Variant report

Variant	rs1796799
Chromosome Location	chr1:76467354-76467355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76465512..76468433-chr1:76470100..76472168,2	K562	blood:

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11162053	0.90[ASN][1000 genomes]
rs11162066	0.83[ASN][1000 genomes]
rs12064158	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]
rs12410724	0.90[ASN][1000 genomes]
rs1251531	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251539	0.90[ASN][1000 genomes]
rs1251550	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251551	0.92[AFR][1000 genomes];0.98[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	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1251587	0.82[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]
rs1340684	0.89[ASN][1000 genomes]
rs1361487	0.85[ASN][1000 genomes]
rs1417402	0.87[ASN][1000 genomes]
rs1438175	0.85[ASN][1000 genomes]
rs1438176	0.90[ASN][1000 genomes]
rs1658737	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
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]
rs1770876	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1796812	0.81[ASN][1000 genomes]
rs1890967	0.90[ASN][1000 genomes]
rs1938321	0.86[ASN][1000 genomes]
rs1938322	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1938323	0.90[ASN][1000 genomes]
rs2066213	0.86[ASN][1000 genomes]
rs2792664	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34574524	0.90[ASN][1000 genomes]
rs3920847	0.87[ASN][1000 genomes]
rs4949619	0.90[ASN][1000 genomes]
rs4949685	0.90[ASN][1000 genomes]
rs7418941	0.87[ASN][1000 genomes]
rs7524665	0.81[ASN][1000 genomes]

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
rs1796799	MSH4	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76467000-76476600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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