Variant report

Variant	rs1566478
Chromosome Location	chr3:20710619-20710620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1566479	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17808771	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17809304	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17809565	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2366311	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4857964	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4857967	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4857968	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55964255	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs56168640	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56286961	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs62234989	0.83[AFR][1000 genomes]
rs62237468	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62237495	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62237497	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62237499	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62237500	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62237501	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62237509	0.83[AMR][1000 genomes]
rs62242111	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62242112	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv876598	chr3:20242143-20970042	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv876599	chr3:20264950-20813009	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv876603	chr3:20626326-20727885	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv460460	chr3:20638228-20718124	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
7	nsv589866	chr3:20638228-20718124	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
8	nsv876604	chr3:20646486-20710994	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20708000-20711400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:20708000-20711600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:20708200-20711600	Enhancers	NHDF-Ad	bronchial
4	chr3:20709200-20711200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:20709200-20711400	Enhancers	Fetal Heart	heart
6	chr3:20709400-20711000	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr3:20709400-20711000	Enhancers	NH-A	brain
8	chr3:20709400-20711600	Enhancers	Ovary	ovary
9	chr3:20709400-20711600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr3:20709400-20712400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr3:20709800-20711400	Enhancers	Brain Germinal Matrix	brain
12	chr3:20709800-20711800	Enhancers	Brain Cingulate Gyrus	brain
13	chr3:20710000-20711000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr3:20710000-20711000	Enhancers	Right Atrium	heart
15	chr3:20710000-20711400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:20710000-20711400	Enhancers	Brain Angular Gyrus	brain
17	chr3:20710000-20711400	Enhancers	Fetal Brain Male	brain
18	chr3:20710000-20711600	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr3:20710000-20711600	Enhancers	Brain Substantia Nigra	brain
20	chr3:20710000-20711600	Enhancers	Fetal Muscle Leg	muscle
21	chr3:20710000-20711600	Enhancers	Left Ventricle	heart
22	chr3:20710000-20711600	Enhancers	Pancreas	Pancrea
23	chr3:20710000-20711600	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr3:20710000-20711600	Enhancers	Stomach Smooth Muscle	stomach
25	chr3:20710000-20711800	Enhancers	Psoas Muscle	Psoas
26	chr3:20710200-20710800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:20710200-20711000	Enhancers	Brain Anterior Caudate	brain
28	chr3:20710200-20711200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:20710200-20711600	Enhancers	Aorta	Aorta
30	chr3:20710400-20711000	Enhancers	Colon Smooth Muscle	Colon
31	chr3:20710400-20711200	Enhancers	Adipose Nuclei	Adipose
32	chr3:20710600-20711000	Flanking Active TSS	Brain Hippocampus Middle	brain
33	chr3:20710600-20711000	Enhancers	Pancreatic Islets	Pancreatic Islet

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