Variant report

Variant	rs10873808
Chromosome Location	chr1:76406767-76406768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10518521	0.83[EUR][1000 genomes]
rs10782602	0.83[EUR][1000 genomes]
rs10873787	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873788	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11161845	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12118399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568447	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1417405	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565717	0.80[AMR][1000 genomes]
rs1689275	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17650138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770885	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1770887	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029683	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2347962	0.84[AFR][1000 genomes]
rs4949683	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4949686	0.83[EUR][1000 genomes]
rs4949885	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs5745433	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61770550	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770556	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61770557	1.00[ASN][1000 genomes]
rs7538800	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs931507	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1004669	chr1:76301198-76409451	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10873808	MSH4	cis	Nerve Tibial	GTEx
rs10873808	MSH4	cis	Artery Tibial	GTEx
rs10873808	MSH4	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76402800-76420000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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