Variant report

Variant	esv3440138
Chromosome Location	chr1:239850754-239853302
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	chr1:239845517..239847518-chr1:239849321..239851318,2	MCF-7	breast:

Extended variants
information (count: 85 )
Associated
traits (count: 87 )

Variant overlapped rSNPs/rCNVs (count:85 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs181778686	chr1:239850815-239850816	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs186171796	chr1:239850826-239850827	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs558955955	chr1:239850897-239850898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs577257598	chr1:239850911-239850912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs544652300	chr1:239850918-239850919	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs374358496	chr1:239850931-239850932	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs561826465	chr1:239850965-239850966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs529027334	chr1:239850973-239850974	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs116431493	chr1:239850997-239850998	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs542062745	chr1:239851053-239851054	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs547462754	chr1:239851060-239851061	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs560461892	chr1:239851101-239851102	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs527612722	chr1:239851161-239851162	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs543308538	chr1:239851193-239851194	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs76026452	chr1:239851216-239851217	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs145738731	chr1:239851257-239851258	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs549803650	chr1:239851258-239851259	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs188926457	chr1:239851300-239851301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs112491516	chr1:239851301-239851302	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs536430121	chr1:239851338-239851339	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs548399112	chr1:239851386-239851387	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs566817659	chr1:239851421-239851422	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs534549328	chr1:239851464-239851465	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs138626635	chr1:239851481-239851482	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs558995743	chr1:239851500-239851501	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs570777087	chr1:239851530-239851531	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs537873412	chr1:239851555-239851556	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs556586963	chr1:239851580-239851581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs575022186	chr1:239851581-239851582	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs542023851	chr1:239851614-239851615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs113939519	chr1:239851616-239851617	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs147776364	chr1:239851642-239851643	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs141164509	chr1:239851653-239851654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs369517323	chr1:239851731-239851732	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs538689902	chr1:239851822-239851823	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs181377122	chr1:239851839-239851840	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs372563357	chr1:239851851-239851852	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs556820977	chr1:239851871-239851872	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs531300833	chr1:239851894-239851895	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs2883621	chr1:239851931-239851932	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs58574752	chr1:239851936-239851937	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs182795547	chr1:239851975-239851976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs548363796	chr1:239851982-239851983	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs62634805	chr1:239851989-239851990	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs575175612	chr1:239851998-239851999	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs527882717	chr1:239852013-239852014	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs552806457	chr1:239852017-239852018	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs571075054	chr1:239852020-239852021	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs538223205	chr1:239852021-239852022	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs61834820	chr1:239852024-239852025	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:87)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Liposarcoma	21253554	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
abnormal development	18461090	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Hepatocellular carcinoma	16750200	CNVD
Arrhythmogenic right ventricular cardiomyopathy	17576883	CNVD
Multiple myeloma	16616336	CNVD
Developmental delay	21147756	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239836600-239856200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:239840000-239853200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:239841000-239854000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:239845000-239855200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:239845000-239879800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:239849800-239856600	Weak transcription	Fetal Intestine Small	intestine
7	chr1:239850600-239850800	Enhancers	Fetal Intestine Large	intestine
8	chr1:239852600-239852800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr1:239852600-239853200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:239852600-239853200	Active TSS	Ovary	ovary
11	chr1:239852800-239853200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr1:239852800-239853200	Active TSS	Fetal Lung	lung
13	chr1:239852800-239853200	Active TSS	A549	lung
14	chr1:239853200-239853400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:239853200-239853400	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr1:239853200-239853400	Enhancers	Fetal Lung	lung
17	chr1:239853200-239853400	Enhancers	Ovary	ovary
18	chr1:239853200-239853600	Active TSS	Breast Myoepithelial Primary Cells	Breast

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