Variant report

Variant	esv3452297
Chromosome Location	chr1:62652564-62657162
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:62656643-62656653	HepG2	liver:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-L1TD1-1	chr1:62656194-62656598	NONHSAT003628
2	lnc-L1TD1-2	chr1:62654803-62655175	NONHSAT003627
3	lnc-L1TD1-2	chr1:62655541-62655625	NONHSAT003627

Variant related genes	Relation type
RPS15AP7	TF binding region
L1TD1	TF binding region
PIGPP2	TF binding region

Extended variants
information (count: 223 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:223 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs142672622	chr1:62652594-62652595	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs533208280	chr1:62652607-62652608	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs370351745	chr1:62652619-62652620	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs560022940	chr1:62652630-62652631	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs527257864	chr1:62652639-62652640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs12093895	chr1:62652640-62652641	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs567270220	chr1:62652650-62652651	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs531846458	chr1:62652704-62652705	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs550065958	chr1:62652759-62652760	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs572312099	chr1:62652767-62652768	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs571505937	chr1:62652784-62652785	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs560132866	chr1:62652794-62652795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs533929028	chr1:62652800-62652801	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs566071646	chr1:62652866-62652867	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs376024150	chr1:62652907-62652908	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs536763968	chr1:62652935-62652936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs554624804	chr1:62652951-62652952	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs183340200	chr1:62652956-62652957	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs576385911	chr1:62653029-62653030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs555777897	chr1:62653034-62653035	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs139709901	chr1:62653038-62653039	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs112983540	chr1:62653054-62653055	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs200050864	chr1:62653063-62653064	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs557122355	chr1:62653064-62653065	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs371699792	chr1:62653065-62653066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs577894700	chr1:62653066-62653067	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs28878237	chr1:62653077-62653078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs376667333	chr1:62653078-62653079	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs4915798	chr1:62653083-62653084	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs11207920	chr1:62653086-62653087	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs74764142	chr1:62653087-62653088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs575733496	chr1:62653104-62653105	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs572011417	chr1:62653105-62653106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs542717593	chr1:62653128-62653129	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs560676632	chr1:62653132-62653133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs376922798	chr1:62653139-62653140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs188917605	chr1:62653164-62653165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs142296589	chr1:62653198-62653199	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs565274206	chr1:62653212-62653213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs193067357	chr1:62653225-62653226	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs185357055	chr1:62653237-62653238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs563656981	chr1:62653250-62653251	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs528037813	chr1:62653252-62653253	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs145916090	chr1:62653292-62653293	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs536300504	chr1:62653317-62653318	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs548682715	chr1:62653319-62653320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs2457818	chr1:62653341-62653342	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs34626505	chr1:62653369-62653370	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs558645118	chr1:62653388-62653389	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs576951408	chr1:62653401-62653402	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:92)

Disease	PMID	Source
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
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
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
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Breast cancer	16620391	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
small cell lung cancer	20016488	CNVD
Developmental delay	21147756	CNVD
Breast cancer	17133270	CNVD
Myelofibrosis	22110671	CNVD
CNS Malformation Syndrome	17530927	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Colorectal cancer	20459617	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62646600-62660400	Weak transcription	Right Atrium	heart
2	chr1:62649800-62660000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:62650400-62658400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:62650400-62658800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:62652000-62660200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:62656000-62657400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr1:62656800-62658600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:62657000-62657200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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