Variant report

Variant	nsv1007543
Chromosome Location	chr2:53129090-53148411
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	CEBPB	chr2:53131724-53132020	MCF-7	breast:	n/a	chr2:53131973-53131984
2	CEBPB	chr2:53145642-53146180	IMR90	lung:	n/a	chr2:53145956-53145969
3	CEBPB	chr2:53131722-53132000	Hela-S3	cervix:	n/a	chr2:53131973-53131984
4	CEBPB	chr2:53145768-53146137	Hela-S3	cervix:	n/a	chr2:53145956-53145969
5	E2F4	chr2:53145806-53146165	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr2:53145804-53146064	Hela-S3	cervix:	n/a	n/a
7	FAM48A	chr2:53145968-53146007	GM12878	blood:	n/a	n/a
8	FOS	chr2:53145670-53146111	MCF10A-Er-Src	breast:	n/a	chr2:53145743-53145753 chr2:53145771-53145783
9	FOS	chr2:53145720-53146051	MCF10A-Er-Src	breast:	n/a	chr2:53145743-53145753 chr2:53145771-53145783
10	FOS	chr2:53145642-53146071	MCF10A-Er-Src	breast:	n/a	chr2:53145743-53145753 chr2:53145771-53145783
11	FOS	chr2:53145714-53146071	MCF10A-Er-Src	breast:	n/a	chr2:53145743-53145753 chr2:53145771-53145783
12	FOXA1	chr2:53147553-53147731	T-47D	breast:	n/a	n/a
13	FOXA1	chr2:53147533-53147819	T-47D	breast:	n/a	n/a
14	GATA3	chr2:53147559-53147730	T-47D	breast:	n/a	n/a
15	GATA3	chr2:53147559-53147840	T-47D	breast:	n/a	n/a
16	MXI1	chr2:53137866-53138008	H1-hESC	embryonic stem cell:	n/a	n/a
17	NFYA	chr2:53138258-53138441	GM12878	blood:	n/a	n/a
18	NR2F2	chr2:53131739-53132236	MCF-7	breast:	n/a	n/a
19	POLR2A	chr2:53139526-53139595	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr2:53147574-53147580	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr2:53146740-53146849	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr2:53137929-53137963	MCF10A-Er-Src	breast:	n/a	n/a
23	PRDM1	chr2:53145696-53146192	Hela-S3	cervix:	n/a	n/a
24	RAD21	chr2:53145621-53146269	IMR90	lung:	n/a	n/a
25	STAT3	chr2:53145727-53146089	MCF10A-Er-Src	breast:	n/a	chr2:53145901-53145909 chr2:53145899-53145910
26	STAT3	chr2:53137672-53137871	MCF10A-Er-Src	breast:	n/a	n/a
27	STAT3	chr2:53145714-53146060	MCF10A-Er-Src	breast:	n/a	chr2:53145901-53145909 chr2:53145899-53145910
28	STAT3	chr2:53145437-53146122	MCF10A-Er-Src	breast:	n/a	chr2:53145901-53145909 chr2:53145899-53145910 chr2:53145548-53145559
29	STAT3	chr2:53145763-53146103	Hela-S3	cervix:	n/a	chr2:53145901-53145909 chr2:53145899-53145910
30	STAT3	chr2:53145723-53146096	MCF10A-Er-Src	breast:	n/a	chr2:53145901-53145909 chr2:53145899-53145910
31	STAT3	chr2:53142448-53142618	MCF10A-Er-Src	breast:	n/a	n/a
32	TCF7L2	chr2:53132666-53132849	HepG2	liver:	n/a	n/a
33	USF2	chr2:53141074-53141168	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:53132852..53133808-chr20:52198265..52198765,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ASB3-1	chr2:53137102-53137158	ENSG00000228033
2	lnc-ASB3-1	chr2:53137102-53137158	ENSG00000228033

Variant related genes	Relation type
ENSG00000228033	TF binding region

Extended variants
information (count: 987 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:987 , 50 per page) page: 1 2 3 4 5 6 7 ... 20

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2839750	chr2:53129090-53129091	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs191268742	chr2:53129103-53129104	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs373794591	chr2:53129143-53129144	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs561550354	chr2:53129155-53129156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs530458355	chr2:53129210-53129211	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs544026622	chr2:53129300-53129301	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs563875972	chr2:53129336-53129337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs150316726	chr2:53129368-53129369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs78095939	chr2:53129411-53129412	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs571192981	chr2:53129414-53129415	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs527268791	chr2:53129509-53129510	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs547021224	chr2:53129549-53129550	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs182313370	chr2:53129601-53129602	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs75553153	chr2:53129610-53129611	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs565876813	chr2:53129652-53129653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs549528085	chr2:53129694-53129695	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs78766470	chr2:53129701-53129702	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs114453500	chr2:53129702-53129703	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs56357423	chr2:53129718-53129719	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs572538533	chr2:53129719-53129720	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs535006975	chr2:53129727-53129728	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs555049023	chr2:53129764-53129765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs575139461	chr2:53129787-53129788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs557266834	chr2:53129789-53129790	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs544137312	chr2:53129791-53129792	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs187876767	chr2:53129795-53129796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs13014773	chr2:53129815-53129816	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs546403951	chr2:53129843-53129844	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs564811386	chr2:53129865-53129866	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs527418969	chr2:53129888-53129889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs140759671	chr2:53129890-53129891	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs560563708	chr2:53129939-53129940	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs199986842	chr2:53130031-53130032	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs529907376	chr2:53130071-53130072	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs368201430	chr2:53130080-53130081	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs549687832	chr2:53130082-53130083	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs569963454	chr2:53130091-53130092	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs538440385	chr2:53130113-53130114	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs552391290	chr2:53130121-53130122	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs193140228	chr2:53130141-53130142	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs539694413	chr2:53130204-53130205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs372467853	chr2:53130205-53130206	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs554961444	chr2:53130223-53130224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs376715565	chr2:53130264-53130265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs537711524	chr2:53130265-53130266	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs374889720	chr2:53130276-53130277	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs79529481	chr2:53130285-53130286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs114494596	chr2:53130291-53130292	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs577498692	chr2:53130324-53130325	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs201220044	chr2:53130336-53130337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53109400-53145600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:53131400-53131800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:53131400-53132000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr2:53131400-53132000	Enhancers	Fetal Muscle Leg	muscle
5	chr2:53131400-53132400	Enhancers	Hela-S3	cervix
6	chr2:53144200-53144400	Enhancers	Fetal Intestine Large	intestine
7	chr2:53144200-53144400	Enhancers	Hela-S3	cervix
8	chr2:53144400-53145400	Weak transcription	Hela-S3	cervix
9	chr2:53145400-53146000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:53145400-53147000	Enhancers	Hela-S3	cervix
11	chr2:53145400-53147200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:53145400-53147200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:53145600-53146200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr2:53145600-53146400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:53145600-53147200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:53146400-53147200	Enhancers	Fetal Intestine Small	intestine
17	chr2:53146400-53148000	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr2:53146400-53160000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr2:53146800-53147000	Enhancers	Fetal Intestine Large	intestine
20	chr2:53147000-53147600	Enhancers	Stomach Mucosa	stomach

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