Variant report

Variant	rs6886088
Chromosome Location	chr5:152460791-152460792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10515680	0.86[EUR][1000 genomes]
rs1123202	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152961	0.86[AFR][1000 genomes]
rs12516389	0.86[AFR][1000 genomes]
rs12517903	0.86[AFR][1000 genomes]
rs12518081	0.86[AFR][1000 genomes]
rs12518199	0.86[AFR][1000 genomes]
rs13154170	0.86[AFR][1000 genomes]
rs13168691	0.86[AFR][1000 genomes]
rs1438935	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17490495	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17490523	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17490621	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17490669	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17491791	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493016	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493121	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17493476	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17494099	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17576736	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17578068	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17578717	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2349021	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34244108	0.86[AFR][1000 genomes]
rs34316705	0.86[AFR][1000 genomes]
rs35029802	0.86[AFR][1000 genomes]
rs35708928	0.86[AFR][1000 genomes]
rs4958332	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958603	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958605	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4958608	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60221066	0.86[EUR][1000 genomes]
rs67942753	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6887416	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71588075	0.86[AFR][1000 genomes]
rs71588077	0.86[AFR][1000 genomes]
rs71588079	0.86[AFR][1000 genomes]
rs72808724	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73284261	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73284269	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73284276	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73284282	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73284294	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73284298	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7443245	0.86[AFR][1000 genomes]
rs998275	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv600089	chr5:152200109-152488891	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017812	chr5:152220845-152467431	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv537928	chr5:152220845-152467431	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv883050	chr5:152277537-152540026	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv949596	chr5:152343943-152548821	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6886088	MYOZ3	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152458600-152461000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr5:152459200-152463800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:152459400-152461000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:152460000-152461200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:152460000-152462800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:152460400-152462000	Enhancers	Pancreatic Islets	Pancreatic Islet
7	chr5:152460600-152461400	Enhancers	HMEC	breast
8	chr5:152460600-152461400	Enhancers	NHEK	skin

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