Variant report

Variant	rs17559185
Chromosome Location	chr11:56609719-56609720
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10501358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17549606	0.91[CEU][hapmap]
rs17559037	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17559600	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17640103	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55815178	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61889065	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61889069	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61889071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61889072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61889073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61889075	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61889076	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61889078	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61889108	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61902501	0.82[EUR][1000 genomes]
rs61902503	0.82[EUR][1000 genomes]
rs61902504	0.82[EUR][1000 genomes]
rs61902517	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61902556	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61903997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7107067	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7116073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7122752	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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	nsv1048328	chr11:56471984-56649908	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	esv2830406	chr11:56481955-56650124	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv468577	chr11:56503728-56704042	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv555101	chr11:56503728-56704042	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv469960	chr11:56605222-56704042	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17559185	PRG3	cis	parietal	SCAN
rs17559185	OR5B3	cis	parietal	SCAN
rs17559185	TPCN2	trans	cerebellum	SCAN
rs17559185	OR5AS1	cis	cerebellum	SCAN
rs17559185	OR5R1	cis	parietal	SCAN
rs17559185	OR4D10	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:56608800-56610200	Enhancers	HMEC	breast
2	chr11:56609000-56609800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:56609000-56609800	Enhancers	Fetal Intestine Large	intestine
4	chr11:56609000-56610800	Enhancers	Fetal Lung	lung
5	chr11:56609000-56611000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr11:56609000-56611600	Enhancers	Stomach Mucosa	stomach
7	chr11:56609200-56610000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:56609200-56613800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr11:56609200-56614000	Weak transcription	Fetal Kidney	kidney
10	chr11:56609400-56610800	Enhancers	A549	lung
11	chr11:56609400-56613800	Weak transcription	NHEK	skin

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