Variant report

Variant	esv3409706
Chromosome Location	chr20:11347552-11352350
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: 230 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:230 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs184684412	chr20:11347567-11347568	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs564378817	chr20:11347597-11347598	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs188661113	chr20:11347649-11347650	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs546871734	chr20:11347665-11347666	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs2143874	chr20:11347678-11347679	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs2143873	chr20:11347685-11347686	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs56128758	chr20:11347701-11347702	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs569270465	chr20:11347734-11347735	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs566844411	chr20:11347743-11347744	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs201320196	chr20:11347748-11347749	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs560680507	chr20:11347822-11347823	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs551358081	chr20:11347829-11347830	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs571251401	chr20:11347836-11347837	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs533927694	chr20:11347837-11347838	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs532721162	chr20:11347891-11347892	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs553534022	chr20:11347930-11347931	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs6108937	chr20:11347940-11347941	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs79167786	chr20:11347960-11347961	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs149098758	chr20:11347977-11347978	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs80007661	chr20:11347982-11347983	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs544277512	chr20:11348029-11348030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs569564966	chr20:11348035-11348036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs564548161	chr20:11348075-11348076	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs578025021	chr20:11348078-11348079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs8118110	chr20:11348115-11348116	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs560592515	chr20:11348152-11348153	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs529473952	chr20:11348166-11348167	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs549606924	chr20:11348172-11348173	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs563126117	chr20:11348175-11348176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs532076901	chr20:11348181-11348182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs181365719	chr20:11348190-11348191	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs571254438	chr20:11348199-11348200	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs146715137	chr20:11348207-11348208	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs372593976	chr20:11348208-11348209	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs185890815	chr20:11348216-11348217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs535995491	chr20:11348230-11348231	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs4813055	chr20:11348281-11348282	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs141308588	chr20:11348362-11348363	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs34360160	chr20:11348419-11348420	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs538960677	chr20:11348421-11348422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs557848383	chr20:11348465-11348466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs4813056	chr20:11348505-11348506	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs373900023	chr20:11348561-11348562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs560528400	chr20:11348577-11348578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs574182590	chr20:11348601-11348602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs62193969	chr20:11348625-11348626	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs563136890	chr20:11348728-11348729	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs575304708	chr20:11348777-11348778	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs370851773	chr20:11348809-11348810	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs1883970	chr20:11348857-11348858	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	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:58 , 50 per page) page: 1 2

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	chr20:11347200-11348000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr20:11347400-11347600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:11347400-11347800	Enhancers	NH-A	brain
9	chr20:11347600-11347800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:11347600-11347800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr20:11347600-11347800	Enhancers	HMEC	breast
12	chr20:11347800-11348800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr20:11347800-11349000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr20:11347800-11356000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr20:11348000-11354400	Weak transcription	HMEC	breast
16	chr20:11348800-11349600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr20:11348800-11349600	Enhancers	Fetal Brain Male	brain
18	chr20:11348800-11349800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr20:11348800-11350200	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr20:11349000-11349800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr20:11349400-11350400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr20:11349600-11349800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
23	chr20:11349600-11350000	ZNF genes & repeats	Esophagus	oesophagus
24	chr20:11349600-11350200	Active TSS	Fetal Lung	lung
25	chr20:11349600-11350400	ZNF genes & repeats	Aorta	Aorta
26	chr20:11349600-11350400	ZNF genes & repeats	Fetal Kidney	kidney
27	chr20:11349600-11350400	Enhancers	Gastric	stomach
28	chr20:11349600-11350400	Enhancers	Pancreas	Pancrea
29	chr20:11349600-11350600	ZNF genes & repeats	Fetal Brain Male	brain
30	chr20:11349600-11352000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr20:11349800-11350200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr20:11349800-11350400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr20:11349800-11353200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr20:11350000-11350200	Weak transcription	Esophagus	oesophagus
35	chr20:11350000-11353800	Weak transcription	Right Atrium	heart
36	chr20:11350200-11350400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr20:11350200-11350400	Enhancers	Esophagus	oesophagus
38	chr20:11350200-11350400	Flanking Bivalent TSS/Enh	Fetal Lung	lung
39	chr20:11350200-11350600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr20:11350400-11351200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr20:11350400-11352800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr20:11350400-11353200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr20:11350400-11353800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr20:11350400-11353800	Weak transcription	Esophagus	oesophagus
45	chr20:11350400-11356600	Weak transcription	Fetal Kidney	kidney
46	chr20:11350400-11360200	Weak transcription	Pancreas	Pancrea
47	chr20:11350600-11350800	Enhancers	Brain Germinal Matrix	brain
48	chr20:11350600-11353200	Weak transcription	Fetal Brain Male	brain
49	chr20:11350600-11353600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr20:11351000-11353200	Weak transcription	Brain Germinal Matrix	brain

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