Variant report

Variant	nsv528961
Chromosome Location	chr5:5494739-5496480
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	chr19:2060401..2061330-chr5:5494671..5495442,2	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 94 )

Variant overlapped rSNPs/rCNVs (count:83 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2578539	chr5:5494739-5494740	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs527284785	chr5:5494765-5494766	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
3	rs190641247	chr5:5494825-5494826	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs374469418	chr5:5494852-5494853	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs145540018	chr5:5494873-5494874	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs529976990	chr5:5494893-5494894	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs549926275	chr5:5494901-5494902	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs569772955	chr5:5495009-5495010	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs538713040	chr5:5495027-5495028	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs372824553	chr5:5495033-5495034	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs145494777	chr5:5495042-5495043	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs558635084	chr5:5495049-5495050	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs532216110	chr5:5495053-5495054	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs565690950	chr5:5495149-5495150	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs115819634	chr5:5495162-5495163	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs192216868	chr5:5495200-5495201	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs575064205	chr5:5495219-5495220	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs74807459	chr5:5495227-5495228	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs138312922	chr5:5495252-5495253	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs577520353	chr5:5495260-5495261	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs545077284	chr5:5495270-5495271	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs76452084	chr5:5495280-5495281	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs184540115	chr5:5495289-5495290	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs541004785	chr5:5495309-5495310	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs79951533	chr5:5495355-5495356	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs252940	chr5:5495373-5495374	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs549823671	chr5:5495413-5495414	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs563103388	chr5:5495458-5495459	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs372530765	chr5:5495462-5495463	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs532180729	chr5:5495487-5495488	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs553932627	chr5:5495503-5495504	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs115366743	chr5:5495524-5495525	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs188617535	chr5:5495526-5495527	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs534841874	chr5:5495531-5495532	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs116758845	chr5:5495546-5495547	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs535357176	chr5:5495567-5495568	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs537706780	chr5:5495584-5495585	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs112872902	chr5:5495597-5495598	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs577656471	chr5:5495610-5495611	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs540026449	chr5:5495629-5495630	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs553635922	chr5:5495635-5495636	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs13180360	chr5:5495671-5495672	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs181367569	chr5:5495672-5495673	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs13163164	chr5:5495710-5495711	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs28626791	chr5:5495727-5495728	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs252939	chr5:5495743-5495744	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs150905883	chr5:5495747-5495748	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs563239740	chr5:5495806-5495807	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs532313912	chr5:5495824-5495825	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs551939412	chr5:5495849-5495850	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:94)

Disease	PMID	Source
Glioblastoma multiforme	22286061	CNVD
Lung cancer	21911935	CNVD
Cri-du chat syndrome	21549014	CNVD
Cervical squamous cell carcinoma	21590768	CNVD
Melanoma	18172304	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Sudden cardiac death	19188705	CNVD
renal disease	17924346	CNVD
abnormal development	18461090	CNVD
Lung cancer	19547694	CNVD
Cri-du chat syndrome	22283845	CNVD
Disorders of sex development	21048976	CNVD
Non-small cell lung cancer	20864512	CNVD
Cancer	21183584	CNVD
Honadal dysgenesis	21048976	CNVD
Cancer	16751803	CNVD
Breast cancer	17133270	CNVD
Hepatocellular carcinoma	22174799	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Salivary gland tumor	18059337	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Kartagener syndrome	16639409	CNVD
Medulloblastoma	21979893	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	16783165	CNVD
Thyroid cancer	19087340	CNVD
Liposarcoma	21253554	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Cervical Cancer	21857958	CNVD
Cervical cancer	21062161	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Oral cancer	21386901	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Ewing''s sarcoma	17952124	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Cervical cancer	18559093	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Cancer	20164919	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Multiple myeloma	17550852	CNVD
Developmental delay	21147756	CNVD
prenatal diagnosis	22389664	CNVD
Bladder cancer	21909424	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Breast cancer	21858162	CNVD
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Melanoma	22183965	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
lymphocytic leukemia	21291569	CNVD
Autism	22495311	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Schizophrenia	23813976	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	16608533	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Breast cancer	22522925	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:248 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5433400-5495200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:5458600-5495000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr5:5465200-5495000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:5475400-5495000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:5477200-5497600	Weak transcription	Brain Angular Gyrus	brain
6	chr5:5482200-5495000	Weak transcription	NHEK	skin
7	chr5:5482800-5497600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:5487400-5495000	Weak transcription	Gastric	stomach
9	chr5:5490200-5495000	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:5490200-5495000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:5490600-5497200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr5:5490600-5497600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:5490800-5496400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:5491400-5495000	Weak transcription	Lung	lung
15	chr5:5491400-5496400	Weak transcription	Hela-S3	cervix
16	chr5:5492200-5495400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr5:5492800-5497400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr5:5493600-5495600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr5:5493800-5494800	Enhancers	NHDF-Ad	bronchial
20	chr5:5493800-5495200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:5493800-5495400	Enhancers	Fetal Heart	heart
22	chr5:5493800-5495400	Bivalent Enhancer	Fetal Stomach	stomach
23	chr5:5493800-5495800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:5494000-5494800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
25	chr5:5494000-5494800	Enhancers	HMEC	breast
26	chr5:5494000-5495000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr5:5494000-5495000	Enhancers	Fetal Intestine Small	intestine
28	chr5:5494000-5495200	Enhancers	Primary T cells from cord blood	blood
29	chr5:5494000-5495200	Enhancers	Placenta	Placenta
30	chr5:5494000-5495400	Enhancers	Primary hematopoietic stem cells	blood
31	chr5:5494000-5495400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
32	chr5:5494000-5495400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:5494000-5495400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr5:5494000-5495400	Enhancers	Esophagus	oesophagus
35	chr5:5494000-5495400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr5:5494000-5495400	Enhancers	Fetal Brain Male	brain
37	chr5:5494000-5495400	Enhancers	Spleen	Spleen
38	chr5:5494000-5495600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:5494000-5495600	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr5:5494000-5495600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr5:5494000-5496200	Enhancers	Psoas Muscle	Psoas
42	chr5:5494000-5496400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:5494200-5495000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr5:5494200-5495000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:5494200-5495000	Enhancers	Adipose Nuclei	Adipose
46	chr5:5494200-5495000	Enhancers	Brain Germinal Matrix	brain
47	chr5:5494200-5495200	Enhancers	Stomach Mucosa	stomach
48	chr5:5494200-5495400	Enhancers	K562	blood
49	chr5:5494400-5494800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:5494400-5494800	Flanking Active TSS	Primary B cells from cord blood	blood

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