Variant report

Variant	rs11856476
Chromosome Location	chr15:54527011-54527012
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10518760	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11071064	1.00[CEU][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs11635437	0.82[CHB][hapmap]
rs12899415	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12899426	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12901994	0.86[CEU][hapmap]
rs12902112	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906606	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12906904	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12907062	0.84[EUR][1000 genomes]
rs12907862	0.85[ASN][1000 genomes]
rs12908409	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12911007	1.00[CEU][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs12911131	0.84[EUR][1000 genomes]
rs12911506	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12917522	0.90[EUR][1000 genomes]
rs1807348	0.86[EUR][1000 genomes]
rs2414287	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2414289	0.84[EUR][1000 genomes]
rs2899536	1.00[CEU][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4774689	0.82[ASN][1000 genomes]
rs4776215	0.82[ASN][1000 genomes]
rs4776216	0.89[CHB][hapmap];0.84[ASN][1000 genomes]
rs6493667	0.83[EUR][1000 genomes]
rs68018837	0.84[EUR][1000 genomes]
rs7162346	0.89[CHB][hapmap];0.83[CHD][hapmap];0.84[ASN][1000 genomes]
rs7183052	0.84[ASN][1000 genomes]
rs7183952	0.89[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs719211	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs8024165	0.86[CEU][hapmap]
rs8025731	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8028549	0.84[EUR][1000 genomes]
rs8032432	0.89[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs8036716	0.86[CEU][hapmap]
rs8039848	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9302174	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052235	chr15:53677524-54618723	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv542388	chr15:53677524-54618723	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1043666	chr15:54415970-54548495	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1043823	chr15:54468477-54532985	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11856476	USP8	cis	parietal	SCAN
rs11856476	SPPL2A	cis	cerebellum	SCAN
rs11856476	ATP8B4	cis	cerebellum	SCAN
rs11856476	GALK2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54516800-54529000	Weak transcription	Fetal Lung	lung
2	chr15:54519000-54554400	Weak transcription	Aorta	Aorta
3	chr15:54519400-54549600	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links