Variant report

Variant	rs9289962
Chromosome Location	chr3:155887479-155887480
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	chr3:155882700..155884920-chr3:155887109..155888631,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1118418	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1353812	0.83[CEU][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1499052	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1499054	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17170	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2173492	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3935399	0.83[ASN][1000 genomes]
rs3936002	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4076087	0.97[ASN][1000 genomes]
rs4234309	0.81[AMR][1000 genomes]
rs4234310	0.91[ASN][1000 genomes]
rs4234311	0.97[ASN][1000 genomes]
rs4258915	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4453801	1.00[JPT][hapmap]
rs4472010	1.00[CHB][hapmap]
rs4488791	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4505650	1.00[JPT][hapmap]
rs4533601	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4577423	1.00[JPT][hapmap]
rs4580504	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4611771	0.93[ASN][1000 genomes]
rs4634068	1.00[JPT][hapmap]
rs4679763	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4679765	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4680238	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]
rs4680239	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6441039	0.97[ASN][1000 genomes]
rs6441040	0.97[ASN][1000 genomes]
rs6441045	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6441046	1.00[JPT][hapmap]
rs6441047	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6775600	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6784723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7372394	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7625226	0.97[ASN][1000 genomes]
rs7625723	0.97[ASN][1000 genomes]
rs7627105	1.00[CEU][hapmap]
rs7629439	0.83[MEX][hapmap]
rs9816126	0.83[MEX][hapmap]
rs9818040	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9832745	1.00[CHB][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9289962	SCARNA7	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155870400-155917800	Weak transcription	Aorta	Aorta
2	chr3:155887400-155887600	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links