Variant report

Variant	esv3354044
Chromosome Location	chr2:50245898-50248196
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	chr2:50246112-50246386	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr2:50245918-50246489	Hela-S3	cervix:	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	FOS	chr2:50245946-50246474	MCF10A-Er-Src	breast:	n/a	chr2:50246199-50246211
8	FOS	chr2:50246004-50246475	MCF10A-Er-Src	breast:	n/a	chr2:50246199-50246211
9	FOS	chr2:50246060-50246463	MCF10A-Er-Src	breast:	n/a	chr2:50246199-50246211
10	FOS	chr2:50246040-50246476	MCF10A-Er-Src	breast:	n/a	chr2:50246199-50246211
11	JUN	chr2:50246151-50246351	H1-hESC	embryonic stem cell:	n/a	chr2:50246254-50246267 chr2:50246199-50246211 chr2:50246239-50246252
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	JUND	chr2:50246095-50246413	HepG2	liver:	n/a	chr2:50246199-50246211
15	JUND	chr2:50246175-50246440	H1-hESC	embryonic stem cell:	n/a	chr2:50246199-50246211
16	JUND	chr2:50246092-50246407	Hela-S3	cervix:	n/a	chr2:50246199-50246211
17	KAP1	chr2:50245328-50246485	U2OS	brain:	n/a	n/a
18	MAX	chr2:50246105-50246368	Hela-S3	cervix:	n/a	chr2:50246256-50246265
19	MYC	chr2:50246075-50246353	MCF10A-Er-Src	breast:	n/a	chr2:50246256-50246265
20	MYC	chr2:50246073-50246360	MCF10A-Er-Src	breast:	n/a	chr2:50246256-50246265
21	POLR2A	chr2:50247797-50248119	MCF10A-Er-Src	breast:	n/a	n/a
22	PRDM1	chr2:50246077-50246320	Hela-S3	cervix:	n/a	chr2:50246206-50246221
23	RCOR1	chr2:50246132-50246333	Hela-S3	cervix:	n/a	n/a
24	RFX5	chr2:50246156-50246332	Hela-S3	cervix:	n/a	n/a
25	SETDB1	chr2:50245869-50246628	U2OS	brain:	n/a	n/a
26	SMC3	chr2:50246164-50246377	Hela-S3	cervix:	n/a	n/a
27	STAT3	chr2:50245955-50246405	MCF10A-Er-Src	breast:	n/a	n/a
28	STAT3	chr2:50246135-50246416	MCF10A-Er-Src	breast:	n/a	n/a
29	STAT3	chr2:50245975-50246442	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr2:50245931-50246399	MCF10A-Er-Src	breast:	n/a	n/a
31	STAT3	chr2:50245957-50246385	Hela-S3	cervix:	n/a	n/a
32	TCF7L2	chr2:50246089-50246379	Hela-S3	cervix:	n/a	n/a
33	USF2	chr2:50246245-50246445	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
NRXN1	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534952608	chr2:50245907-50245908	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs553296142	chr2:50245987-50245988	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs375590034	chr2:50246017-50246018	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs566128269	chr2:50246027-50246028	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs536257468	chr2:50246091-50246092	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs554909607	chr2:50246123-50246124	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs544711052	chr2:50246182-50246183	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs140183289	chr2:50246205-50246206	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs543871159	chr2:50246214-50246215	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs7571903	chr2:50246224-50246225	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs146211469	chr2:50246233-50246234	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs373856264	chr2:50246235-50246236	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs7586095	chr2:50246249-50246250	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs377305326	chr2:50246272-50246273	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs529880973	chr2:50246299-50246300	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs541371609	chr2:50246361-50246362	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs559621729	chr2:50246370-50246371	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs79131040	chr2:50246400-50246401	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs80238440	chr2:50246402-50246403	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs184290934	chr2:50246408-50246409	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs541473137	chr2:50246548-50246549	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs553318000	chr2:50247825-50247826	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs145559178	chr2:50247892-50247893	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs6754803	chr2:50247942-50247943	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs558216565	chr2:50247990-50247991	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs527909664	chr2:50248008-50248009	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs548057581	chr2:50248016-50248017	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs557631787	chr2:50248035-50248036	Inactive region	TF binding region	1 gene(s)	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:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50242600-50246000	Enhancers	Brain Germinal Matrix	brain
2	chr2:50244000-50246200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr2:50244600-50246600	Enhancers	Hela-S3	cervix
4	chr2:50245000-50246000	Enhancers	Brain Substantia Nigra	brain
5	chr2:50245400-50246000	Enhancers	Brain Hippocampus Middle	brain
6	chr2:50245400-50246000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr2:50245400-50246000	Enhancers	Fetal Brain Female	brain
8	chr2:50245400-50246400	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:50245600-50246000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr2:50245600-50246000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:50245600-50246400	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr2:50245600-50246400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:50245800-50246200	Enhancers	HUES64 Cell Line	embryonic stem cell

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