Variant report

Variant	rs2160052
Chromosome Location	chr3:118641879-118641880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11927719	0.89[CEU][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs12487299	0.83[EUR][1000 genomes]
rs12489856	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829163	0.89[CEU][hapmap];0.92[EUR][1000 genomes]
rs1879552	0.91[EUR][1000 genomes]
rs2110368	0.89[CEU][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes]
rs2110369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215811	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866317	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36052974	0.91[EUR][1000 genomes]
rs58464946	0.92[EUR][1000 genomes]
rs6765168	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs6782002	1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6786886	0.93[ASW][hapmap]
rs6795936	0.89[CEU][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs6802658	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73183699	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73185803	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610212	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs9289117	0.93[ASW][hapmap]
rs9848979	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9854506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9878706	0.93[ASW][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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2160052	IGSF11	cis	cerebellum	SCAN
rs2160052	B4GALT4	cis	parietal	SCAN
rs2160052	IGSF11	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118619800-118651400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:118620200-118663200	Weak transcription	Pancreas	Pancrea
3	chr3:118622000-118644600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:118627800-118642200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:118641400-118643000	Enhancers	Brain Substantia Nigra	brain
6	chr3:118641600-118642000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:118641600-118642200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:118641600-118642200	Strong transcription	Ovary	ovary
9	chr3:118641600-118642600	Enhancers	Brain Cingulate Gyrus	brain
10	chr3:118641600-118642800	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:118641600-118642800	Enhancers	Brain Angular Gyrus	brain
12	chr3:118641600-118642800	Enhancers	Brain Anterior Caudate	brain
13	chr3:118641600-118642800	Enhancers	Brain Hippocampus Middle	brain
14	chr3:118641800-118644600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links