Variant report

Variant	rs953994
Chromosome Location	chr15:54679346-54679347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11629500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11629831	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs11629995	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11630912	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs11633330	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs11633475	1.00[CEU][hapmap]
rs11633514	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11633544	0.85[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11633674	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11634047	0.85[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11634125	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11634629	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11634764	0.85[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11634781	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11635260	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11637336	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11638441	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11638760	0.86[AMR][1000 genomes]
rs11638833	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11638875	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1355506	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1355507	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1355508	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1355509	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17237571	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34270881	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4506835	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs57505610	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59738575	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73415771	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73417782	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs981450	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv1845471	chr15:54556063-54685463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs953994	PDZD8	trans	brain	seeQTL
rs953994	RRAD	trans	brain	seeQTL
rs953994	VAV3	trans	brain	seeQTL
rs953994	RBM28	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54678800-54679400	Flanking Active TSS	Aorta	Aorta
2	chr15:54679000-54679800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr15:54679000-54679800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links