Variant report

Variant	rs6495132
Chromosome Location	chr15:75255322-75255323
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12050494	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12050759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12592377	0.81[ASN][1000 genomes]
rs12594897	0.81[ASN][1000 genomes]
rs1867153	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.80[ASN][1000 genomes]
rs2004278	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57684159	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59270710	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60228621	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60740187	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67271490	0.80[ASN][1000 genomes]

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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv1612	chr15:75247725-75281284	Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6495132	SCAMP5	cis	cerebellum	SCAN
rs6495132	ULK3	cis	multi-tissue	Pritchard
rs6495132	SCAMP5	cis	Artery Tibial	GTEx
rs6495132	POLR2J	trans	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75252000-75255400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:75252000-75256400	Weak transcription	Lung	lung
3	chr15:75252000-75257200	Weak transcription	Pancreas	Pancrea
4	chr15:75252400-75255600	Enhancers	Brain Germinal Matrix	brain
5	chr15:75252400-75256800	Weak transcription	NHDF-Ad	bronchial
6	chr15:75252800-75255800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:75253000-75255800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:75254000-75256200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:75254200-75257000	Weak transcription	A549	lung
10	chr15:75254200-75257000	Weak transcription	Hela-S3	cervix
11	chr15:75254800-75255800	Weak transcription	HUVEC	blood vessel
12	chr15:75255200-75255400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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