Variant report

Variant	nsv557601
Chromosome Location	chr12:12538135-12541869
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	chr12:12539967..12541683-chr12:12547549..12549266,2	MCF-7	breast:
2	chr12:12538899..12542001-chr12:12714080..12716309,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111266	chromatin interactions

Extended variants
information (count: 166 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:166 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs575959798	chr12:12538150-12538151	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
2	rs556623115	chr12:12538152-12538153	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
3	rs115427265	chr12:12538158-12538159	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
4	rs542317936	chr12:12538182-12538183	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3'	n/a	n/a	Overlapped CNVs	n/a
5	rs554102480	chr12:12538242-12538243	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs538518283	chr12:12538248-12538249	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs540151552	chr12:12538285-12538286	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs565210613	chr12:12538294-12538295	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs147976409	chr12:12538307-12538308	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs544385029	chr12:12538308-12538309	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs562691692	chr12:12538351-12538352	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs112022357	chr12:12538415-12538416	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs568909483	chr12:12538448-12538449	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs548713148	chr12:12538504-12538505	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs113115954	chr12:12538531-12538532	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs185502399	chr12:12538534-12538535	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs552574393	chr12:12538538-12538539	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs544599685	chr12:12538607-12538608	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs12815074	chr12:12538631-12538632	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs12814371	chr12:12538632-12538633	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs12820101	chr12:12538676-12538677	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs140451452	chr12:12538686-12538687	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs561393236	chr12:12538693-12538694	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs556311644	chr12:12538701-12538702	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs12815134	chr12:12538704-12538705	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs568324638	chr12:12538706-12538707	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs113726959	chr12:12538722-12538723	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs554695504	chr12:12538728-12538729	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs542495141	chr12:12538763-12538764	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs572726842	chr12:12538823-12538824	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs556928117	chr12:12538875-12538876	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs144309833	chr12:12538886-12538887	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs191332115	chr12:12538890-12538891	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs373487346	chr12:12538912-12538913	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs560241187	chr12:12538939-12538940	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs147499050	chr12:12538973-12538974	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs544524104	chr12:12538974-12538975	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs113000160	chr12:12538981-12538982	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs112981463	chr12:12539003-12539004	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs562634601	chr12:12539009-12539010	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs574728038	chr12:12539038-12539039	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs140099056	chr12:12539085-12539086	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs560665453	chr12:12539107-12539108	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs527671300	chr12:12539116-12539117	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs150054372	chr12:12539131-12539132	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs145422045	chr12:12539132-12539133	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs375919171	chr12:12539133-12539134	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs560642791	chr12:12539136-12539137	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs528248046	chr12:12539155-12539156	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs183135760	chr12:12539196-12539197	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Hepatocellular carcinoma	16750200	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	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
Testicular germ cell tumor	18059402	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Breast cancer	21509527	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	21611746	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Lung cancer	18438408	CNVD
Myelofibrosis	22110671	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Squamous cell cancer	19607727	CNVD
Prostate cancer	16573809	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute myeloid leukemia	17268525	CNVD
Acute monocytic leukemia	16498392	CNVD
Prostate cancer	16461572	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Prostate cancer	21088497	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:289 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12511400-12540600	Weak transcription	HSMM	muscle
2	chr12:12511600-12540000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:12511600-12550600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:12512000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:12512200-12540400	Weak transcription	HMEC	breast
6	chr12:12512400-12540600	Weak transcription	Psoas Muscle	Psoas
7	chr12:12516400-12540000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr12:12519200-12549800	Weak transcription	Aorta	Aorta
9	chr12:12519600-12540400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr12:12521800-12542800	Weak transcription	Adipose Nuclei	Adipose
11	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:12525400-12550200	Weak transcription	Fetal Stomach	stomach
13	chr12:12526000-12541600	Weak transcription	Brain Germinal Matrix	brain
14	chr12:12526400-12540400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:12526400-12540400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr12:12529600-12541400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:12531600-12539000	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr12:12532400-12540000	Weak transcription	NHEK	skin
20	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
21	chr12:12533000-12542800	Weak transcription	Placenta	Placenta
22	chr12:12533000-12545800	Weak transcription	Pancreas	Pancrea
23	chr12:12533400-12540400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr12:12533400-12555800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:12533600-12555400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:12533800-12540000	Weak transcription	NHDF-Ad	bronchial
27	chr12:12533800-12540200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:12533800-12540400	Weak transcription	NHLF	lung
29	chr12:12533800-12540400	Weak transcription	Osteobl	bone
30	chr12:12535000-12539400	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr12:12535400-12539600	Weak transcription	Esophagus	oesophagus
32	chr12:12535400-12542800	Weak transcription	Right Ventricle	heart
33	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr12:12535600-12540400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:12535600-12540400	Weak transcription	A549	lung
36	chr12:12535800-12542600	Weak transcription	Lung	lung
37	chr12:12536000-12538800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr12:12536200-12538200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:12536200-12538800	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr12:12536400-12538600	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr12:12536400-12539000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr12:12536600-12538600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr12:12536600-12538600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:12536600-12539400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:12536800-12538400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:12537000-12538800	Enhancers	Fetal Thymus	thymus
47	chr12:12537000-12539800	Enhancers	Primary T cells fromperipheralblood	blood
48	chr12:12537000-12540000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:12537000-12540200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:12537000-12540400	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links