Variant report

Variant	rs4680238
Chromosome Location	chr3:155873269-155873270
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1118418	0.82[EUR][1000 genomes]
rs1353812	0.88[MEX][hapmap]
rs1499052	0.82[EUR][1000 genomes]
rs1499054	0.82[EUR][1000 genomes]
rs17170	1.00[CHB][hapmap]
rs2173492	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs3935399	0.86[ASN][1000 genomes]
rs3936002	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MKK][hapmap];0.97[ASN][1000 genomes]
rs4076087	0.82[ASN][1000 genomes]
rs4234309	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4234311	0.82[ASN][1000 genomes]
rs4258915	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4453801	1.00[JPT][hapmap]
rs4472010	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs4488791	0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs4505650	1.00[JPT][hapmap]
rs4533601	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4577423	1.00[JPT][hapmap]
rs4580504	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4634068	1.00[JPT][hapmap]
rs4679763	0.87[EUR][1000 genomes]
rs4679765	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs4680239	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs55858430	0.91[ASN][1000 genomes]
rs6441038	0.91[ASN][1000 genomes]
rs6441039	0.82[ASN][1000 genomes]
rs6441040	0.82[ASN][1000 genomes]
rs6441045	0.90[CEU][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs6441046	1.00[JPT][hapmap]
rs6441047	0.84[EUR][1000 genomes]
rs6775600	0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap]
rs6784723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7372394	0.82[EUR][1000 genomes]
rs7625226	0.82[ASN][1000 genomes]
rs7625723	0.82[ASN][1000 genomes]
rs7627105	0.90[CEU][hapmap]
rs7627867	0.91[ASN][1000 genomes]
rs7629439	0.89[MEX][hapmap]
rs9289962	0.80[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9816126	0.89[MEX][hapmap]
rs9818040	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs9832745	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs9862554	0.85[CEU][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	nsv592085	chr3:155827634-156012679	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4680238	SCARNA7	cis	cerebellum	SCAN
rs4680238	VEPH1	cis	cerebellum	SCAN
rs4680238	MLF1	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155870200-155874200	Weak transcription	Left Ventricle	heart
2	chr3:155870200-155875800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:155870200-155876400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:155870400-155917800	Weak transcription	Aorta	Aorta
5	chr3:155873200-155873800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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