Variant report

Variant	rs17161607
Chromosome Location	chr5:108442828-108442829
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10035329	0.86[ASN][1000 genomes]
rs10036203	0.85[AMR][1000 genomes]
rs10040665	0.92[CEU][hapmap]
rs10056059	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10063768	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10074425	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10076453	0.82[AMR][1000 genomes]
rs1036214	0.80[MEX][hapmap]
rs10477951	0.85[EUR][1000 genomes]
rs10900651	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.80[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11749630	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11957989	0.86[EUR][1000 genomes]
rs12332736	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13362578	0.96[ASN][1000 genomes]
rs17450338	0.81[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534846	0.96[ASN][1000 genomes]
rs28433735	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797845	0.81[AMR][1000 genomes]
rs55699307	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58724822	0.95[ASN][1000 genomes]
rs59616337	0.86[ASN][1000 genomes]
rs67436896	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6882531	0.94[ASW][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes]
rs72796568	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72796571	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72796593	0.81[EUR][1000 genomes]
rs72796595	0.81[EUR][1000 genomes]
rs72796596	0.81[EUR][1000 genomes]
rs7709466	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7709482	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7724901	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7729990	0.93[ASN][1000 genomes]
rs7731193	0.93[LWK][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9326758	0.85[CEU][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs972278	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830443	chr5:108326491-108496723	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv882692	chr5:108391660-108474166	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882693	chr5:108391660-108502493	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv882694	chr5:108391660-108524416	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17161607	DCP2	cis	cerebellum	SCAN
rs17161607	EFNA5	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:108422800-108444800	Weak transcription	Left Ventricle	heart
2	chr5:108435600-108446800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:108441400-108445400	Enhancers	Fetal Heart	heart
4	chr5:108441600-108447400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:108441600-108455600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:108441800-108455600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:108442000-108443000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:108442000-108443000	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr5:108442000-108443200	Enhancers	NHDF-Ad	bronchial
10	chr5:108442000-108445000	Weak transcription	Brain Anterior Caudate	brain
11	chr5:108442000-108446800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:108442000-108497400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr5:108442200-108443000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr5:108442200-108444200	Enhancers	HUVEC	blood vessel
15	chr5:108442400-108449000	Weak transcription	Pancreas	Pancrea
16	chr5:108442600-108443600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:108442600-108444200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:108442800-108445200	Weak transcription	Osteobl	bone
19	chr5:108442800-108446000	Weak transcription	HSMM	muscle
20	chr5:108442800-108455600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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