Variant report

Variant	esv3441185
Chromosome Location	chr12:57287885-57292183
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57287877..57290636-chr12:57297614..57299721,2	MCF-7	breast:
2	chr12:57290248..57293772-chr12:57294284..57296377,4	K562	blood:
3	chr1:149214913..149215694-chr12:57291472..57291972,2	NB4	blood:
4	chr12:57287853..57289367-chr12:57293884..57295708,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MYO1A-2	chr12:57288927-57289598	ucscGeneNc_uc001sqq_1

Variant related genes	Relation type
ENSG00000252826	chromatin interactions

Extended variants
information (count: 168 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:168 , 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	rs530282795	chr12:57287898-57287899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs191273989	chr12:57287909-57287910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs548237069	chr12:57287941-57287942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs199968026	chr12:57287984-57287985	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs570344229	chr12:57288013-57288014	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs201663797	chr12:57288035-57288036	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs199856484	chr12:57288037-57288038	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs147625402	chr12:57288038-57288039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs58435855	chr12:57288040-57288041	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs71446589	chr12:57288041-57288042	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs547702154	chr12:57288056-57288057	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs75217706	chr12:57288072-57288073	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs147749941	chr12:57288170-57288171	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs551878788	chr12:57288182-57288183	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs570389338	chr12:57288186-57288187	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs141011734	chr12:57288224-57288225	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs552995889	chr12:57288317-57288318	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs4418849	chr12:57288321-57288322	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs535247658	chr12:57288365-57288366	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs60262411	chr12:57288428-57288429	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs150192280	chr12:57288432-57288433	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs12321987	chr12:57288449-57288450	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs558683086	chr12:57288506-57288507	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs55720321	chr12:57288507-57288508	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs541183074	chr12:57288606-57288607	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs559870599	chr12:57288616-57288617	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs530347823	chr12:57288617-57288618	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs201910992	chr12:57288618-57288619	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs7315229	chr12:57288668-57288669	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs566520851	chr12:57288669-57288670	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs564013289	chr12:57288675-57288676	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs531122240	chr12:57288752-57288753	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs34490499	chr12:57288765-57288766	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs188418202	chr12:57288769-57288770	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs372052206	chr12:57288825-57288826	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs78406706	chr12:57288850-57288851	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs555361717	chr12:57288851-57288852	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs528071821	chr12:57288863-57288864	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs374530456	chr12:57288877-57288878	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs4415812	chr12:57288900-57288901	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs567811163	chr12:57288920-57288921	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs145723104	chr12:57288942-57288943	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs4237807	chr12:57288997-57288998	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs193209398	chr12:57289009-57289010	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs79705650	chr12:57289040-57289041	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs35426019	chr12:57289041-57289042	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs539374067	chr12:57289091-57289092	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs557997723	chr12:57289103-57289104	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs577203853	chr12:57289105-57289106	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs141097513	chr12:57289156-57289157	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

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
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	18194544	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
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Bladder cancer	21909424	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Autism	20531469	CNVD
Rhabdomyosarcoma	16790082	CNVD
Renal cell carcinoma	18765545	CNVD
Urothelial cell carcinoma	18451213	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21138945	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Leukemia	18628472	CNVD
Glioblastoma multiforme	22291905	CNVD
Glioblastoma multiforme	19435819	CNVD
Myelofibrosis	22110671	CNVD
Phyllodes tumor	17334353	CNVD
Glaucoma	21310917	CNVD
Breast cancer	16272173	CNVD
Mental retardation	19951919	CNVD
Glaucoma	21447600	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Developmental delay	21267005	CNVD
12q14 microdeletion syndrome	21267005	CNVD
Developmental delay	19277063	CNVD
Dwarfism	19277063	CNVD
Fibroblasts	20926602	CNVD
Follicular lymphoma	18703704	CNVD
Acute myeloid leukemia	21251322	CNVD
Glycogen storage disease	18421352	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Glioblastoma multiforme	20080666	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	17133270	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Osteosarcoma	21215367	CNVD

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57275600-57291200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:57285800-57288200	Weak transcription	Liver	Liver
3	chr12:57288200-57293600	Enhancers	Liver	Liver
4	chr12:57288400-57289200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:57289200-57291800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:57289600-57290200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:57289800-57290000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:57289800-57290200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:57289800-57290200	ZNF genes & repeats	Fetal Kidney	kidney
10	chr12:57289800-57290200	Active TSS	Fetal Lung	lung
11	chr12:57289800-57290200	Enhancers	Gastric	stomach
12	chr12:57289800-57290200	Enhancers	Lung	lung
13	chr12:57289800-57290200	ZNF genes & repeats	Pancreas	Pancrea
14	chr12:57289800-57290400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr12:57289800-57290400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
16	chr12:57289800-57290400	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr12:57289800-57290400	Enhancers	Esophagus	oesophagus
18	chr12:57290000-57290200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:57290000-57290200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr12:57290000-57290200	Enhancers	K562	blood
21	chr12:57290200-57290400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:57290200-57293600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr12:57290200-57293600	Weak transcription	Gastric	stomach
24	chr12:57290200-57293600	Weak transcription	Lung	lung
25	chr12:57290400-57293600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:57291000-57295600	Enhancers	HMEC	breast
27	chr12:57291200-57292800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:57291200-57295800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr12:57291600-57291800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr12:57291600-57293000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr12:57291600-57293000	Enhancers	NHEK	skin
32	chr12:57291800-57292600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr12:57291800-57292600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr12:57291800-57296800	Enhancers	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links