Variant report

Variant	nsv431002
Chromosome Location	chr2:50243349-50259749
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	chr2:50246112-50246411	HepG2	liver:	n/a	n/a
2	CEBPB	chr2:50245918-50246489	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr2:50246112-50246386	H1-hESC	embryonic stem cell:	n/a	n/a
4	CHD2	chr2:50246157-50246357	Hela-S3	cervix:	n/a	n/a
5	E2F4	chr2:50246109-50246340	MCF10A-Er-Src	breast:	n/a	n/a
6	EP300	chr2:50246059-50246447	Hela-S3	cervix:	n/a	chr2:50246254-50246268
7	EP300	chr2:50249956-50250058	GM12878	blood:	n/a	n/a
8	FOS	chr2:50246004-50246475	MCF10A-Er-Src	breast:	n/a	chr2:50246199-50246211
9	FOS	chr2:50245946-50246474	MCF10A-Er-Src	breast:	n/a	chr2:50246199-50246211
10	FOS	chr2:50246060-50246463	MCF10A-Er-Src	breast:	n/a	chr2:50246199-50246211
11	FOS	chr2:50246040-50246476	MCF10A-Er-Src	breast:	n/a	chr2:50246199-50246211
12	JUN	chr2:50246107-50246425	Hela-S3	cervix:	n/a	chr2:50246254-50246267 chr2:50246199-50246211 chr2:50246239-50246252
13	JUN	chr2:50246109-50246397	HepG2	liver:	n/a	chr2:50246254-50246267 chr2:50246199-50246211 chr2:50246239-50246252
14	JUN	chr2:50246151-50246351	H1-hESC	embryonic stem cell:	n/a	chr2:50246254-50246267 chr2:50246199-50246211 chr2:50246239-50246252
15	JUND	chr2:50244756-50244966	HepG2	liver:	n/a	chr2:50244859-50244866 chr2:50244858-50244867 chr2:50244857-50244868 chr2:50244859-50244867 chr2:50244859-50244868
16	JUND	chr2:50246175-50246440	H1-hESC	embryonic stem cell:	n/a	chr2:50246199-50246211
17	JUND	chr2:50246092-50246407	Hela-S3	cervix:	n/a	chr2:50246199-50246211
18	JUND	chr2:50246095-50246413	HepG2	liver:	n/a	chr2:50246199-50246211
19	KAP1	chr2:50245328-50246485	U2OS	brain:	n/a	n/a
20	MAX	chr2:50246105-50246368	Hela-S3	cervix:	n/a	chr2:50246256-50246265
21	MYC	chr2:50257366-50257501	H1-hESC	embryonic stem cell:	n/a	n/a
22	MYC	chr2:50246075-50246353	MCF10A-Er-Src	breast:	n/a	chr2:50246256-50246265
23	MYC	chr2:50246073-50246360	MCF10A-Er-Src	breast:	n/a	chr2:50246256-50246265
24	POLR2A	chr2:50243528-50243692	MCF10A-Er-Src	breast:	n/a	n/a
25	POLR2A	chr2:50258639-50258688	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr2:50244110-50244570	H1-neurons	neurons:	n/a	n/a
27	POLR2A	chr2:50247797-50248119	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr2:50259009-50259209	MCF10A-Er-Src	breast:	n/a	n/a
29	PRDM1	chr2:50246077-50246320	Hela-S3	cervix:	n/a	chr2:50246206-50246221
30	RCOR1	chr2:50246132-50246333	Hela-S3	cervix:	n/a	n/a
31	RFX5	chr2:50246156-50246332	Hela-S3	cervix:	n/a	n/a
32	SETDB1	chr2:50245869-50246628	U2OS	brain:	n/a	n/a
33	SMC3	chr2:50246164-50246377	Hela-S3	cervix:	n/a	n/a
34	STAT3	chr2:50245957-50246385	Hela-S3	cervix:	n/a	n/a
35	STAT3	chr2:50245955-50246405	MCF10A-Er-Src	breast:	n/a	n/a
36	STAT3	chr2:50246135-50246416	MCF10A-Er-Src	breast:	n/a	n/a
37	STAT3	chr2:50245931-50246399	MCF10A-Er-Src	breast:	n/a	n/a
38	STAT3	chr2:50250389-50250706	MCF10A-Er-Src	breast:	n/a	chr2:50250577-50250585
39	STAT3	chr2:50244475-50244549	MCF10A-Er-Src	breast:	n/a	n/a
40	STAT3	chr2:50245975-50246442	MCF10A-Er-Src	breast:	n/a	n/a
41	TCF7L2	chr2:50246089-50246379	Hela-S3	cervix:	n/a	n/a
42	USF2	chr2:50246245-50246445	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:49987705..49990073-chr2:50256678..50259583,2	K562	blood:
2	chr2:50245424..50247273-chr2:50250002..50252375,2	K562	blood:

Variant related genes	Relation type
NRXN1	TF binding region
ENSG00000179915	chromatin interactions

Extended variants
information (count: 437 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:437 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536154348	chr2:50243366-50243367	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs13003111	chr2:50243386-50243387	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs6731061	chr2:50243402-50243403	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs553581287	chr2:50243417-50243418	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs74447449	chr2:50243449-50243450	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs542554992	chr2:50243451-50243452	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs561233257	chr2:50243453-50243454	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs538708927	chr2:50243498-50243499	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs531460425	chr2:50243502-50243503	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs558827396	chr2:50243504-50243505	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs552942833	chr2:50243508-50243509	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs544605158	chr2:50243510-50243511	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs373810473	chr2:50243531-50243532	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs181602757	chr2:50243547-50243548	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs572598587	chr2:50243607-50243608	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs376920329	chr2:50243640-50243641	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs560707100	chr2:50243641-50243642	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs76188810	chr2:50243650-50243651	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs10196157	chr2:50243651-50243652	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs80066171	chr2:50243654-50243655	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs112820530	chr2:50243661-50243662	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs138291317	chr2:50243688-50243689	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs374150463	chr2:50243701-50243702	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs538121039	chr2:50243702-50243703	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs143782907	chr2:50243703-50243704	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs571136485	chr2:50243712-50243713	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs116198233	chr2:50243724-50243725	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs115236407	chr2:50243725-50243726	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs544020566	chr2:50243738-50243739	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs146372594	chr2:50243740-50243741	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs536042368	chr2:50243743-50243744	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs185441158	chr2:50243754-50243755	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs6746395	chr2:50243779-50243780	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs576302353	chr2:50243799-50243800	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs543329240	chr2:50243856-50243857	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs562426957	chr2:50243870-50243871	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs72889512	chr2:50243886-50243887	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs200776653	chr2:50243923-50243924	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs79616272	chr2:50243924-50243925	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs190642681	chr2:50243932-50243933	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs112323286	chr2:50243935-50243936	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs10172768	chr2:50243938-50243939	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs549568449	chr2:50243954-50243955	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs561294313	chr2:50244025-50244026	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs532061794	chr2:50244073-50244074	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs182778072	chr2:50244126-50244127	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs10181439	chr2:50244128-50244129	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs549482551	chr2:50244183-50244184	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs538244876	chr2:50244192-50244193	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs546943518	chr2:50244226-50244227	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:104)

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
Bladder cancer	21909424	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
small cell lung cancer	20016488	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
Lung cancer	17297452	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20433910	CNVD
Autism	21701786	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Austim spectrum disorder	21302340	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	20553308	CNVD
Autism	22241247	CNVD
Myelofibrosis	22110671	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Mental retardation	19521722	CNVD
Schizophrenia	18990708	CNVD
Schizophrenia	18940311	CNVD
Schizophrenia	19348701	CNVD
Schizophrenia	18945720	CNVD
Schizophrenia	19571808	CNVD
Prostate cancer	16573809	CNVD
Neuroticism	17667963	CNVD
Schizophrenia	19443537	CNVD
Schizophrenia	19546859	CNVD
Autism	17322880	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
Basal cell lymphoma	21115979	CNVD
Cognitive impairment	21505072	CNVD
Psychiatric disorder	19734545	CNVD
Autism	20844286	CNVD
Schizophrenia	20838587	CNVD
Schizophrenia	20718829	CNVD
Autism	19218893	CNVD
Autism	22209245	CNVD
Neuropsychiatric disorder	21827697	CNVD
Schizophrenia	22118685	CNVD
Autism	20663923	CNVD
Schizophrenia	21285140	CNVD
Breast cancer	22522925	CNVD
Breast cancer	21990379	CNVD
Schizophrenia	22885689	CNVD
Autism	20964600	CNVD
Schizophrenia	19521646	CNVD
Attention deficit hyperactivity disorder	22214315	CNVD
Chronic motor tic disorder	22214315	CNVD
Schizophrenia	22214315	CNVD
Mental retardation	19896112	CNVD

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50234200-50245600	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr2:50237800-50245800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr2:50241200-50245600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr2:50242600-50245400	Weak transcription	Brain Angular Gyrus	brain
5	chr2:50242600-50246000	Enhancers	Brain Germinal Matrix	brain
6	chr2:50242800-50245400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:50243800-50244000	Enhancers	Fetal Brain Female	brain
8	chr2:50244000-50246200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:50244200-50244600	Enhancers	Brain Substantia Nigra	brain
10	chr2:50244200-50245400	Weak transcription	Fetal Brain Female	brain
11	chr2:50244600-50245000	Weak transcription	Brain Substantia Nigra	brain
12	chr2:50244600-50246600	Enhancers	Hela-S3	cervix
13	chr2:50245000-50246000	Enhancers	Brain Substantia Nigra	brain
14	chr2:50245400-50245600	Enhancers	Brain Angular Gyrus	brain
15	chr2:50245400-50246000	Enhancers	Brain Hippocampus Middle	brain
16	chr2:50245400-50246000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr2:50245400-50246000	Enhancers	Fetal Brain Female	brain
18	chr2:50245400-50246400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr2:50245600-50246000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr2:50245600-50246000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:50245600-50246400	Enhancers	HUES48 Cell Line	embryonic stem cell
22	chr2:50245600-50246400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:50245800-50246200	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr2:50250000-50250400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:50250000-50250800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr2:50250400-50252200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:50250800-50252200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:50252200-50253800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:50252200-50254800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:50252400-50252600	Enhancers	Fetal Heart	heart
31	chr2:50252600-50253600	Enhancers	Primary hematopoietic stem cells	blood
32	chr2:50253000-50253400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr2:50253200-50253400	Enhancers	Fetal Heart	heart
34	chr2:50253800-50256200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:50254800-50256600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:50256200-50257000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:50256600-50256800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:50259200-50265200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links