Variant report

Variant	esv3471522
Chromosome Location	chr5:5495931-5497962
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:5497022..5497900-chr5:6745484..6746132,2	MCF-7	breast:
2	chr5:5497053..5497738-chr5:5886888..5887554,2	MCF-7	breast:
3	chr5:5497229..5497886-chr5:6576751..6577654,2	MCF-7	breast:
4	chr5:5497029..5497914-chr5:6525976..6526639,2	MCF-7	breast:
5	chr5:5497214..5497881-chr5:5886985..5887597,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112941	chromatin interactions

Extended variants
information (count: 91 )
Associated
traits (count: 94 )

Variant overlapped rSNPs/rCNVs (count:91 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs557753284	chr5:5495934-5495935	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
2	rs143983226	chr5:5495952-5495953	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
3	rs572860905	chr5:5495958-5495959	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
4	rs114850113	chr5:5495996-5495997	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
5	rs13163639	chr5:5496011-5496012	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
6	rs534822093	chr5:5496039-5496040	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
7	rs34836345	chr5:5496040-5496041	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs77979853	chr5:5496052-5496053	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs397883327	chr5:5496054-5496055	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs114935397	chr5:5496106-5496107	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs571142340	chr5:5496124-5496125	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
12	rs116531058	chr5:5496127-5496128	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs373870952	chr5:5496131-5496132	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs368002035	chr5:5496161-5496162	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs544458911	chr5:5496184-5496185	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs574614532	chr5:5496201-5496202	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs13181223	chr5:5496203-5496204	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs563422871	chr5:5496229-5496230	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs573492471	chr5:5496237-5496238	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs534674306	chr5:5496247-5496248	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs554371481	chr5:5496256-5496257	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs574524170	chr5:5496284-5496285	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs543043007	chr5:5496285-5496286	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs368851471	chr5:5496291-5496292	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs530643237	chr5:5496305-5496306	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs145146333	chr5:5496319-5496320	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs144877459	chr5:5496375-5496376	Bivalent Enhancer Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs182021425	chr5:5496433-5496434	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
29	rs559090595	chr5:5496473-5496474	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
30	rs252938	chr5:5496480-5496481	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs542051836	chr5:5496498-5496499	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
32	rs562030529	chr5:5496500-5496501	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
33	rs148612070	chr5:5496507-5496508	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
34	rs77656540	chr5:5496528-5496529	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs528046891	chr5:5496534-5496535	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
36	rs142196905	chr5:5496544-5496545	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs533633577	chr5:5496568-5496569	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs151218885	chr5:5496584-5496585	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs140452337	chr5:5496589-5496590	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs186998499	chr5:5496596-5496597	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs535668894	chr5:5496610-5496611	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs145431266	chr5:5496631-5496632	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs568048495	chr5:5496634-5496635	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs36125417	chr5:5496682-5496683	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs192379158	chr5:5496707-5496708	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs116984924	chr5:5496768-5496769	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs202120264	chr5:5496809-5496810	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs576449167	chr5:5496825-5496826	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs568653829	chr5:5496846-5496847	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs545643713	chr5:5496879-5496880	Enhancers Weak transcription 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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5477200-5497600	Weak transcription	Brain Angular Gyrus	brain
2	chr5:5482800-5497600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:5490600-5497200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:5490600-5497600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:5490800-5496400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:5491400-5496400	Weak transcription	Hela-S3	cervix
7	chr5:5492800-5497400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:5494000-5496200	Enhancers	Psoas Muscle	Psoas
9	chr5:5494000-5496400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr5:5494400-5496200	Weak transcription	Brain Substantia Nigra	brain
11	chr5:5494800-5497200	Weak transcription	HMEC	breast
12	chr5:5494800-5503800	Weak transcription	GM12878-XiMat	blood
13	chr5:5495200-5496400	Weak transcription	Fetal Brain Female	brain
14	chr5:5495200-5497000	Weak transcription	Colon Smooth Muscle	Colon
15	chr5:5495200-5497200	Weak transcription	Brain Anterior Caudate	brain
16	chr5:5495200-5498400	Enhancers	Brain Germinal Matrix	brain
17	chr5:5495400-5496000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr5:5495400-5496600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:5495400-5496600	Weak transcription	Fetal Brain Male	brain
20	chr5:5495400-5496800	Enhancers	Adipose Nuclei	Adipose
21	chr5:5495400-5497000	Weak transcription	Primary B cells from peripheral blood	blood
22	chr5:5495400-5497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
23	chr5:5495400-5497200	Weak transcription	Liver	Liver
24	chr5:5495400-5497200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr5:5495400-5497200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:5495400-5497600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr5:5495400-5497600	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:5495400-5497800	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr5:5495600-5496000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:5495600-5496000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:5495600-5496000	Weak transcription	Gastric	stomach
32	chr5:5495600-5497200	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr5:5495600-5497200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:5495800-5496800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:5495800-5497000	Enhancers	Brain Hippocampus Middle	brain
36	chr5:5496000-5496600	Enhancers	Gastric	stomach
37	chr5:5496000-5496800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:5496000-5497200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
39	chr5:5496000-5497600	Enhancers	Brain Cingulate Gyrus	brain
40	chr5:5496200-5496400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
41	chr5:5496200-5496400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
42	chr5:5496200-5497600	Enhancers	Brain Substantia Nigra	brain
43	chr5:5496200-5497600	Weak transcription	Psoas Muscle	Psoas
44	chr5:5496400-5496600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
45	chr5:5496400-5496600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
46	chr5:5496400-5496600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
47	chr5:5496400-5497200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
48	chr5:5496400-5497800	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr5:5496400-5498000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr5:5496400-5498000	Enhancers	Fetal Brain Female	brain

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