Variant report

Variant	nsv590926
Chromosome Location	chr3:89379935-89417287
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:89350735..89353187-chr3:89378356..89381194,2	MCF-7	breast:
2	chr3:89362727..89364940-chr3:89377326..89380080,2	MCF-7	breast:
3	chr3:89374362..89376361-chr3:89384187..89386718,2	MCF-7	breast:
4	chr3:89374528..89377645-chr3:89392593..89395332,3	MCF-7	breast:

Extended variants
information (count: 1372 )
Associated
traits (count: 78 )

Variant overlapped rSNPs/rCNVs (count:1372 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9866959	chr3:89379935-89379936	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs530210163	chr3:89379936-89379937	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs181427124	chr3:89379969-89379970	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs562392979	chr3:89380005-89380006	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs550541628	chr3:89380072-89380073	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs529648717	chr3:89380108-89380109	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs375097049	chr3:89380194-89380195	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs535232787	chr3:89380203-89380204	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs151174129	chr3:89380210-89380211	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs115339270	chr3:89380217-89380218	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs12152482	chr3:89380232-89380233	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs570354353	chr3:89380251-89380252	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs568932755	chr3:89380270-89380271	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs539627035	chr3:89380283-89380284	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs527382305	chr3:89380325-89380326	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs557618495	chr3:89380365-89380366	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs547213050	chr3:89380370-89380371	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs141030224	chr3:89380408-89380409	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs539190682	chr3:89380411-89380412	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs540209383	chr3:89380412-89380413	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs73846143	chr3:89380433-89380434	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs149819257	chr3:89380464-89380465	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs375788710	chr3:89380470-89380471	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs145832031	chr3:89380486-89380487	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs573320226	chr3:89380514-89380515	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs369630549	chr3:89380524-89380525	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs534022781	chr3:89380552-89380553	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs558375587	chr3:89380556-89380557	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs185666165	chr3:89380612-89380613	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs543960435	chr3:89380644-89380645	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs149004825	chr3:89380692-89380693	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs189974184	chr3:89380752-89380753	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs541847354	chr3:89380765-89380766	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs555374567	chr3:89380817-89380818	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs145921581	chr3:89380851-89380852	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs527428989	chr3:89380892-89380893	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs11923303	chr3:89380944-89380945	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs533905019	chr3:89380954-89380955	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs564131532	chr3:89380977-89380978	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs553573854	chr3:89380993-89380994	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs532769269	chr3:89381021-89381022	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs551166544	chr3:89381030-89381031	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs180774245	chr3:89381048-89381049	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs536529898	chr3:89381069-89381070	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs548603128	chr3:89381150-89381151	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs150463549	chr3:89381200-89381201	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs187505120	chr3:89381214-89381215	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs191836835	chr3:89381232-89381233	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs558634621	chr3:89381237-89381238	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs576890732	chr3:89381242-89381243	Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:78)

Disease	PMID	Source
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
Acute myeloid leukemia	20729466	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	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
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Metanephric adenoma	20802469	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Wilms tumour	21544195	CNVD
Soft tissue tumor	16732325	CNVD
small cell lung cancer	20016488	CNVD
Neurodevelopmental disorder	22521361	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
craniofacial dysmorphism	21918468	CNVD
Cancer	20164920	CNVD
Non-small cell lung cancer	21829676	CNVD
Lung cancer	19547694	CNVD
Cancer	20164919	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:89378200-89380200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:89378400-89380200	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:89378600-89380200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:89378800-89381000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:89379400-89384000	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:89379800-89380200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:89380000-89382400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr3:89380000-89382800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:89380200-89380400	Enhancers	H9 Cell Line	embryonic stem cell
10	chr3:89380200-89381200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr3:89380200-89381400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr3:89380200-89382600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr3:89380200-89383000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:89380400-89381200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:89380600-89381400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr3:89381000-89382400	Enhancers	Brain Germinal Matrix	brain
17	chr3:89381000-89382800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:89381200-89381800	Enhancers	Psoas Muscle	Psoas
19	chr3:89381200-89382000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:89381200-89382000	Enhancers	H9 Cell Line	embryonic stem cell
21	chr3:89381200-89382000	Enhancers	Stomach Smooth Muscle	stomach
22	chr3:89381200-89382200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:89381200-89382200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr3:89381200-89382400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr3:89381200-89382400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr3:89381200-89382400	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr3:89381200-89382800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:89381200-89383000	Enhancers	Fetal Brain Female	brain
29	chr3:89381400-89381800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr3:89381400-89382000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr3:89381400-89382000	Enhancers	Brain Angular Gyrus	brain
32	chr3:89381400-89382200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:89381400-89382200	Enhancers	Brain Substantia Nigra	brain
34	chr3:89381600-89382000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:89381600-89382000	Enhancers	Brain Anterior Caudate	brain
36	chr3:89381600-89382000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr3:89381600-89382000	Enhancers	Fetal Muscle Leg	muscle
38	chr3:89381600-89382200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:89381600-89382200	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr3:89381600-89382200	Enhancers	Spleen	Spleen
41	chr3:89381600-89382400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:89381800-89383000	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr3:89382000-89383600	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr3:89382200-89382600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:89382200-89382600	Weak transcription	Spleen	Spleen
46	chr3:89382200-89382800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:89382200-89383200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:89382400-89383400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:89382400-89383800	Enhancers	iPS-20b Cell Line	embryonic stem cell
50	chr3:89382400-89391200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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