Variant report

Variant	rs28713425
Chromosome Location	chr5:15366545-15366546
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10045262	0.83[AMR][1000 genomes]
rs10053676	0.83[AMR][1000 genomes]
rs10059008	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10060027	0.83[AMR][1000 genomes]
rs10063263	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10069407	0.83[AMR][1000 genomes]
rs10077393	1.00[EUR][1000 genomes]
rs10475048	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs11133817	1.00[EUR][1000 genomes]
rs13356380	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs13358244	0.83[AMR][1000 genomes]
rs13359958	0.83[AMR][1000 genomes]
rs1447279	0.83[AMR][1000 genomes]
rs1529487	1.00[EUR][1000 genomes]
rs16903856	0.83[AMR][1000 genomes]
rs16903858	0.83[AMR][1000 genomes]
rs16903864	1.00[EUR][1000 genomes]
rs16903892	1.00[EUR][1000 genomes]
rs188592	1.00[EUR][1000 genomes]
rs2402164	1.00[EUR][1000 genomes]
rs28503726	0.83[AMR][1000 genomes]
rs28536119	0.83[AMR][1000 genomes]
rs28570342	0.83[AMR][1000 genomes]
rs28710989	0.83[AMR][1000 genomes]
rs28716171	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2896211	1.00[EUR][1000 genomes]
rs304557	1.00[EUR][1000 genomes]
rs304559	1.00[EUR][1000 genomes]
rs304560	1.00[EUR][1000 genomes]
rs304561	1.00[EUR][1000 genomes]
rs304562	1.00[EUR][1000 genomes]
rs4701626	1.00[EUR][1000 genomes]
rs4701628	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4701629	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4702074	1.00[EUR][1000 genomes]
rs4702075	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4702077	1.00[EUR][1000 genomes]
rs512861	1.00[EUR][1000 genomes]
rs572051	1.00[EUR][1000 genomes]
rs575014	1.00[EUR][1000 genomes]
rs57991493	1.00[EUR][1000 genomes]
rs598853	1.00[EUR][1000 genomes]
rs609984	1.00[EUR][1000 genomes]
rs623156	1.00[EUR][1000 genomes]
rs633807	1.00[EUR][1000 genomes]
rs652985	1.00[EUR][1000 genomes]
rs6554885	1.00[EUR][1000 genomes]
rs683393	1.00[EUR][1000 genomes]
rs685706	1.00[EUR][1000 genomes]
rs73751952	1.00[EUR][1000 genomes]
rs73751955	1.00[EUR][1000 genomes]
rs7709371	1.00[EUR][1000 genomes]
rs7710669	0.83[AMR][1000 genomes]
rs7717617	1.00[EUR][1000 genomes]
rs7736609	0.83[AMR][1000 genomes]
rs9312883	0.83[AMR][1000 genomes]
rs9312884	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9312885	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9312886	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9968651	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv516929	chr5:15087791-15870300	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1023068	chr5:15095221-15863583	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv869040	chr5:15097602-15866117	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530222	chr5:15151662-15851485	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv881558	chr5:15291398-15420775	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:15363600-15368800	Enhancers	Fetal Heart	heart
2	chr5:15364400-15368000	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr5:15364600-15366600	Enhancers	HUVEC	blood vessel
4	chr5:15364800-15366600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:15364800-15371400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:15365000-15366800	Weak transcription	Brain Substantia Nigra	brain
7	chr5:15365200-15366800	Enhancers	Fetal Lung	lung
8	chr5:15365200-15367000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:15365600-15367000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr5:15366400-15366800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:15366400-15367200	Enhancers	Right Ventricle	heart
12	chr5:15366400-15367800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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