Variant report

Variant	rs2399407
Chromosome Location	chr3:111904539-111904540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10511308	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10934154	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10934155	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10934156	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10934157	0.80[EUR][1000 genomes]
rs10934159	0.80[EUR][1000 genomes]
rs10934160	0.80[EUR][1000 genomes]
rs10934161	0.80[EUR][1000 genomes]
rs1119339	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11917180	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11918129	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11919901	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11924882	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11926448	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11926649	0.80[EUR][1000 genomes]
rs11926968	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12486083	0.80[EUR][1000 genomes]
rs12486177	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13061801	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13069541	0.80[EUR][1000 genomes]
rs13072156	0.80[EUR][1000 genomes]
rs13078927	0.80[EUR][1000 genomes]
rs13080696	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13086724	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13087387	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13090086	0.80[EUR][1000 genomes]
rs13090344	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13090432	0.80[EUR][1000 genomes]
rs13090629	0.80[EUR][1000 genomes]
rs13091981	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13092810	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13095956	0.80[EUR][1000 genomes]
rs13096855	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13097307	0.80[EUR][1000 genomes]
rs1586873	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1586874	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1602673	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2399406	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34043603	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34399151	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4234414	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4260401	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4274721	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4279068	0.80[EUR][1000 genomes]
rs4279069	0.80[EUR][1000 genomes]
rs4438628	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4440097	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4481127	0.81[EUR][1000 genomes]
rs4552323	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4592997	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4602356	0.80[EUR][1000 genomes]
rs4613425	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4618193	0.81[EUR][1000 genomes]
rs4682099	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4682371	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682386	0.80[ASN][1000 genomes]
rs4682387	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4682388	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4682389	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4682390	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57890482	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57964682	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6781137	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6796241	0.91[EUR][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	nsv1010219	chr3:111856709-111923647	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv967051	chr3:111902412-111904661	Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
3	nsv10307	chr3:111903974-112087686	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111885400-111904600	Weak transcription	Left Ventricle	heart
2	chr3:111892400-111904600	Weak transcription	Thymus	Thymus
3	chr3:111904200-111904800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:111904200-111905000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr3:111904400-111904600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:111904400-111904600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:111904400-111904600	Enhancers	Fetal Muscle Leg	muscle
8	chr3:111904400-111904800	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr3:111904400-111904800	Active TSS	iPS-18 Cell Line	embryonic stem cell
10	chr3:111904400-111904800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:111904400-111904800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:111904400-111904800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:111904400-111904800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:111904400-111904800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:111904400-111904800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:111904400-111904800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:111904400-111904800	Enhancers	Esophagus	oesophagus
18	chr3:111904400-111905000	Active TSS	H1 Cell Line	embryonic stem cell
19	chr3:111904400-111905000	Active TSS	H9 Cell Line	embryonic stem cell
20	chr3:111904400-111905000	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr3:111904400-111905000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:111904400-111905000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:111904400-111905000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:111904400-111905000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:111904400-111905000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:111904400-111905000	Active TSS	Brain Angular Gyrus	brain
27	chr3:111904400-111905000	Active TSS	Brain Hippocampus Middle	brain
28	chr3:111904400-111905000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr3:111904400-111905000	Active TSS	Fetal Brain Female	brain
30	chr3:111904400-111905000	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr3:111904400-111905200	Active TSS	HUES6 Cell Line	embryonic stem cell
32	chr3:111904400-111905200	Active TSS	iPS-15b Cell Line	embryonic stem cell

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