Variant report

Variant	nsv1004550
Chromosome Location	chr2:50250335-50274067
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	chr2:50271154-50271446	HepG2	liver:	n/a	chr2:50271251-50271262 chr2:50271290-50271301
2	EBF1	chr2:50269267-50269547	GM12878	blood:	n/a	n/a
3	EP300	chr2:50266645-50266872	SK-N-SH_RA	brain:	n/a	n/a
4	EP300	chr2:50266517-50267135	SK-N-SH	brain:	n/a	chr2:50266883-50266891
5	EP300	chr2:50266622-50266833	SK-N-SH_RA	brain:	n/a	n/a
6	GATA2	chr2:50266597-50266977	SH-SY5Y	brain:	n/a	chr2:50266825-50266842 chr2:50266829-50266850 chr2:50266836-50266843 chr2:50266831-50266847 chr2:50266834-50266843
7	GATA3	chr2:50266677-50267063	SH-SY5Y	brain:	n/a	chr2:50266825-50266842 chr2:50266829-50266850 chr2:50266836-50266843 chr2:50267013-50267025 chr2:50266831-50266847 chr2:50266834-50266843
8	JUN	chr2:50264659-50264798	K562	blood:	n/a	n/a
9	MAFK	chr2:50262326-50262523	HepG2	liver:	n/a	chr2:50262375-50262386
10	MYC	chr2:50257366-50257501	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr2:50266455-50266521	ProgFib	skin:	n/a	n/a
12	POLR2A	chr2:50259009-50259209	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr2:50258639-50258688	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr2:50268763-50268851	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr2:50273143-50273160	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr2:50260562-50260728	ProgFib	skin:	n/a	n/a
17	SPI1	chr2:50270015-50270274	HL-60	blood:	n/a	n/a
18	STAT3	chr2:50250389-50250706	MCF10A-Er-Src	breast:	n/a	chr2:50250577-50250585
19	STAT3	chr2:50261176-50261287	MCF10A-Er-Src	breast:	n/a	n/a
20	USF1	chr2:50263721-50263971	H1-hESC	embryonic stem cell:	n/a	n/a
21	USF1	chr2:50263698-50264018	H1-hESC	embryonic stem cell:	n/a	n/a
22	ZNF143	chr2:50269511-50269604	GM12878	blood:	n/a	n/a

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

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

Extended variants
information (count: 787 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:787 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4971634	chr2:50250335-50250336	Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs538457504	chr2:50250350-50250351	Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs188399890	chr2:50250428-50250429	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs4971635	chr2:50250447-50250448	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs12476030	chr2:50250448-50250449	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs562149687	chr2:50250472-50250473	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs573944374	chr2:50250481-50250482	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs373638590	chr2:50250483-50250484	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs58756415	chr2:50250495-50250496	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs562977930	chr2:50250523-50250524	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs533427964	chr2:50250524-50250525	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs553695395	chr2:50250554-50250555	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs76881045	chr2:50250577-50250578	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs552023388	chr2:50250581-50250582	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs560644131	chr2:50250593-50250594	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs181571982	chr2:50250610-50250611	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs60750261	chr2:50250622-50250623	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs577769062	chr2:50250623-50250624	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs368836040	chr2:50250624-50250625	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs567299095	chr2:50250729-50250730	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs138271099	chr2:50250755-50250756	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs17494917	chr2:50250758-50250759	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs59497317	chr2:50250763-50250764	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs538318627	chr2:50250787-50250788	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs58018074	chr2:50250823-50250824	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs565724777	chr2:50250841-50250842	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs536592436	chr2:50250857-50250858	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs554565918	chr2:50250911-50250912	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs4971636	chr2:50250919-50250920	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs185673122	chr2:50250921-50250922	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs556567348	chr2:50250957-50250958	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs149602785	chr2:50250983-50250984	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs191563599	chr2:50251007-50251008	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs184204918	chr2:50251010-50251011	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs572454665	chr2:50251048-50251049	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs187132256	chr2:50251074-50251075	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs9677968	chr2:50251100-50251101	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs561432019	chr2:50251117-50251118	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs191137783	chr2:50251133-50251134	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs549389191	chr2:50251141-50251142	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs570888305	chr2:50251158-50251159	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs182166848	chr2:50251207-50251208	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs532111682	chr2:50251217-50251218	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs187233701	chr2:50251228-50251229	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs146126179	chr2:50251232-50251233	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs545775941	chr2:50251237-50251238	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs138998119	chr2:50251297-50251298	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs6712956	chr2:50251332-50251333	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs191647523	chr2:50251356-50251357	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs6712970	chr2:50251363-50251364	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	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:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50250000-50250400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:50250000-50250800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:50250400-50252200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:50250800-50252200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:50252200-50253800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:50252200-50254800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr2:50252400-50252600	Enhancers	Fetal Heart	heart
8	chr2:50252600-50253600	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:50253000-50253400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr2:50253200-50253400	Enhancers	Fetal Heart	heart
11	chr2:50253800-50256200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:50254800-50256600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:50256200-50257000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:50256600-50256800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:50259200-50265200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:50263800-50264200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr2:50265200-50265800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:50265800-50269800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr2:50266200-50266600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:50266400-50267200	Enhancers	Fetal Heart	heart
21	chr2:50268800-50269000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr2:50269000-50270000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr2:50269600-50270000	Enhancers	Fetal Intestine Large	intestine
24	chr2:50269800-50270200	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr2:50270000-50271000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:50270000-50271200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:50270000-50271600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr2:50270200-50270600	Enhancers	Fetal Intestine Large	intestine
29	chr2:50270200-50270600	Enhancers	Fetal Intestine Small	intestine
30	chr2:50270200-50271000	Enhancers	Primary hematopoietic stem cells	blood

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