Variant report

Variant	rs959813
Chromosome Location	chr20:1446580-1446581
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1444656..1446589-chr20:1449305..1450879,2	K562	blood:
2	chr20:1422183..1425116-chr20:1445369..1447221,2	K562	blood:
3	chr20:1446155..1447724-chr20:1468382..1469913,2	MCF-7	breast:
4	chr20:1306070..1308541-chr20:1446001..1448028,2	MCF-7	breast:
5	chr20:1437321..1440209-chr20:1445376..1448458,3	MCF-7	breast:
6	chr20:1436244..1441221-chr20:1444525..1448562,4	MCF-7	breast:
7	chr20:361485..363213-chr20:1446007..1447644,2	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction
ENSG00000125775	Chromatin interaction
ENSG00000101255	Chromatin interaction
ENSG00000266085	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11696447	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1474879	1.00[ASN][1000 genomes]
rs1474880	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16994239	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1884390	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064645	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064646	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2873522	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41308086	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58194712	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58718584	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59239479	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105101	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6105140	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109837	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109838	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6109962	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109984	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109986	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109989	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6109992	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66497853	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8124855	0.88[AMR][1000 genomes];1.00[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	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv833893	chr20:1414615-1527779	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv3375230	chr20:1446177-1448725	Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1433600-1446600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:1442000-1446600	Weak transcription	Aorta	Aorta
3	chr20:1445200-1446600	Enhancers	Pancreas	Pancrea
4	chr20:1445400-1446600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr20:1445600-1446600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr20:1445600-1446800	Flanking Active TSS	Colon Smooth Muscle	Colon
7	chr20:1445800-1446600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr20:1445800-1446600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr20:1445800-1446800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:1445800-1446800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
11	chr20:1445800-1446800	Flanking Active TSS	Brain Cingulate Gyrus	brain
12	chr20:1445800-1447000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr20:1445800-1447000	Flanking Active TSS	Rectal Smooth Muscle	rectum
14	chr20:1445800-1447400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr20:1445800-1447800	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr20:1446000-1446600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr20:1446000-1446600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:1446000-1446600	Flanking Active TSS	Ovary	ovary
19	chr20:1446000-1446600	Flanking Active TSS	Psoas Muscle	Psoas
20	chr20:1446000-1446800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr20:1446000-1446800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr20:1446000-1446800	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr20:1446000-1446800	Flanking Active TSS	Brain Germinal Matrix	brain
24	chr20:1446000-1446800	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr20:1446000-1446800	Flanking Active TSS	Colonic Mucosa	Colon
26	chr20:1446000-1446800	Flanking Active TSS	Fetal Brain Female	brain
27	chr20:1446000-1446800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr20:1446000-1446800	Flanking Active TSS	NHEK	skin
29	chr20:1446000-1447000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr20:1446000-1447000	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr20:1446000-1447000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr20:1446000-1447000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr20:1446000-1447000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr20:1446000-1447000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr20:1446000-1447200	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr20:1446000-1447800	Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr20:1446200-1446600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr20:1446200-1446600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr20:1446200-1446600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr20:1446200-1446600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr20:1446200-1446600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
42	chr20:1446200-1446600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr20:1446200-1446600	Weak transcription	Esophagus	oesophagus
44	chr20:1446200-1446600	Enhancers	Fetal Thymus	thymus
45	chr20:1446200-1446600	Enhancers	Small Intestine	intestine
46	chr20:1446200-1446600	Flanking Active TSS	HSMMtube	muscle
47	chr20:1446200-1446600	Flanking Active TSS	NHDF-Ad	bronchial
48	chr20:1446200-1446600	Flanking Active TSS	NHLF	lung
49	chr20:1446200-1446800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr20:1446200-1446800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--

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