Variant report

Variant	esv3452295
Chromosome Location	chr1:62654286-62657413
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	CTCF	chr1:62657260-62657410	HepG2	liver:	n/a	n/a
2	MAX	chr1:62656643-62656653	HepG2	liver:	n/a	n/a
3	STAT3	chr1:62657352-62657552	MCF10A-Er-Src	breast:	n/a	n/a

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

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

Extended variants
information (count: 146 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:146 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547607595	chr1:62654331-62654332	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs536473666	chr1:62654381-62654382	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs143066575	chr1:62654391-62654392	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs76064380	chr1:62654397-62654398	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs181783937	chr1:62654411-62654412	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs146107327	chr1:62654482-62654483	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs66784185	chr1:62654491-62654492	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs35291979	chr1:62654505-62654506	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs536576112	chr1:62654510-62654511	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs186803717	chr1:62654511-62654512	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs576473326	chr1:62654551-62654552	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs541360292	chr1:62654557-62654558	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs560025085	chr1:62654584-62654585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs369545115	chr1:62654587-62654588	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs370740141	chr1:62654614-62654615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs112201120	chr1:62654627-62654628	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs530217640	chr1:62654632-62654633	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs542375865	chr1:62654633-62654634	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs563894595	chr1:62654636-62654637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs530979218	chr1:62654676-62654677	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs555553467	chr1:62654703-62654704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs369955363	chr1:62654710-62654711	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs140152841	chr1:62654727-62654728	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs570849383	chr1:62654758-62654759	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs143683287	chr1:62654760-62654761	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs7551899	chr1:62654775-62654776	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs78348068	chr1:62654777-62654778	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs115661571	chr1:62654805-62654806	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs191249394	chr1:62654806-62654807	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs554312719	chr1:62654809-62654810	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs12737213	chr1:62654820-62654821	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs536742640	chr1:62654822-62654823	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs577946433	chr1:62654864-62654865	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs558279421	chr1:62654921-62654922	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs576743348	chr1:62654944-62654945	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs538246679	chr1:62654946-62654947	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs75380838	chr1:62654959-62654960	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs552710831	chr1:62654972-62654973	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs74790914	chr1:62654996-62654997	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs542161986	chr1:62655034-62655035	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs563832535	chr1:62655070-62655071	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs575949242	chr1:62655084-62655085	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs546315226	chr1:62655085-62655086	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs541108313	chr1:62655090-62655091	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
45	rs564598560	chr1:62655095-62655096	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs552931641	chr1:62655116-62655117	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs182614853	chr1:62655130-62655131	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
48	rs184950686	chr1:62655177-62655178	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs74403686	chr1:62655180-62655181	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs201396062	chr1:62655211-62655212	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:15 , 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
9	chr1:62657200-62657400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr1:62657200-62657400	Bivalent Enhancer	K562	blood
11	chr1:62657400-62657600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:62657400-62657600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr1:62657400-62657600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:62657400-62658400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr1:62657400-62659000	Enhancers	ES-I3 Cell Line	embryonic stem cell

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