Variant report

Variant	esv3352570
Chromosome Location	chr20:52527249-52527533
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52523557..52527351-chr20:55838528..55843177,6	MCF-7	breast:
2	chr20:49378353..49380763-chr20:52526997..52528562,2	MCF-7	breast:
3	chr17:59477246..59479573-chr20:52526014..52528128,2	MCF-7	breast:
4	chr20:52526939..52530902-chr3:43731432..43734302,3	MCF-7	breast:
5	chr20:45986485..45988930-chr20:52526541..52529264,2	MCF-7	breast:
6	chr20:52518754..52529234-chr20:55834628..55846143,16	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PFDN4-3	chr20:52527092-52527460	NONHSAT080410

No data

Variant related genes	Relation type
ENSG00000121068	chromatin interactions
ENSG00000160746	chromatin interactions
ENSG00000226308	chromatin interactions
ENSG00000011198	chromatin interactions
ENSG00000101144	chromatin interactions
ENSG00000267131	chromatin interactions

Extended variants
information (count: 21 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs551166251	chr20:52527261-52527262	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
2	rs571071924	chr20:52527274-52527275	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
3	rs536841669	chr20:52527275-52527276	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
4	rs6064022	chr20:52527297-52527298	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
5	rs73914427	chr20:52527321-52527322	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs145064553	chr20:52527322-52527323	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
7	rs118156812	chr20:52527330-52527331	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
8	rs552664040	chr20:52527339-52527340	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
9	rs572976201	chr20:52527344-52527345	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
10	rs73914429	chr20:52527351-52527352	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs558675443	chr20:52527352-52527353	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
12	rs77779826	chr20:52527355-52527356	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
13	rs529996071	chr20:52527362-52527363	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
14	rs57069132	chr20:52527380-52527381	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
15	rs184670648	chr20:52527417-52527418	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
16	rs144159523	chr20:52527426-52527427	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region lncRNA	6 gene(s)	Overlapped CNVs	n/a
17	rs369601102	chr20:52527469-52527470	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
18	rs531643227	chr20:52527470-52527471	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
19	rs532483757	chr20:52527499-52527500	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
20	rs75503806	chr20:52527505-52527506	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
21	rs538727136	chr20:52527507-52527508	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Gastric cancer	17908304	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Medulloblastoma	21979893	CNVD
Urothelial carcinoma	21177765	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Colorectal cancer	21645411	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	21693616	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Endometrial cancer	22040021	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
colon cancer	17210682	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	22028636	CNVD
Breast cancer	21264507	CNVD
Thyroid cancer	19087340	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Colorectal cancer	19359472	CNVD
Gastric cancer	17167181	CNVD
Myeloproliferative neoplasm	19047681	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Breast cancer	17603634	CNVD
Melanoma	18172304	CNVD
Breast cancer	16608533	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17133270	CNVD
Oral cancer	21386901	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Myelodysplastic syndrome	21251322	CNVD
Ductal carcinoma	22052326	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Gastric cancer	20585902	CNVD
Ductal carcinoma	18381933	CNVD
Cancer	21129771	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	20864512	CNVD
Ovarian cancer	22174824	CNVD
Lung cancer	16740712	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16620391	CNVD
Okamoto syndrome	17623483	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21785460	CNVD
Bladder cancer	21909424	CNVD
Biliary cancer	19435499	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Cervical cancer	16585170	CNVD
Ovarian cancer	20844748	CNVD
Hirschsprung''s Disease	21712996	CNVD
Breast cancer	21364760	CNVD
Breast cancer	20459607	CNVD
Gastric cancer	18160780	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52516800-52531200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr20:52517000-52530800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr20:52518400-52528800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr20:52518600-52529800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr20:52518600-52532000	Weak transcription	Esophagus	oesophagus
6	chr20:52518800-52531000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr20:52518800-52532000	Weak transcription	Gastric	stomach
8	chr20:52519000-52530800	Weak transcription	Adipose Nuclei	Adipose
9	chr20:52519200-52529000	Weak transcription	Lung	lung
10	chr20:52519200-52530800	Weak transcription	Right Atrium	heart
11	chr20:52520800-52530400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr20:52523800-52528600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr20:52523800-52531200	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr20:52523800-52531800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr20:52524000-52529800	Weak transcription	HSMM	muscle
16	chr20:52524000-52529800	Weak transcription	HSMMtube	muscle
17	chr20:52524400-52529200	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr20:52524800-52530000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr20:52525000-52528400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:52525000-52529800	Weak transcription	HMEC	breast
21	chr20:52525000-52529800	Weak transcription	NHEK	skin
22	chr20:52525000-52530000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr20:52525200-52528000	Weak transcription	K562	blood
24	chr20:52525600-52530000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:52525600-52530600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr20:52525600-52530800	Weak transcription	Stomach Mucosa	stomach
27	chr20:52525800-52528400	Weak transcription	A549	lung
28	chr20:52525800-52530000	Weak transcription	NHLF	lung
29	chr20:52525800-52530400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr20:52525800-52530800	Weak transcription	Thymus	Thymus
31	chr20:52526000-52528600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr20:52526000-52530000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr20:52526000-52530600	Weak transcription	Fetal Kidney	kidney
34	chr20:52526200-52529000	Weak transcription	NHDF-Ad	bronchial
35	chr20:52526200-52529800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr20:52526200-52529800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr20:52526200-52530000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr20:52526200-52530600	Weak transcription	Fetal Intestine Large	intestine
39	chr20:52526200-52530600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr20:52526200-52530800	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr20:52526200-52530800	Weak transcription	GM12878-XiMat	blood
42	chr20:52526200-52531000	Weak transcription	Hela-S3	cervix
43	chr20:52526400-52529800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr20:52526400-52530400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr20:52526800-52527600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr20:52526800-52527600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr20:52527000-52530400	Weak transcription	Primary B cells from cord blood	blood
48	chr20:52527000-52530800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr20:52527200-52528600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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