Variant report

Variant	rs6582686
Chromosome Location	chr12:47313346-47313347
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10785646	0.92[EUR][1000 genomes]
rs10881009	0.85[EUR][1000 genomes]
rs10881011	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10881013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11183625	0.80[CHB][hapmap]
rs11183661	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11183665	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11183666	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11183671	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183672	0.92[EUR][1000 genomes]
rs11609950	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12229470	0.85[EUR][1000 genomes]
rs12423364	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1986584	0.85[EUR][1000 genomes]
rs2253630	0.84[EUR][1000 genomes]
rs2465221	0.80[EUR][1000 genomes]
rs2465222	0.80[EUR][1000 genomes]
rs2465223	0.80[EUR][1000 genomes]
rs2465227	0.80[EUR][1000 genomes]
rs2465228	0.80[EUR][1000 genomes]
rs2465229	0.83[EUR][1000 genomes]
rs2465230	0.82[CEU][hapmap];0.85[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2465232	0.84[EUR][1000 genomes]
rs2465597	0.84[EUR][1000 genomes]
rs2465617	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2465627	0.84[EUR][1000 genomes]
rs2465628	0.84[EUR][1000 genomes]
rs2465630	0.84[EUR][1000 genomes]
rs4374015	0.80[CHB][hapmap]
rs4405401	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4586261	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7137808	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7138703	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7295618	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7963326	0.85[EUR][1000 genomes]
rs7966987	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7975211	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6582686	CCNT1	cis	parietal	SCAN
rs6582686	RAPGEF3	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47309200-47314800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:47310200-47313400	Weak transcription	Fetal Lung	lung
3	chr12:47311000-47315800	Weak transcription	Placenta	Placenta
4	chr12:47311200-47313600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:47311200-47313600	Weak transcription	Fetal Muscle Leg	muscle
6	chr12:47311200-47314800	Weak transcription	Fetal Stomach	stomach
7	chr12:47311400-47313400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:47311400-47313400	Weak transcription	NHLF	lung
9	chr12:47311400-47314800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr12:47311400-47315000	Weak transcription	Osteobl	bone
11	chr12:47311600-47313400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:47311600-47315000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:47311600-47315000	Weak transcription	HMEC	breast
14	chr12:47311800-47314800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:47313000-47313600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr12:47313000-47314000	Enhancers	HSMMtube	muscle
17	chr12:47313200-47313600	Enhancers	NHDF-Ad	bronchial
18	chr12:47313200-47314000	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr12:47313200-47314000	Enhancers	HSMM	muscle
20	chr12:47313200-47315000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:47313200-47316200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:47313200-47316400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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