Variant report

Variant	esv3388930
Chromosome Location	chr20:11348452-11351550
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:11351053..11352921-chr20:11353499..11355342,2	MCF-7	breast:

Extended variants
information (count: 154 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:154 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs557848383	chr20:11348465-11348466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs4813056	chr20:11348505-11348506	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs373900023	chr20:11348561-11348562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs560528400	chr20:11348577-11348578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs574182590	chr20:11348601-11348602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs62193969	chr20:11348625-11348626	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs563136890	chr20:11348728-11348729	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs575304708	chr20:11348777-11348778	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs370851773	chr20:11348809-11348810	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs1883970	chr20:11348857-11348858	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs189519706	chr20:11348864-11348865	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs34501789	chr20:11348874-11348875	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs57261719	chr20:11348886-11348887	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs565460859	chr20:11348924-11348925	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs527253028	chr20:11348925-11348926	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs546992771	chr20:11348939-11348940	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs75058343	chr20:11348982-11348983	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs529781512	chr20:11348989-11348990	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs1883969	chr20:11349014-11349015	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs533069456	chr20:11349017-11349018	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs181989016	chr20:11349062-11349063	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs538482313	chr20:11349146-11349147	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs558784152	chr20:11349178-11349179	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs7361981	chr20:11349186-11349187	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs35602600	chr20:11349215-11349216	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs77769468	chr20:11349303-11349304	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs187410063	chr20:11349373-11349374	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs534133237	chr20:11349393-11349394	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs554252677	chr20:11349395-11349396	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs2143872	chr20:11349422-11349423	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs532271933	chr20:11349509-11349510	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs78285334	chr20:11349512-11349513	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs35819105	chr20:11349562-11349563	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs116107385	chr20:11349582-11349583	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs145047350	chr20:11349583-11349584	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs60059631	chr20:11349586-11349587	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs117246789	chr20:11349591-11349592	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs369223746	chr20:11349597-11349598	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs574739101	chr20:11349604-11349605	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs529720686	chr20:11349614-11349615	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs549822394	chr20:11349618-11349619	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs569669453	chr20:11349624-11349625	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs190345977	chr20:11349625-11349626	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs552087413	chr20:11349673-11349674	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs565959653	chr20:11349675-11349676	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs35695473	chr20:11349680-11349681	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs201360880	chr20:11349686-11349687	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs534954783	chr20:11349704-11349705	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs554191460	chr20:11349705-11349706	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs567689853	chr20:11349724-11349725	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:52)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Glaucoma	21310917	CNVD
Alagille syndrome	22470819	CNVD
Lung cancer	16773561	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21804112	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Myelofibrosis	22110671	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	20409316	CNVD

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:11335000-11355400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr20:11345400-11360000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:11346600-11358600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr20:11346800-11348800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr20:11346800-11360000	Weak transcription	Psoas Muscle	Psoas
6	chr20:11347800-11348800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr20:11347800-11349000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr20:11347800-11356000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr20:11348000-11354400	Weak transcription	HMEC	breast
10	chr20:11348800-11349600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr20:11348800-11349600	Enhancers	Fetal Brain Male	brain
12	chr20:11348800-11349800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr20:11348800-11350200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr20:11349000-11349800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr20:11349400-11350400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr20:11349600-11349800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
17	chr20:11349600-11350000	ZNF genes & repeats	Esophagus	oesophagus
18	chr20:11349600-11350200	Active TSS	Fetal Lung	lung
19	chr20:11349600-11350400	ZNF genes & repeats	Aorta	Aorta
20	chr20:11349600-11350400	ZNF genes & repeats	Fetal Kidney	kidney
21	chr20:11349600-11350400	Enhancers	Gastric	stomach
22	chr20:11349600-11350400	Enhancers	Pancreas	Pancrea
23	chr20:11349600-11350600	ZNF genes & repeats	Fetal Brain Male	brain
24	chr20:11349600-11352000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr20:11349800-11350200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr20:11349800-11350400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr20:11349800-11353200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr20:11350000-11350200	Weak transcription	Esophagus	oesophagus
29	chr20:11350000-11353800	Weak transcription	Right Atrium	heart
30	chr20:11350200-11350400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr20:11350200-11350400	Enhancers	Esophagus	oesophagus
32	chr20:11350200-11350400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
33	chr20:11350200-11350600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr20:11350400-11351200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr20:11350400-11352800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr20:11350400-11353200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr20:11350400-11353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr20:11350400-11353800	Weak transcription	Esophagus	oesophagus
39	chr20:11350400-11356600	Weak transcription	Fetal Kidney	kidney
40	chr20:11350400-11360200	Weak transcription	Pancreas	Pancrea
41	chr20:11350600-11350800	Enhancers	Brain Germinal Matrix	brain
42	chr20:11350600-11353200	Weak transcription	Fetal Brain Male	brain
43	chr20:11350600-11353600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr20:11351000-11353200	Weak transcription	Brain Germinal Matrix	brain
45	chr20:11351200-11358600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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