Variant report

Variant	esv3519315
Chromosome Location	chr1:104668122-104670754
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMY1C-2	chr1:104668179-104668541	XLOC_000326
2	lnc-AMY1C-2	chr1:104668178-104668541	NONHSAT004905

Extended variants
information (count: 83 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:83 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs548106065	chr1:104668209-104668210	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
2	rs943964	chr1:104668220-104668221	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs533882138	chr1:104668242-104668243	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs558726269	chr1:104668253-104668254	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs570559135	chr1:104668274-104668275	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs537869753	chr1:104668309-104668310	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs115145474	chr1:104668320-104668321	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs575049047	chr1:104668362-104668363	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs542482395	chr1:104668390-104668391	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs138712052	chr1:104668402-104668403	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs572562968	chr1:104668460-104668461	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs115037923	chr1:104668475-104668476	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs149389145	chr1:104668483-104668484	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs370400994	chr1:104668493-104668494	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs181216934	chr1:104668501-104668502	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs538963452	chr1:104668581-104668582	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs543425899	chr1:104668589-104668590	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs374893742	chr1:104668646-104668647	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs114005236	chr1:104668678-104668679	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs529947460	chr1:104668692-104668693	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs147477066	chr1:104668705-104668706	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs557678759	chr1:104668707-104668708	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs184971596	chr1:104668802-104668803	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs527530621	chr1:104668812-104668813	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs552378847	chr1:104668860-104668861	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs77545683	chr1:104668870-104668871	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs116045227	chr1:104668874-104668875	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs555910519	chr1:104668899-104668900	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs375815036	chr1:104668900-104668901	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs535786608	chr1:104669028-104669029	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs554480781	chr1:104669060-104669061	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs17019073	chr1:104669145-104669146	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs17476187	chr1:104669154-104669155	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs557892367	chr1:104669275-104669276	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs113139986	chr1:104669276-104669277	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs71655848	chr1:104669285-104669286	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs576133127	chr1:104669375-104669376	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs543485071	chr1:104669390-104669391	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs138142041	chr1:104669397-104669398	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs189519831	chr1:104669447-104669448	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs113460109	chr1:104669471-104669472	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs56175747	chr1:104669474-104669475	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs541044432	chr1:104669492-104669493	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs532990437	chr1:104669503-104669504	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs527573391	chr1:104669515-104669516	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs111875953	chr1:104669625-104669626	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs111264518	chr1:104669632-104669633	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs28438397	chr1:104669650-104669651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs374359933	chr1:104669693-104669694	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs55816437	chr1:104669811-104669812	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:100)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Medulloblastoma	21979893	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ovarian cancer	21720365	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Cancer	22429812	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Esophageal adenocarcinoma	18820669	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Glioblastoma multiforme	21922591	CNVD
Autism	17483303	CNVD
Intestinal disease	21956041	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Schizophrenia	17879154	CNVD
Mental retardation	17124404	CNVD
Intestinal disease	17828263	CNVD
lymphocytic leukemia	21291569	CNVD
Colorectal cancer	16774939	CNVD
Myelofibrosis	22110671	CNVD
Lung adenocarcinoma	17086460	CNVD
Immune disease	21076436	CNVD
Immune disease	21042300	CNVD
Lung cancer	17086460	CNVD
Gastric cancer	16891809	CNVD
Multiple myeloma	17550852	CNVD

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:104667800-104669000	Enhancers	Primary hematopoietic stem cells	blood
2	chr1:104667800-104669000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:104667800-104669200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:104668000-104668400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:104668000-104668400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:104668000-104669400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:104668200-104668800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:104668400-104674800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:104668600-104669000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:104669400-104678400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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