes]
rs11162066	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs1146648	0.82[JPT][hapmap]
rs12022506	0.84[ASN][1000 genomes]
rs12044211	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs12064158	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12076093	0.82[JPT][hapmap]
rs12090712	0.82[JPT][hapmap]
rs12095069	0.81[ASN][1000 genomes]
rs12401729	0.81[JPT][hapmap]
rs12402230	0.91[ASN][1000 genomes]
rs12402347	0.84[ASN][1000 genomes]
rs12405994	0.84[ASN][1000 genomes]
rs12408897	0.84[ASN][1000 genomes]
rs12410373	0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs12410724	0.81[ASN][1000 genomes]
rs1251272	0.85[JPT][hapmap]
rs1251531	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251539	0.88[ASN][1000 genomes]
rs1251550	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251551	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251556	0.88[ASN][1000 genomes]
rs1251560	0.88[ASN][1000 genomes]
rs1251579	0.96[ASN][1000 genomes]
rs1251580	0.96[ASN][1000 genomes]
rs1251581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251582	0.83[ASN][1000 genomes]
rs1251583	0.86[ASN][1000 genomes]
rs1251588	0.96[ASN][1000 genomes]
rs1251591	0.94[ASN][1000 genomes]
rs1251594	0.94[ASN][1000 genomes]
rs12567390	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs12732495	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1303870	0.82[JPT][hapmap]
rs1340684	0.80[ASN][1000 genomes]
rs1361487	0.85[ASN][1000 genomes]
rs1417402	0.84[ASN][1000 genomes]
rs1438175	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1438176	0.81[ASN][1000 genomes]
rs1498313	0.82[JPT][hapmap]
rs1572859	0.81[ASN][1000 genomes]
rs1603734	0.83[JPT][hapmap]
rs1658737	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1689271	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17097681	0.86[JPT][hapmap]
rs17097695	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs17097821	0.81[ASN][1000 genomes]
rs17097836	0.81[ASN][1000 genomes]
rs17097837	0.81[ASN][1000 genomes]
rs17097841	0.81[ASN][1000 genomes]
rs17097863	0.81[ASN][1000 genomes]
rs17097864	0.81[ASN][1000 genomes]
rs17097867	0.80[ASN][1000 genomes]
rs17649675	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs1770876	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796799	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1796812	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1873894	0.86[ASN][1000 genomes]
rs1890967	0.81[ASN][1000 genomes]
rs1908089	0.82[JPT][hapmap]
rs1938322	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1938323	0.81[ASN][1000 genomes]
rs2028212	0.81[ASN][1000 genomes]
rs2066213	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2307077	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2792664	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34574524	0.81[ASN][1000 genomes]
rs3765682	0.81[JPT][hapmap]
rs3795251	0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs3920847	0.84[ASN][1000 genomes]
rs4949619	0.81[ASN][1000 genomes]
rs4949681	0.86[ASN][1000 genomes]
rs4949685	0.81[ASN][1000 genomes]
rs5745354	0.81[JPT][hapmap]
rs5745451	0.86[JPT][hapmap]
rs5745465	0.81[JPT][hapmap]
rs5745523	0.86[JPT][hapmap]
rs5745532	0.83[JPT][hapmap]
rs5745542	0.86[JPT][hapmap]
rs5745546	0.87[JPT][hapmap]
rs58722308	0.91[ASN][1000 genomes]
rs6685657	0.87[ASN][1000 genomes]
rs6693002	0.85[ASN][1000 genomes]
rs7418941	0.84[ASN][1000 genomes]
rs7514912	0.83[JPT][hapmap]
rs7520312	0.84[ASN][1000 genomes]
rs7521538	0.91[ASN][1000 genomes]
rs7524665	0.94[ASN][1000 genomes]
rs7545057	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7548391	0.83[JPT][hapmap]
rs931506	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]

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	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1251587	MSH4	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76421000-76424600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:76421000-76430000	Weak transcription	HMEC	breast
3	chr1:76422000-76423200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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