Variant report

Variant	rs12086546
Chromosome Location	chr1:56039069-56039070
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10493196	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10789002	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10789003	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10789004	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888931	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10888933	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10888934	0.95[AFR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11206618	0.85[ASN][1000 genomes]
rs11206620	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11206622	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11206625	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11206629	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11206638	0.83[EUR][1000 genomes]
rs11807964	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12026971	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12040862	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12041985	0.82[EUR][1000 genomes]
rs12044949	0.87[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12069408	0.81[ASN][1000 genomes]
rs12128185	0.85[ASN][1000 genomes]
rs12128337	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12142554	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12401977	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1392128	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1392129	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1499658	0.85[ASN][1000 genomes]
rs1604016	0.83[EUR][1000 genomes]
rs17112402	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17417716	0.82[EUR][1000 genomes]
rs1875068	0.85[ASN][1000 genomes]
rs4339898	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4927249	0.83[ASN][1000 genomes]
rs56169646	0.82[EUR][1000 genomes]
rs61774741	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61776360	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61776375	0.82[EUR][1000 genomes]
rs61776377	0.82[EUR][1000 genomes]
rs6588566	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6669248	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6675850	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72667832	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs72667838	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72667846	0.85[ASN][1000 genomes]
rs7513395	0.83[EUR][1000 genomes]
rs7544458	0.83[EUR][1000 genomes]
rs7546899	0.83[EUR][1000 genomes]
rs7555929	0.83[EUR][1000 genomes]
rs9436973	0.83[ASN][1000 genomes]
rs9787362	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56035400-56043200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:56036400-56039400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:56036400-56039400	Enhancers	Osteobl	bone
4	chr1:56036400-56041000	Weak transcription	Fetal Lung	lung
5	chr1:56037200-56039800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr1:56037200-56047200	Weak transcription	Esophagus	oesophagus
7	chr1:56037800-56039600	Enhancers	NH-A	brain
8	chr1:56038000-56039200	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr1:56038000-56039400	Enhancers	NHDF-Ad	bronchial
10	chr1:56038000-56039600	Enhancers	Hela-S3	cervix
11	chr1:56038000-56042000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:56038200-56042200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:56038400-56039200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr1:56038400-56039200	Enhancers	Psoas Muscle	Psoas
15	chr1:56038400-56039400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:56038400-56039400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr1:56038400-56039400	Enhancers	HSMMtube	muscle
18	chr1:56038400-56039600	Enhancers	Placenta Amnion	Placenta Amnion
19	chr1:56038400-56042200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr1:56038600-56039200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:56038600-56039200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:56038600-56039600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr1:56038800-56039600	Enhancers	Fetal Stomach	stomach
24	chr1:56038800-56041000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:56039000-56039200	Enhancers	Brain Substantia Nigra	brain
26	chr1:56039000-56041200	Weak transcription	HSMM	muscle
27	chr1:56039000-56045200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:56039000-56045800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:56039000-56046000	Weak transcription	NHLF	lung
30	chr1:56039000-56046800	Weak transcription	Skeletal Muscle Female	skeletal muscle

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