Variant report

Variant	rs1251550
Chromosome Location	chr1:76462321-76462322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10732724	0.87[CHB][hapmap]
rs10873804	0.82[CHB][hapmap]
rs10873863	0.85[CEU][hapmap]
rs11161887	0.81[JPT][hapmap]
rs11162053	0.90[ASN][1000 genomes]
rs11162066	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs12044211	0.83[CHB][hapmap]
rs12064158	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs12095069	0.90[ASN][1000 genomes]
rs12402347	0.87[ASN][1000 genomes]
rs12405994	0.87[ASN][1000 genomes]
rs12408897	0.87[ASN][1000 genomes]
rs12410373	0.82[CHB][hapmap]
rs12410724	0.90[ASN][1000 genomes]
rs1251531	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251539	0.90[ASN][1000 genomes]
rs1251551	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251556	0.90[ASN][1000 genomes]
rs1251560	0.91[ASN][1000 genomes]
rs1251579	0.82[ASN][1000 genomes]
rs1251580	0.82[ASN][1000 genomes]
rs1251581	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251587	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251588	0.82[ASN][1000 genomes]
rs1251591	0.81[ASN][1000 genomes]
rs1251594	0.81[ASN][1000 genomes]
rs12567390	0.86[CHB][hapmap]
rs12732495	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs1340684	0.89[ASN][1000 genomes]
rs1361487	0.85[ASN][1000 genomes]
rs1417402	0.87[ASN][1000 genomes]
rs1438175	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs1438176	0.90[ASN][1000 genomes]
rs1498313	0.85[CEU][hapmap]
rs1658737	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1658739	0.92[CEU][hapmap]
rs1689271	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs17097695	0.82[CHB][hapmap]
rs17097821	0.90[ASN][1000 genomes]
rs17097836	0.90[ASN][1000 genomes]
rs17097837	0.90[ASN][1000 genomes]
rs17097841	0.90[ASN][1000 genomes]
rs17097863	0.90[ASN][1000 genomes]
rs17097864	0.90[ASN][1000 genomes]
rs17097867	0.89[ASN][1000 genomes]
rs17649675	0.83[CHB][hapmap]
rs1770876	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770880	0.82[AFR][1000 genomes]
rs1796799	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796812	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1890967	0.90[ASN][1000 genomes]
rs1938321	0.86[ASN][1000 genomes]
rs1938322	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938323	0.90[ASN][1000 genomes]
rs2066213	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][1000 genomes]
rs2307077	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2792664	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34574524	0.90[ASN][1000 genomes]
rs3795251	0.82[CHB][hapmap]
rs3920847	0.87[ASN][1000 genomes]
rs4949619	0.90[ASN][1000 genomes]
rs4949685	0.90[ASN][1000 genomes]
rs5745451	0.81[JPT][hapmap]
rs5745523	0.82[JPT][hapmap]
rs5745542	0.82[JPT][hapmap]
rs7418941	0.87[ASN][1000 genomes]
rs7524665	0.81[ASN][1000 genomes]
rs7545057	0.83[CHB][hapmap]
rs931506	0.85[CHB][hapmap];0.82[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
rs1251550	MSH4	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76458200-76466600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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