Variant report

Variant	rs12198549
Chromosome Location	chr6:145569151-145569152
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10080573	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747272	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11155407	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11966141	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12192050	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12197362	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12198531	0.83[AFR][1000 genomes]
rs12212061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1321528	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1474614	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546864	0.95[ASN][1000 genomes]
rs1546865	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1546866	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17074868	0.80[ASN][1000 genomes]
rs1884955	0.87[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2328651	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2328652	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2876615	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs491131	0.80[ASN][1000 genomes]
rs491794	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs507942	0.87[ASN][1000 genomes]
rs513966	0.87[AFR][1000 genomes]
rs546717	0.84[AFR][1000 genomes]
rs553160	0.87[AFR][1000 genomes]
rs559366	0.81[AFR][1000 genomes]
rs562811	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6899332	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6917361	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917689	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6924190	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6932885	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6933246	0.88[ASN][1000 genomes]
rs6942333	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs715030	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs715031	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs737436	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7744166	0.88[ASN][1000 genomes]
rs7755038	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9484958	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9484959	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9484961	0.87[EUR][1000 genomes];0.89[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	nsv1016747	chr6:144917411-145599874	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1022965	chr6:145374851-145635385	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:145567000-145570200	Weak transcription	Liver	Liver
2	chr6:145568000-145569200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:145568400-145569600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:145568600-145569200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:145568600-145569200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:145568600-145569200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:145568600-145569200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:145568600-145569400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:145568600-145569400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:145568600-145569400	Enhancers	A549	lung
11	chr6:145568600-145569400	Enhancers	HepG2	liver
12	chr6:145568600-145569400	Enhancers	NHDF-Ad	bronchial
13	chr6:145568600-145569400	Enhancers	NHEK	skin
14	chr6:145568600-145569600	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:145568800-145569200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr6:145568800-145569200	Flanking Active TSS	Osteobl	bone
17	chr6:145569000-145569200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:145569000-145569400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr6:145569000-145569400	Flanking Active TSS	Hela-S3	cervix
20	chr6:145569000-145569400	Flanking Active TSS	NH-A	brain

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