Variant report

Variant	rs12490031
Chromosome Location	chr3:156994234-156994235
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10428149	0.83[EUR][1000 genomes]
rs10936082	0.95[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11709487	1.00[ASW][hapmap];1.00[CEU][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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11718332	0.80[TSI][hapmap]
rs12489852	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12491378	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12496692	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1500913	0.88[MEX][hapmap]
rs1500914	0.88[MEX][hapmap];0.80[TSI][hapmap]
rs1500926	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1566520	0.80[TSI][hapmap]
rs17388505	1.00[ASW][hapmap];1.00[CEU][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];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915952	0.89[YRI][hapmap]
rs2305621	0.86[CEU][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs34650246	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56003856	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56375731	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61068670	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61473987	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279638	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279639	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62279641	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62281371	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62281372	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62281373	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6441125	0.81[EUR][1000 genomes]
rs67643214	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6769039	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6793166	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6803886	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73154644	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73154694	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7618171	0.95[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs9864194	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12490031	KCNAB1	cis	cerebellum	SCAN
rs12490031	SSR3	cis	cerebellum	SCAN

Chromatin state (count:22 , 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	chr3:156990800-156994600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:156991000-156994600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:156991200-156994600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:156991800-156995200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:156992000-156996800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:156992400-156994400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:156992400-156994400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr3:156992600-157000200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:156992800-156994400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:156993800-156995400	Enhancers	H9 Cell Line	embryonic stem cell
19	chr3:156994000-157000000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr3:156994200-156997000	Weak transcription	Osteobl	bone
21	chr3:156994200-156997200	Weak transcription	NHDF-Ad	bronchial
22	chr3:156994200-156998800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links