Variant report

Variant	rs7641474
Chromosome Location	chr3:55821111-55821112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12631767	0.91[ASN][1000 genomes]
rs1495368	0.89[ASN][1000 genomes]
rs1495369	0.89[ASN][1000 genomes]
rs17272960	0.93[ASN][1000 genomes]
rs17332241	0.92[ASN][1000 genomes]
rs17714443	0.83[ASN][1000 genomes]
rs2168818	0.88[ASN][1000 genomes]
rs35664654	0.89[ASN][1000 genomes]
rs4129821	0.88[ASN][1000 genomes]
rs4129822	0.88[ASN][1000 genomes]
rs4129823	0.87[ASN][1000 genomes]
rs4260395	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4299453	0.92[ASN][1000 genomes]
rs4459870	0.82[ASN][1000 genomes]
rs4493400	0.88[ASN][1000 genomes]
rs4521190	0.93[ASN][1000 genomes]
rs4955877	0.88[CHB][hapmap];0.91[JPT][hapmap]
rs4955878	0.88[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs4955879	0.92[ASN][1000 genomes]
rs4955880	0.90[ASN][1000 genomes]
rs4955881	0.92[ASN][1000 genomes]
rs4955882	0.85[ASN][1000 genomes]
rs4955883	0.93[ASN][1000 genomes]
rs4955884	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4974144	0.89[ASN][1000 genomes]
rs4974145	0.88[ASN][1000 genomes]
rs4974146	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56912263	0.93[ASN][1000 genomes]
rs57802485	0.93[ASN][1000 genomes]
rs60551886	0.89[ASN][1000 genomes]
rs61072124	0.89[ASN][1000 genomes]
rs72877116	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73076938	0.89[ASN][1000 genomes]
rs73076939	0.89[ASN][1000 genomes]
rs73076947	0.91[ASN][1000 genomes]
rs9809248	0.82[AMR][1000 genomes]
rs9838012	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840522	0.80[ASN][1000 genomes]
rs9846380	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9853067	0.91[JPT][hapmap]
rs9860951	0.80[ASN][1000 genomes]
rs9866297	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[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	nsv876814	chr3:55802749-55860526	Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7641474	HESX1	cis	cerebellum	SCAN
rs7641474	RRP9	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55817200-55830600	Weak transcription	Pancreas	Pancrea
2	chr3:55819600-55821800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:55820200-55822200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:55820600-55821600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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