Variant report

Variant	rs6790079
Chromosome Location	chr3:111485020-111485021
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10212300	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10470303	0.96[ASN][1000 genomes]
rs10934106	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10934107	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710738	1.00[ASN][1000 genomes]
rs12490166	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490595	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496925	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12496971	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497012	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13069980	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13074817	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13079085	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4284954	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4431081	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682057	0.95[ASN][1000 genomes]
rs4682305	1.00[ASN][1000 genomes]
rs62273780	1.00[ASN][1000 genomes]
rs6438003	0.86[EUR][1000 genomes]
rs6438008	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6438009	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6764720	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6768713	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6777540	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6784753	0.97[ASN][1000 genomes]
rs6786386	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6786612	0.98[ASN][1000 genomes]
rs6790072	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6792493	0.84[ASN][1000 genomes]
rs6802995	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7427201	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7609653	0.96[ASN][1000 genomes]
rs7614443	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9818574	0.96[ASN][1000 genomes]
rs9823974	0.96[ASN][1000 genomes]
rs9825915	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9834030	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9838371	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863403	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9868171	1.00[ASN][1000 genomes]
rs9870823	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111480200-111492000	Enhancers	Liver	Liver
2	chr3:111480600-111486000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr3:111481000-111487400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:111481000-111487400	Weak transcription	Right Atrium	heart
5	chr3:111481800-111485200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:111482000-111487400	Weak transcription	Pancreas	Pancrea
7	chr3:111482200-111487200	Weak transcription	Fetal Heart	heart
8	chr3:111482200-111487400	Weak transcription	Left Ventricle	heart
9	chr3:111482600-111487400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr3:111482800-111487200	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:111482800-111487400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:111483000-111487400	Weak transcription	Fetal Stomach	stomach
13	chr3:111483200-111487600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:111483200-111489200	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:111483400-111487200	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:111483400-111487400	Weak transcription	Fetal Lung	lung
17	chr3:111483800-111487600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:111484000-111486800	Weak transcription	NH-A	brain
19	chr3:111484000-111487400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:111484200-111486000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:111484200-111487000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:111484200-111487000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr3:111484200-111487200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:111484200-111487200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:111484200-111487200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:111484200-111487600	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:111484400-111486000	Weak transcription	HSMM	muscle
28	chr3:111484400-111486000	Weak transcription	HSMMtube	muscle
29	chr3:111484400-111486000	Weak transcription	NHLF	lung
30	chr3:111484400-111486400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr3:111484400-111486800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:111484400-111486800	Weak transcription	Stomach Mucosa	stomach
33	chr3:111484400-111487000	Weak transcription	Hela-S3	cervix
34	chr3:111484400-111487000	Weak transcription	HepG2	liver
35	chr3:111484400-111487000	Weak transcription	NHEK	skin
36	chr3:111484400-111487200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr3:111484400-111487400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:111484400-111487600	Weak transcription	Colon Smooth Muscle	Colon
39	chr3:111484400-111487600	Weak transcription	Fetal Intestine Small	intestine
40	chr3:111484400-111487800	Weak transcription	Fetal Intestine Large	intestine
41	chr3:111484600-111486000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:111484600-111486000	Weak transcription	HMEC	breast
43	chr3:111484600-111487000	Enhancers	A549	lung
44	chr3:111484600-111487200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr3:111484600-111487400	Weak transcription	Adipose Nuclei	Adipose
46	chr3:111484600-111487600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:111484800-111485400	Weak transcription	NHDF-Ad	bronchial
48	chr3:111484800-111486000	Weak transcription	Osteobl	bone
49	chr3:111484800-111487200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr3:111484800-111487400	Weak transcription	Rectal Smooth Muscle	rectum

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