Variant report

Variant	nsv1012098
Chromosome Location	chr3:56040905-56055908
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	chr3:56037511..56039135-chr3:56041080..56043477,2	MCF-7	breast:

Extended variants
information (count: 531 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:531 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs557580656	chr3:56040917-56040918	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs577321039	chr3:56040950-56040951	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs139923453	chr3:56040955-56040956	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs545997529	chr3:56040970-56040971	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs368783997	chr3:56040977-56040978	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs1379716	chr3:56040980-56040981	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs143429249	chr3:56040984-56040985	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs374378213	chr3:56040992-56040993	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs541455448	chr3:56040994-56040995	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs372669910	chr3:56040996-56040997	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs561333623	chr3:56041038-56041039	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs534939921	chr3:56041138-56041139	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs1379715	chr3:56041187-56041188	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs184897007	chr3:56041192-56041193	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs1379714	chr3:56041193-56041194	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs370188469	chr3:56041300-56041301	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs374466939	chr3:56041326-56041327	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs367999451	chr3:56041335-56041336	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs146206948	chr3:56041371-56041372	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs188627745	chr3:56041374-56041375	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs560390710	chr3:56041397-56041398	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs566744545	chr3:56041449-56041450	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs139239193	chr3:56041463-56041464	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs373488899	chr3:56041530-56041531	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs555036347	chr3:56041552-56041553	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs568352568	chr3:56041580-56041581	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs181141779	chr3:56041594-56041595	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs75406331	chr3:56041602-56041603	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs550313223	chr3:56041678-56041679	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs577385016	chr3:56041680-56041681	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs565851260	chr3:56041692-56041693	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs545959550	chr3:56041702-56041703	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs553133212	chr3:56041725-56041726	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs9830643	chr3:56041726-56041727	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs186181819	chr3:56041751-56041752	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs561771488	chr3:56041753-56041754	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs142492409	chr3:56041765-56041766	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs6805479	chr3:56041908-56041909	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs555826846	chr3:56041936-56041937	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs563988934	chr3:56041964-56041965	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs190459197	chr3:56041984-56041985	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs546844038	chr3:56042025-56042026	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs566654527	chr3:56042026-56042027	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs150937213	chr3:56042072-56042073	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs549252645	chr3:56042081-56042082	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs34947176	chr3:56042153-56042154	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs568451788	chr3:56042169-56042170	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs34633564	chr3:56042170-56042171	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs34761117	chr3:56042172-56042173	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs77392726	chr3:56042176-56042177	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

Disease	PMID	Source
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
Acute myeloid leukemia	20729466	CNVD
Glioblastoma multiforme	21080181	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Breast cancer	21785460	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Squamous cell cancer	20885788	CNVD
Breast cancer	16608533	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Renal cell carcinoma	18765545	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21509527	CNVD
Prostate cancer	18632612	CNVD
Cancer	20164919	CNVD
Myelofibrosis	22110671	CNVD
Urothelial cell carcinoma	18451213	CNVD
Breast cancer	19490591	CNVD
Autism	18414403	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-small cell lung cancer	20864512	CNVD
Metastatic melanoma	17975146	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56033000-56052000	Weak transcription	Brain Germinal Matrix	brain
2	chr3:56033200-56046800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:56036000-56041400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:56037800-56041400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:56039200-56041600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:56039200-56041800	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr3:56039800-56052400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:56040000-56041200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr3:56040400-56041600	Enhancers	iPS-20b Cell Line	embryonic stem cell
10	chr3:56040600-56041400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:56040600-56041600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:56041200-56041400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:56041400-56041800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:56041400-56041800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr3:56041400-56041800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:56041400-56046600	Weak transcription	Fetal Brain Female	brain
17	chr3:56041600-56044400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:56041600-56054400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:56041800-56045600	Weak transcription	Fetal Heart	heart
20	chr3:56041800-56054000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:56044400-56044600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr3:56045600-56048600	Enhancers	Fetal Heart	heart
23	chr3:56046200-56046400	Enhancers	Lung	lung
24	chr3:56046200-56047200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr3:56046200-56047200	Enhancers	Gastric	stomach
26	chr3:56046400-56046600	Enhancers	Fetal Intestine Large	intestine
27	chr3:56046400-56047600	Enhancers	Stomach Mucosa	stomach
28	chr3:56046600-56047200	Enhancers	Fetal Brain Female	brain
29	chr3:56046600-56047400	Weak transcription	Fetal Intestine Large	intestine
30	chr3:56046600-56047600	Enhancers	Fetal Kidney	kidney
31	chr3:56046800-56047000	Bivalent Enhancer	Fetal Lung	lung
32	chr3:56046800-56047200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:56046800-56047200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:56047200-56047400	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr3:56047200-56048200	Weak transcription	Gastric	stomach
36	chr3:56047200-56049400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:56047200-56052400	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:56047200-56052400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:56047400-56047600	Enhancers	Fetal Intestine Large	intestine
40	chr3:56047600-56048200	Weak transcription	Fetal Kidney	kidney
41	chr3:56048200-56048400	Enhancers	Fetal Kidney	kidney
42	chr3:56048200-56048600	Enhancers	Fetal Stomach	stomach
43	chr3:56048200-56048600	Enhancers	Gastric	stomach
44	chr3:56048400-56048600	Enhancers	Fetal Intestine Large	intestine
45	chr3:56048600-56052600	Weak transcription	Fetal Stomach	stomach
46	chr3:56048600-56059000	Weak transcription	Fetal Intestine Large	intestine
47	chr3:56051200-56051800	Enhancers	HUES6 Cell Line	embryonic stem cell
48	chr3:56051600-56051800	Weak transcription	Ovary	ovary
49	chr3:56051800-56052000	Enhancers	Ovary	ovary
50	chr3:56051800-56052600	Bivalent Enhancer	Fetal Heart	heart

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