Variant report

Variant	esv3490563
Chromosome Location	chr12:87530442-87533556
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	chr12:87523604..87525877-chr12:87529351..87531918,2	MCF-7	breast:

Extended variants
information (count: 115 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:115 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs539018443	chr12:87530461-87530462	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs552944734	chr12:87530471-87530472	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs535149124	chr12:87530502-87530503	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs572964279	chr12:87530530-87530531	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs535591592	chr12:87530549-87530550	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs552681127	chr12:87530572-87530573	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs568962396	chr12:87530613-87530614	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs34393616	chr12:87530620-87530621	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs142899372	chr12:87530751-87530752	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs554589201	chr12:87530797-87530798	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs544432079	chr12:87530807-87530808	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs557864698	chr12:87530809-87530810	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs577869629	chr12:87530819-87530820	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs540221304	chr12:87530824-87530825	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs181928906	chr12:87530841-87530842	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs548379022	chr12:87530866-87530867	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs531927067	chr12:87530909-87530910	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs571709527	chr12:87530910-87530911	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs542749864	chr12:87530985-87530986	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs562660250	chr12:87531005-87531006	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs111464794	chr12:87531018-87531019	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs531762242	chr12:87531038-87531039	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs371536188	chr12:87531108-87531109	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs76618043	chr12:87531123-87531124	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs571808069	chr12:87531135-87531136	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs528030840	chr12:87531167-87531168	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs546274656	chr12:87531172-87531173	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs566500371	chr12:87531180-87531181	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs186300097	chr12:87531222-87531223	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs368961493	chr12:87531229-87531230	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs556951813	chr12:87531231-87531232	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs563355555	chr12:87531233-87531234	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs553041160	chr12:87531259-87531260	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs190055468	chr12:87531276-87531277	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs568992023	chr12:87531289-87531290	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs151096080	chr12:87531298-87531299	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs112727646	chr12:87531314-87531315	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs11104307	chr12:87531321-87531322	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs73412087	chr12:87531402-87531403	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs540551028	chr12:87531417-87531418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs553736894	chr12:87531419-87531420	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs377261172	chr12:87531489-87531490	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs35037661	chr12:87531515-87531516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs537703090	chr12:87531580-87531581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs181701039	chr12:87531639-87531640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs542633618	chr12:87531729-87531730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs562597130	chr12:87531754-87531755	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs140160599	chr12:87531787-87531788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs144033636	chr12:87531793-87531794	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs565519207	chr12:87531801-87531802	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:67)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lung cancer	18438408	CNVD
Breast cancer	17899364	CNVD
Cancer	16751803	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	21251322	CNVD
Prostate cancer	18632612	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	22032731	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Ovarian cancer	21720365	CNVD
Acute myeloid leukemia	20729466	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Renal cell carcinoma	18194544	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	21364760	CNVD
Multiple myeloma	17550852	CNVD
Melanoma	17363583	CNVD
Urothelial cell carcinoma	18451213	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute lymphoblastic leukemia	17443227	CNVD

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:87521400-87535000	Weak transcription	Fetal Heart	heart
2	chr12:87529200-87530800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:87529400-87530600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr12:87529400-87531000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:87529400-87531200	Enhancers	HMEC	breast
6	chr12:87529600-87530800	Enhancers	NHEK	skin
7	chr12:87529600-87531400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr12:87529800-87530600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr12:87529800-87530800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr12:87529800-87530800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:87530000-87530600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr12:87530200-87530800	Flanking Active TSS	A549	lung
13	chr12:87530400-87530600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:87530400-87530600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
15	chr12:87530400-87530800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:87530400-87530800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:87530400-87530800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:87530400-87530800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr12:87530400-87530800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:87530400-87530800	Flanking Active TSS	Hela-S3	cervix
21	chr12:87530400-87530800	Flanking Active TSS	Osteobl	bone
22	chr12:87530600-87530800	Enhancers	Muscle Satellite Cultured Cells	--
23	chr12:87530600-87531000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:87530800-87531000	Enhancers	A549	lung
25	chr12:87530800-87531400	Enhancers	Hela-S3	cervix
26	chr12:87530800-87533600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:87530800-87534000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:87531000-87533800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr12:87531000-87534000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:87531400-87534000	Weak transcription	Hela-S3	cervix

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