Variant report

Variant	nsv962130
Chromosome Location	chr2:52588159-52598836
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	chr2:52594040-52594190	GM12869	blood:	n/a	n/a
2	EP300	chr2:52596370-52596765	T-47D	breast:	n/a	n/a
3	FOXA1	chr2:52596298-52596674	T-47D	breast:	n/a	n/a
4	FOXA1	chr2:52596382-52596643	T-47D	breast:	n/a	n/a
5	GATA3	chr2:52596389-52596627	T-47D	breast:	n/a	n/a
6	GATA3	chr2:52596387-52596681	T-47D	breast:	n/a	n/a
7	GATA3	chr2:52595386-52595610	T-47D	breast:	n/a	n/a
8	HDAC2	chr2:52596356-52596719	MCF-7	breast:	n/a	n/a
9	POLR2A	chr2:52592176-52592253	GM12878	blood:	n/a	n/a
10	POLR2A	chr2:52595671-52595829	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr2:52597599-52597672	MCF10A-Er-Src	breast:	n/a	n/a
12	SETDB1	chr2:52590883-52591191	U2OS	brain:	n/a	n/a
13	SIN3AK20	chr2:52596288-52596768	MCF-7	breast:	n/a	n/a
14	STAT3	chr2:52597336-52597514	MCF10A-Er-Src	breast:	n/a	n/a
15	ZNF143	chr2:52591010-52591161	H1-hESC	embryonic stem cell:	n/a	n/a
16	ZNF143	chr2:52597455-52597507	GM12878	blood:	n/a	n/a
17	ZNF217	chr2:52596436-52596615	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000225444	TF binding region

Extended variants
information (count: 513 )
Associated
traits (count: 83 )

Variant overlapped rSNPs/rCNVs (count:513 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs116542899	chr2:52588180-52588181	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs138748019	chr2:52588190-52588191	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs148928457	chr2:52588195-52588196	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs534723516	chr2:52588237-52588238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs143631887	chr2:52588243-52588244	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs6706839	chr2:52588260-52588261	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs190530522	chr2:52588269-52588270	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs148116119	chr2:52588288-52588289	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs17042808	chr2:52588289-52588290	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs13432341	chr2:52588340-52588341	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs540129767	chr2:52588349-52588350	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs141875006	chr2:52588353-52588354	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs572049230	chr2:52588368-52588369	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs531760846	chr2:52588408-52588409	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs2955290	chr2:52588411-52588412	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs574402824	chr2:52588417-52588418	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs2955289	chr2:52588483-52588484	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs13432527	chr2:52588506-52588507	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs532218824	chr2:52588517-52588518	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs552029315	chr2:52588527-52588528	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs2969313	chr2:52588534-52588535	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs4971809	chr2:52588622-52588623	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs139220199	chr2:52588673-52588674	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs568447737	chr2:52588685-52588686	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs187082732	chr2:52588686-52588687	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs189567949	chr2:52588687-52588688	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs115688277	chr2:52588739-52588740	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs143349879	chr2:52588774-52588775	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs13012563	chr2:52588775-52588776	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs182497320	chr2:52588822-52588823	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs147533615	chr2:52588848-52588849	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs369111710	chr2:52588873-52588874	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs536158146	chr2:52588922-52588923	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs554226550	chr2:52588947-52588948	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs574413425	chr2:52588961-52588962	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs114975871	chr2:52588970-52588971	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs557045240	chr2:52589005-52589006	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs576610866	chr2:52589033-52589034	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs143626070	chr2:52589062-52589063	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs569293804	chr2:52589069-52589070	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs2262851	chr2:52589138-52589139	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs372808469	chr2:52589160-52589161	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs2356040	chr2:52589185-52589186	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs528326240	chr2:52589197-52589198	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs549931891	chr2:52589199-52589200	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs114167450	chr2:52589203-52589204	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs188061757	chr2:52589235-52589236	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs193087167	chr2:52589240-52589241	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs570991995	chr2:52589259-52589260	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs13398489	chr2:52589282-52589283	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:83)

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
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
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
Pancreatic ductal adenocarcinoma	19077451	CNVD
Ovarian clear cell carcinoma	21343371	CNVD

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:52586600-52590600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:52587800-52591000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr2:52588600-52589800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:52589800-52592000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:52591000-52591600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
6	chr2:52591200-52591400	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:52591400-52591600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:52591600-52591800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:52591600-52591800	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:52591800-52614800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:52592000-52594200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:52595400-52596000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:52596400-52596600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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