Variant report

Variant	esv3403907
Chromosome Location	chr20:25581152-25585550
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25560873..25562976-chr20:25579297..25581436,2	MCF-7	breast:
2	chr20:25581473..25584276-chr20:25603857..25605738,2	K562	blood:
3	chr20:25581299..25586315-chr20:25601577..25606333,5	MCF-7	breast:
4	chr20:25579638..25582269-chr20:25599435..25601779,2	K562	blood:
5	chr20:25578107..25581222-chr20:25601982..25605095,3	MCF-7	breast:
6	chr20:25582607..25585301-chr20:25602976..25605414,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213742	chromatin interactions
ENSG00000170191	chromatin interactions

Extended variants
information (count: 190 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:190 , 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	rs535908573	chr20:25581211-25581212	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs73339343	chr20:25581213-25581214	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs200413207	chr20:25581255-25581256	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs184832096	chr20:25581318-25581319	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs540871118	chr20:25581397-25581398	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs6132850	chr20:25581424-25581425	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs577548514	chr20:25581425-25581426	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs543336055	chr20:25581434-25581435	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs149010266	chr20:25581473-25581474	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs115066894	chr20:25581524-25581525	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs376532989	chr20:25581536-25581537	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs549018545	chr20:25581539-25581540	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs559230203	chr20:25581546-25581547	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs535116680	chr20:25581548-25581549	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs548046207	chr20:25581559-25581560	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs571139842	chr20:25581565-25581566	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs533637881	chr20:25581596-25581597	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs550510778	chr20:25581606-25581607	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs569993670	chr20:25581656-25581657	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs189288322	chr20:25581685-25581686	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs555824868	chr20:25581697-25581698	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs375081801	chr20:25581704-25581705	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs180889811	chr20:25581758-25581759	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs547054920	chr20:25581806-25581807	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs557504351	chr20:25581807-25581808	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs143798460	chr20:25581830-25581831	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs543275330	chr20:25581844-25581845	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs115797456	chr20:25581861-25581862	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs369400337	chr20:25581875-25581876	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs573578683	chr20:25581882-25581883	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs542298823	chr20:25581934-25581935	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs559383719	chr20:25581936-25581937	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs58877578	chr20:25581972-25581973	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
34	rs545145054	chr20:25582055-25582056	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs570432331	chr20:25582149-25582150	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs13040655	chr20:25582197-25582198	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	mRNA abundance
37	rs386813597	chr20:25582220-25582221	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs533574907	chr20:25582228-25582229	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs201367525	chr20:25582237-25582238	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs115866883	chr20:25582238-25582239	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs111143827	chr20:25582239-25582240	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs202109892	chr20:25582246-25582247	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs374082672	chr20:25582247-25582248	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs111721423	chr20:25582249-25582250	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs201153528	chr20:25582261-25582262	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs377434136	chr20:25582266-25582267	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs368562016	chr20:25582271-25582272	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs60947849	chr20:25582285-25582286	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs370799292	chr20:25582292-25582293	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs8124947	chr20:25582295-25582296	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
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
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	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
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Breast cancer	16608533	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Breast cancer	17133270	CNVD
Thrombophilia	17576883	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Hepatocellular carcinoma	22174799	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
Oral cancer	21386901	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25573800-25590400	Weak transcription	Thymus	Thymus
2	chr20:25576000-25585800	Weak transcription	Fetal Stomach	stomach
3	chr20:25580200-25603000	Weak transcription	Fetal Brain Male	brain
4	chr20:25580600-25581400	Enhancers	Fetal Heart	heart
5	chr20:25580600-25582000	Enhancers	Osteobl	bone
6	chr20:25580800-25581400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr20:25581000-25581600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr20:25581000-25582000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr20:25581000-25582200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:25581000-25582200	Enhancers	HSMMtube	muscle
11	chr20:25581000-25583800	Enhancers	HepG2	liver
12	chr20:25581200-25581800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr20:25581200-25581800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr20:25581200-25582000	Enhancers	Adipose Nuclei	Adipose
15	chr20:25581400-25581800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr20:25581600-25594000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr20:25581800-25594000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:25581800-25603800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:25582000-25582400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr20:25582000-25593200	Weak transcription	Adipose Nuclei	Adipose
21	chr20:25582000-25594800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr20:25582000-25602800	Weak transcription	Osteobl	bone
23	chr20:25582200-25585200	Weak transcription	HSMMtube	muscle
24	chr20:25582200-25593000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr20:25582400-25582600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr20:25583600-25594200	Weak transcription	Aorta	Aorta
27	chr20:25583800-25584200	Flanking Active TSS	HepG2	liver
28	chr20:25583800-25584400	Enhancers	Liver	Liver
29	chr20:25584000-25588400	Weak transcription	Dnd41	blood
30	chr20:25584200-25584800	Enhancers	HepG2	liver
31	chr20:25584400-25593800	Weak transcription	Liver	Liver
32	chr20:25584800-25588000	Weak transcription	HepG2	liver
33	chr20:25585200-25585600	Enhancers	Fetal Muscle Trunk	muscle
34	chr20:25585200-25587000	Enhancers	HSMMtube	muscle
35	chr20:25585400-25586400	Enhancers	Fetal Muscle Leg	muscle

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