Variant report

Variant	rs1390083
Chromosome Location	chr3:23299166-23299167
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1027380	0.88[ASN][1000 genomes]
rs11711630	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11715107	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13087416	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095887	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1495133	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1495134	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1552931	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17342342	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2036045	0.83[CEU][hapmap]
rs2047340	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes]
rs2055155	0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2088129	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132145	0.96[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2132147	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2132148	0.88[CEU][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2132149	0.87[CEU][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2201481	0.81[EUR][1000 genomes]
rs36073188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4293660	0.82[ASN][1000 genomes]
rs4334589	0.97[ASN][1000 genomes]
rs4858065	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4858066	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858488	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4858498	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6769959	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6790185	1.00[CEU][hapmap];0.93[CHB][hapmap];0.85[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6799861	0.91[ASN][1000 genomes]
rs6806387	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73149661	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618910	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7629327	0.93[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs7635882	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636532	0.80[ASN][1000 genomes]
rs7648425	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs778493	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap]
rs903519	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs923996	0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs9826103	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9836135	0.84[CEU][hapmap];0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9840015	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9844558	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9848331	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

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	nsv834636	chr3:23138653-23301443	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv589947	chr3:23277838-23403943	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv589948	chr3:23287141-23390221	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23283600-23302200	Weak transcription	Left Ventricle	heart
2	chr3:23292800-23304200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:23292800-23306800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:23293000-23303800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:23293200-23299400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr3:23294800-23299200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr3:23295200-23321800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:23296000-23300600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:23296000-23302000	Weak transcription	Lung	lung
10	chr3:23296400-23302000	Weak transcription	Psoas Muscle	Psoas
11	chr3:23297000-23307000	Weak transcription	Primary B cells from cord blood	blood
12	chr3:23298000-23299800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:23298200-23299800	Enhancers	Brain Cingulate Gyrus	brain
14	chr3:23298400-23299200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:23298400-23300000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:23298400-23302000	Weak transcription	Pancreas	Pancrea
17	chr3:23298400-23305200	Weak transcription	HSMM	muscle
18	chr3:23298600-23299800	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr3:23298600-23300600	Weak transcription	Brain Angular Gyrus	brain
20	chr3:23298600-23300600	Weak transcription	Right Atrium	heart
21	chr3:23298600-23302200	Weak transcription	Brain Anterior Caudate	brain
22	chr3:23298800-23299600	Weak transcription	Brain Substantia Nigra	brain
23	chr3:23298800-23299600	Weak transcription	Osteobl	bone
24	chr3:23298800-23304400	Weak transcription	Right Ventricle	heart
25	chr3:23298800-23311000	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:23298800-23336600	Weak transcription	Thymus	Thymus
27	chr3:23299000-23299200	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr3:23299000-23299400	Weak transcription	A549	lung
29	chr3:23299000-23302200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:23299000-23304200	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:23299000-23304400	Weak transcription	NHEK	skin
32	chr3:23299000-23306800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:23299000-23314200	Weak transcription	Primary T cells from cord blood	blood

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