Variant report

Variant	rs17086188
Chromosome Location	chr5:95845854-95845855
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10515239	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11135463	0.99[ASN][1000 genomes]
rs12519858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12519926	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12519944	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12520029	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12520030	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12520472	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs155211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs155212	0.99[ASN][1000 genomes]
rs156004	1.00[EUR][1000 genomes]
rs156014	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17086176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17086192	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2350243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs261969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869289	0.81[EUR][1000 genomes]
rs4869294	0.87[CEU][hapmap]
rs62365716	0.99[ASN][1000 genomes]
rs7729313	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8180437	1.00[CEU][hapmap]

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	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1026484	chr5:95759910-95961518	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Menarche (age at onset)	25231870	GWAS catalog

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95838400-95849200	Enhancers	Hela-S3	cervix
2	chr5:95844200-95846400	Enhancers	Fetal Intestine Large	intestine
3	chr5:95844200-95846400	Enhancers	Fetal Intestine Small	intestine
4	chr5:95844200-95846800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:95844200-95846800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:95844600-95852400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr5:95844800-95846400	Enhancers	Muscle Satellite Cultured Cells	--
8	chr5:95845000-95846000	Enhancers	Sigmoid Colon	Sigmoid Colon
9	chr5:95845000-95846400	Enhancers	Osteobl	bone
10	chr5:95845200-95846200	Enhancers	NHDF-Ad	bronchial
11	chr5:95845200-95846400	Enhancers	NHLF	lung
12	chr5:95845600-95846200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:95845600-95846200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:95845600-95846200	Active TSS	A549	lung
15	chr5:95845800-95846000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:95845800-95846200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:95845800-95846400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:95845800-95846400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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