Variant report

Variant	rs10484458
Chromosome Location	chr6:113785448-113785449
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11153422	0.82[ASN][1000 genomes]
rs12175106	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12526316	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12527509	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12528387	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1555030	0.92[ASN][1000 genomes]
rs1883170	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2049924	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2092088	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2142638	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142640	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179114	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179115	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179116	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179117	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2348298	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2348299	0.83[ASN][1000 genomes]
rs2348300	0.83[ASN][1000 genomes]
rs2348301	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4945951	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58748285	0.81[EUR][1000 genomes]
rs6903255	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6916484	0.82[ASN][1000 genomes]
rs6925126	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928402	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6936596	0.91[ASN][1000 genomes]
rs721464	0.90[ASN][1000 genomes]
rs724290	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7751070	0.82[ASN][1000 genomes]
rs7766686	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7771683	0.90[ASN][1000 genomes]
rs909542	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9320451	0.80[CEU][hapmap];0.91[CHB][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9320452	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9320460	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9372363	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9372364	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9374402	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9374403	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374405	0.80[ASN][1000 genomes]
rs9384867	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9384868	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9387146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9387147	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9387148	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9387149	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398344	0.90[EUR][1000 genomes]
rs9398345	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398346	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9398347	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9400626	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9400628	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9400629	0.92[ASN][1000 genomes]
rs9400630	0.81[ASN][1000 genomes]
rs9488196	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9488198	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9488199	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9488202	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9488205	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916294	chr6:113518489-113904305	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1034256	chr6:113703567-113793790	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1021815	chr6:113703567-113799956	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv518991	chr6:113760526-113799618	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10484458	GOPC	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:113772400-113785800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr6:113777200-113785600	Weak transcription	A549	lung
3	chr6:113780400-113785600	Weak transcription	NH-A	brain
4	chr6:113780400-113785800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:113780600-113785800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:113783200-113785800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:113784600-113786000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr6:113785000-113787000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:113785000-113787200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:113785200-113788800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr6:113785200-113788800	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr6:113785400-113786000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr6:113785400-113786600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:113785400-113786800	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:113785400-113787000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:113785400-113787000	Enhancers	HMEC	breast
17	chr6:113785400-113787000	Enhancers	HUVEC	blood vessel
18	chr6:113785400-113787000	Enhancers	NHEK	skin
19	chr6:113785400-113787000	Enhancers	NHLF	lung
20	chr6:113785400-113787000	Enhancers	Osteobl	bone
21	chr6:113785400-113787200	Enhancers	Hela-S3	cervix
22	chr6:113785400-113787400	Enhancers	NHDF-Ad	bronchial
23	chr6:113785400-113787800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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