Variant report

Variant	rs2047647
Chromosome Location	chr3:156996988-156996989
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10755111	0.89[CEU][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10804777	1.00[CEU][hapmap];0.95[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];0.98[ASN][1000 genomes]
rs10936076	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10936077	0.87[MEX][hapmap];0.84[AMR][1000 genomes]
rs1157738	0.82[CHB][hapmap]
rs12486155	0.83[AMR][1000 genomes]
rs12486304	0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12490120	0.81[CEU][hapmap];0.86[AMR][1000 genomes]
rs12633099	0.84[AMR][1000 genomes]
rs12634905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12637932	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1403104	0.87[CHB][hapmap]
rs1403105	0.89[CEU][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1403107	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1403109	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs1500927	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1546260	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs16827308	0.86[CHB][hapmap]
rs2062607	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2321743	0.89[CEU][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4679790	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4679791	0.89[CEU][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4680353	0.85[CEU][hapmap];0.87[MEX][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55734537	0.81[AMR][1000 genomes]
rs73156724	0.84[AMR][1000 genomes]
rs7636413	0.91[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7643340	0.82[AMR][1000 genomes]
rs872652	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2047647	SSR3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156967200-157000000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr3:156967200-157000000	Weak transcription	NH-A	brain
3	chr3:156967200-157007800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:156979600-156997000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:156982400-156997000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:156984200-156998200	Weak transcription	HUVEC	blood vessel
7	chr3:156988000-157005800	Weak transcription	Pancreas	Pancrea
8	chr3:156989400-156999800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:156992600-157000200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:156994000-157000000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:156994200-156997000	Weak transcription	Osteobl	bone
12	chr3:156994200-156997200	Weak transcription	NHDF-Ad	bronchial
13	chr3:156994200-156998800	Weak transcription	HSMM	muscle
14	chr3:156994400-156998000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:156994400-156998000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:156994400-156998000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr3:156994600-156998600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:156996400-156997400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:156996800-156997400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr3:156996800-156997600	Enhancers	K562	blood

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