Variant report

Variant	esv3398650
Chromosome Location	chr1:56387164-56390862
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	chr1:56381262..56382928-chr1:56386333..56388137,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRKAA2-11	chr1:56389261-56389531	NONHSAT003427

Extended variants
information (count: 130 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:130 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs41285918	chr1:56387212-56387213	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs569706304	chr1:56387232-56387233	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs41285920	chr1:56387242-56387243	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs555303659	chr1:56387246-56387247	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs12144400	chr1:56387285-56387286	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs11800215	chr1:56387295-56387296	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs575317977	chr1:56387302-56387303	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs557958238	chr1:56387350-56387351	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs34098107	chr1:56387385-56387386	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs541636239	chr1:56387386-56387387	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs553713314	chr1:56387422-56387423	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs577799554	chr1:56387427-56387428	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs539571624	chr1:56387454-56387455	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs557194519	chr1:56387455-56387456	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs574031143	chr1:56387470-56387471	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs542663012	chr1:56387497-56387498	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs559688097	chr1:56387515-56387516	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs527629724	chr1:56387518-56387519	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs541307986	chr1:56387588-56387589	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs564341567	chr1:56387607-56387608	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs80056967	chr1:56387625-56387626	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs578161610	chr1:56387677-56387678	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs544703080	chr1:56387684-56387685	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs549903730	chr1:56387690-56387691	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs34873099	chr1:56387725-56387726	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs143479117	chr1:56387732-56387733	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs528975725	chr1:56387735-56387736	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs148009538	chr1:56387759-56387760	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs182450021	chr1:56387782-56387783	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs535018174	chr1:56387786-56387787	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs558045985	chr1:56387916-56387917	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs571579128	chr1:56387921-56387922	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs537250013	chr1:56387926-56387927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs557487071	chr1:56387951-56387952	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs187085306	chr1:56387976-56387977	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs530411535	chr1:56387986-56387987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs189052170	chr1:56388030-56388031	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs553428444	chr1:56388075-56388076	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs573291981	chr1:56388148-56388149	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs545396204	chr1:56388153-56388154	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs564377781	chr1:56388155-56388156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs72904497	chr1:56388180-56388181	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs543294475	chr1:56388222-56388223	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs563496585	chr1:56388226-56388227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs181482854	chr1:56388277-56388278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs185627429	chr1:56388284-56388285	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs190093673	chr1:56388366-56388367	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs182785661	chr1:56388378-56388379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs115111103	chr1:56388438-56388439	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs550914582	chr1:56388450-56388451	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
Papillary thyroid carcinoma	21436994	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
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
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
Melanoma	17363583	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
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Meckel-Gruber syndrome	21572526	CNVD
Breast cancer	16620391	CNVD
Multiple myeloma	16616336	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21509527	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	19490664	CNVD
Glioblastoma multiforme	22286061	CNVD
Ovarian cancer	21720365	CNVD

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56382600-56393400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:56382800-56392800	Weak transcription	Fetal Lung	lung
3	chr1:56383000-56393400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:56386200-56387600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr1:56386400-56387600	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:56386800-56387800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:56386800-56392800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:56386800-56395400	Weak transcription	Placenta	Placenta
9	chr1:56386800-56396600	Weak transcription	Esophagus	oesophagus
10	chr1:56387000-56387800	Enhancers	Adipose Nuclei	Adipose
11	chr1:56387600-56392400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:56387800-56393000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:56387800-56393400	Weak transcription	Adipose Nuclei	Adipose

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