Variant report

Variant	nsv589292
Chromosome Location	chr3:359160-378069
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	chr3:377988-378086	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr3:360820-360858	Kidney_OC	kidney:	n/a	n/a
3	EP300	chr3:360589-360901	SK-N-SH_RA	brain:	n/a	n/a
4	EP300	chr3:360571-360892	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr3:376998-377287	SK-N-SH_RA	brain:	n/a	n/a
6	IRF1	chr3:371993-372007	K562	blood:	n/a	n/a
7	MAFF	chr3:367223-367524	HepG2	liver:	n/a	chr3:367357-367375
8	MAFF	chr3:367279-367485	K562	blood:	n/a	chr3:367357-367375
9	MAFK	chr3:367250-367564	K562	blood:	n/a	chr3:367359-367374
10	MAFK	chr3:367191-367549	HepG2	liver:	n/a	chr3:367359-367374
11	MAFK	chr3:367204-367516	HepG2	liver:	n/a	chr3:367359-367374
12	MAFK	chr3:367193-367554	IMR90	lung:	n/a	chr3:367359-367374
13	MAFK	chr3:367282-367482	H1-hESC	embryonic stem cell:	n/a	chr3:367359-367374
14	POLR2A	chr3:377490-377521	GM12878	blood:	n/a	n/a
15	POLR2A	chr3:365910-366040	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:367135-367326	MCF10A-Er-Src	breast:	n/a	n/a
17	RFX5	chr3:371145-371169	K562	blood:	n/a	n/a
18	RFX5	chr3:361455-361464	K562	blood:	n/a	n/a
19	STAT3	chr3:369669-369759	MCF10A-Er-Src	breast:	n/a	n/a
20	ZC3H11A	chr3:366197-366400	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:369627..372241-chr3:375088..376630,2	K562	blood:
2	chr3:369627..372241-chr3:375088..376630,2	K562	blood:

Variant related genes	Relation type
CHL1	TF binding region

Extended variants
information (count: 986 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:986 , 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	rs330900	chr3:359160-359161	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs375395547	chr3:359208-359209	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs114300093	chr3:359225-359226	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs189982764	chr3:359251-359252	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs79185595	chr3:359252-359253	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs193184983	chr3:359312-359313	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs370451186	chr3:359332-359333	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs201105154	chr3:359335-359336	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs35799872	chr3:359337-359338	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs77110504	chr3:359338-359339	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs71058763	chr3:359350-359351	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs530043614	chr3:359373-359374	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs528210098	chr3:359375-359376	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs541608532	chr3:359402-359403	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs185413928	chr3:359412-359413	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs530349718	chr3:359418-359419	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs372802028	chr3:359419-359420	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs78344689	chr3:359431-359432	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs4685578	chr3:359454-359455	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs530763711	chr3:359460-359461	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs552171683	chr3:359474-359475	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs570586642	chr3:359478-359479	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs561608468	chr3:359481-359482	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs534774542	chr3:359498-359499	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs189540046	chr3:359557-359558	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs4685579	chr3:359574-359575	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs142189541	chr3:359600-359601	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs541258537	chr3:359614-359615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs374857438	chr3:359642-359643	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs180675854	chr3:359647-359648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs116330921	chr3:359668-359669	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs545447336	chr3:359676-359677	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs557808118	chr3:359768-359769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs572903299	chr3:359788-359789	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs540313644	chr3:359795-359796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs115258984	chr3:359830-359831	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs530226053	chr3:359834-359835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs146332403	chr3:359863-359864	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs550148290	chr3:359874-359875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs547764587	chr3:359886-359887	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs563869209	chr3:359889-359890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs139574437	chr3:359912-359913	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs56270007	chr3:359920-359921	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs528508697	chr3:359924-359925	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs554796402	chr3:359981-359982	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs546686869	chr3:359982-359983	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs568543805	chr3:360003-360004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs377227267	chr3:360022-360023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs144306494	chr3:360027-360028	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs539721711	chr3:360028-360029	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Cancer	20164920	CNVD
Lung cancer	16618734	CNVD
Autism	18349135	CNVD
Breast cancer	20409316	CNVD
Myelofibrosis	22110671	CNVD
Autism	22241247	CNVD
Intellectual disability	22045946	CNVD
Squamous cell cancer	19607727	CNVD
Gastric adenocarcinoma	19115996	CNVD
sporadic birth defects	19047251	CNVD
Mental retardation	17124404	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Sudden cardiac death	19188705	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ovarian cancer	21720365	CNVD
Neuroblastoma	18923191	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Biliary cancer	19435499	CNVD
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	20967226	CNVD
Autism	22543975	CNVD
Attention deficit hyperactivity disorder	19546859	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	17289997	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Tetralogy of Fallot	22912587	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Autism	20685689	CNVD
Melanoma	20877625	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:351000-369800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:358800-359600	Enhancers	Pancreatic Islets	Pancreatic Islet
3	chr3:360000-391800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:365800-366000	Enhancers	Brain Anterior Caudate	brain
5	chr3:366000-410400	Weak transcription	Brain Anterior Caudate	brain
6	chr3:366200-376000	Weak transcription	Ovary	ovary
7	chr3:367600-380400	Weak transcription	Brain Germinal Matrix	brain
8	chr3:367800-375400	Weak transcription	Fetal Brain Female	brain
9	chr3:368600-374400	Weak transcription	Fetal Brain Male	brain
10	chr3:369800-371000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:370200-371000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:371000-386200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:374000-375200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:374200-375000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:374200-377800	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:374400-375800	Enhancers	Fetal Brain Male	brain
17	chr3:374600-375400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:375000-377000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:375400-375600	Enhancers	Fetal Brain Female	brain
20	chr3:375600-389200	Weak transcription	Fetal Brain Female	brain
21	chr3:377000-377400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:377400-380200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:377800-380400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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