Variant report

Variant	nsv557606
Chromosome Location	chr12:12540376-12543233
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: 134 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:134 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs114283534	chr12:12540430-12540431	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs192849657	chr12:12540431-12540432	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs574276601	chr12:12540444-12540445	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs149457117	chr12:12540467-12540468	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs567074590	chr12:12540475-12540476	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs375524972	chr12:12540523-12540524	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs529493024	chr12:12540525-12540526	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs143003873	chr12:12540552-12540553	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs576012249	chr12:12540553-12540554	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs78669475	chr12:12540570-12540571	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs547763209	chr12:12540577-12540578	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs112233999	chr12:12540588-12540589	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs74463206	chr12:12540620-12540621	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs575984660	chr12:12540650-12540651	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs56261569	chr12:12540656-12540657	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs184874259	chr12:12540678-12540679	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs6488520	chr12:12540702-12540703	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs540745279	chr12:12540703-12540704	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs570597373	chr12:12540740-12540741	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs531451635	chr12:12540748-12540749	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs541231619	chr12:12540761-12540762	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs569480606	chr12:12540771-12540772	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs114989930	chr12:12540779-12540780	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs115902484	chr12:12540822-12540823	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs535701066	chr12:12540823-12540824	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs113120590	chr12:12540884-12540885	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs77854659	chr12:12540894-12540895	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs572294010	chr12:12540910-12540911	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs565845592	chr12:12540948-12540949	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs539289266	chr12:12540954-12540955	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs557545660	chr12:12540968-12540969	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs559480307	chr12:12540971-12540972	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs368336734	chr12:12541014-12541015	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs541692852	chr12:12541031-12541032	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs372495052	chr12:12541048-12541049	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs7300993	chr12:12541063-12541064	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs142733273	chr12:12541081-12541082	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs190067742	chr12:12541091-12541092	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs541710468	chr12:12541152-12541153	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs554581592	chr12:12541221-12541222	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs376861009	chr12:12541223-12541224	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs181752841	chr12:12541273-12541274	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs573030284	chr12:12541340-12541341	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs147384218	chr12:12541386-12541387	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs184693532	chr12:12541391-12541392	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs7132813	chr12:12541407-12541408	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs140059707	chr12:12541507-12541508	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs568060064	chr12:12541508-12541509	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs35638977	chr12:12541519-12541520	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs563085333	chr12:12541552-12541553	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:192 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12511400-12540600	Weak transcription	HSMM	muscle
2	chr12:12511600-12550600	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:12512000-12545000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr12:12512200-12540400	Weak transcription	HMEC	breast
5	chr12:12512400-12540600	Weak transcription	Psoas Muscle	Psoas
6	chr12:12519200-12549800	Weak transcription	Aorta	Aorta
7	chr12:12519600-12540400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:12521800-12542800	Weak transcription	Adipose Nuclei	Adipose
9	chr12:12521800-12556200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr12:12525400-12550200	Weak transcription	Fetal Stomach	stomach
11	chr12:12526000-12541600	Weak transcription	Brain Germinal Matrix	brain
12	chr12:12526400-12540400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:12526400-12540400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:12526400-12558800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:12529600-12541400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr12:12532800-12556400	Weak transcription	Spleen	Spleen
17	chr12:12533000-12542800	Weak transcription	Placenta	Placenta
18	chr12:12533000-12545800	Weak transcription	Pancreas	Pancrea
19	chr12:12533400-12540400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:12533400-12555800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr12:12533600-12555400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr12:12533800-12540400	Weak transcription	NHLF	lung
23	chr12:12533800-12540400	Weak transcription	Osteobl	bone
24	chr12:12535400-12542800	Weak transcription	Right Ventricle	heart
25	chr12:12535400-12561400	Weak transcription	Primary B cells from peripheral blood	blood
26	chr12:12535600-12540400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr12:12535600-12540400	Weak transcription	A549	lung
28	chr12:12535800-12542600	Weak transcription	Lung	lung
29	chr12:12537000-12540400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:12537200-12576000	Weak transcription	Primary B cells from cord blood	blood
31	chr12:12538000-12541400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:12538200-12540400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:12538200-12540400	Weak transcription	NH-A	brain
34	chr12:12538200-12540600	Weak transcription	Fetal Lung	lung
35	chr12:12538200-12541800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:12538200-12551000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:12538400-12540400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:12538400-12540400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:12538400-12540400	Weak transcription	Brain Hippocampus Middle	brain
40	chr12:12538400-12540400	Weak transcription	Brain Substantia Nigra	brain
41	chr12:12538400-12540400	Weak transcription	Fetal Heart	heart
42	chr12:12538400-12540400	Weak transcription	HSMMtube	muscle
43	chr12:12538400-12540400	Weak transcription	K562	blood
44	chr12:12538400-12540600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:12538400-12540600	Weak transcription	Brain Angular Gyrus	brain
46	chr12:12538400-12540600	Weak transcription	Brain Cingulate Gyrus	brain
47	chr12:12538400-12540800	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr12:12538400-12545800	Weak transcription	Left Ventricle	heart
49	chr12:12538400-12548600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:12538400-12549200	Weak transcription	Fetal Muscle Leg	muscle

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