Variant report

Variant	rs4949686
Chromosome Location	chr1:76473299-76473300
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10518521	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732723	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10782602	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873787	0.81[EUR][1000 genomes]
rs10873788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs10873808	0.83[EUR][1000 genomes]
rs10873863	0.80[CEU][hapmap]
rs11161836	1.00[CEU][hapmap]
rs11161845	0.81[EUR][1000 genomes]
rs11161857	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11588578	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1159214	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs12090849	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12118399	0.83[EUR][1000 genomes]
rs12122939	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs1318243	1.00[CHB][hapmap]
rs1417405	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1565717	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs1689275	0.80[EUR][1000 genomes]
rs17650138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs1770885	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs1770887	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs2029681	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2029683	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2172507	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs4949683	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs5745336	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs5745427	0.86[CEU][hapmap];1.00[CHB][hapmap]
rs5745433	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs5745442	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs5745449	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs61770550	0.81[EUR][1000 genomes]
rs61770556	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs638947	1.00[CHB][hapmap]
rs6683437	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6699682	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7523573	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7547056	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs7549863	1.00[CHB][hapmap]
rs931507	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4949686	MSH4	cis	Esophagus Muscularis	GTEx
rs4949686	MSH4	cis	Artery Tibial	GTEx

Chromatin state (count:3 , 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
2	chr1:76472400-76473600	Enhancers	Fetal Stomach	stomach
3	chr1:76473200-76474400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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