Variant report

Variant	rs3934640
Chromosome Location	chr5:111891377-111891378
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10038874	0.93[EUR][1000 genomes]
rs10050436	0.95[EUR][1000 genomes]
rs10055787	0.95[EUR][1000 genomes]
rs10055908	0.93[EUR][1000 genomes]
rs10056032	0.95[EUR][1000 genomes]
rs10060366	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10060474	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10062535	0.92[EUR][1000 genomes]
rs10062917	0.95[EUR][1000 genomes]
rs10063938	0.95[EUR][1000 genomes]
rs10064939	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10065383	0.95[ASN][1000 genomes]
rs10065523	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10065629	0.95[EUR][1000 genomes]
rs10070796	0.95[EUR][1000 genomes]
rs10074435	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10077808	0.94[ASN][1000 genomes]
rs10463637	0.95[EUR][1000 genomes]
rs10463640	0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10515442	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs11241169	0.94[EUR][1000 genomes]
rs11241170	0.94[EUR][1000 genomes]
rs11241172	0.92[EUR][1000 genomes]
rs11241173	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11952093	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11955149	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11955894	0.93[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap]
rs13357891	0.95[EUR][1000 genomes]
rs1530508	0.95[EUR][1000 genomes]
rs1530509	0.95[EUR][1000 genomes]
rs1530510	0.95[EUR][1000 genomes]
rs2121162	0.95[EUR][1000 genomes]
rs2121163	0.95[EUR][1000 genomes]
rs2121164	0.93[EUR][1000 genomes]
rs2416291	0.94[EUR][1000 genomes]
rs28671308	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28703859	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs338870	0.80[EUR][1000 genomes]
rs341309	0.81[JPT][hapmap]
rs341314	0.81[JPT][hapmap]
rs341319	0.82[JPT][hapmap]
rs341328	0.82[JPT][hapmap]
rs341331	0.82[JPT][hapmap]
rs456305	0.81[JPT][hapmap]
rs456491	0.81[JPT][hapmap]
rs458508	0.81[JPT][hapmap]
rs463532	0.87[JPT][hapmap]
rs465644	0.82[JPT][hapmap]
rs4958049	0.95[EUR][1000 genomes]
rs4958050	0.95[EUR][1000 genomes]
rs55655201	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55813767	0.91[EUR][1000 genomes]
rs56034571	0.91[EUR][1000 genomes]
rs67793660	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72793937	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72793965	0.95[ASN][1000 genomes]
rs7378714	0.92[EUR][1000 genomes]
rs9790874	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9885457	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv882715	chr5:111836278-111894491	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
3	nsv882716	chr5:111848890-111894491	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:111886400-111891800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr5:111889800-111892200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr5:111890000-111891400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:111890000-111892000	Enhancers	NHLF	lung
5	chr5:111890200-111891400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr5:111890200-111891800	Enhancers	HSMMtube	muscle
7	chr5:111890600-111891400	Enhancers	Adipose Nuclei	Adipose
8	chr5:111890600-111891400	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr5:111890600-111891600	Enhancers	Brain Hippocampus Middle	brain
10	chr5:111890600-111891800	Enhancers	Brain Cingulate Gyrus	brain
11	chr5:111890800-111891400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:111890800-111891400	Enhancers	Brain Substantia Nigra	brain
13	chr5:111890800-111891400	Weak transcription	Fetal Brain Female	brain
14	chr5:111890800-111891600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:111890800-111891600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:111890800-111891600	Enhancers	Osteobl	bone
17	chr5:111890800-111892200	Enhancers	HSMM	muscle
18	chr5:111891000-111891400	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr5:111891000-111891600	Enhancers	Brain Angular Gyrus	brain
20	chr5:111891000-111891800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:111891000-111892200	Weak transcription	Fetal Heart	heart
22	chr5:111891000-111892200	Enhancers	NHDF-Ad	bronchial
23	chr5:111891200-111891400	Enhancers	Left Ventricle	heart
24	chr5:111891200-111891400	Enhancers	Ovary	ovary
25	chr5:111891200-111891400	Enhancers	Stomach Smooth Muscle	stomach
26	chr5:111891200-111891600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:111891200-111891800	Enhancers	Brain Anterior Caudate	brain
28	chr5:111891200-111899200	Weak transcription	Aorta	Aorta

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