Variant report

Variant	nsv430009
Chromosome Location	chr9:25083900-25092100
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	E2F4	chr9:25089914-25090146	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr9:25091584-25091859	SK-N-SH_RA	brain:	n/a	chr9:25091782-25091796
3	FOS	chr9:25089773-25090158	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr9:25087433-25087763	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr9:25089834-25090135	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr9:25087395-25087815	MCF10A-Er-Src	breast:	n/a	n/a
7	FOS	chr9:25089805-25090158	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr9:25087421-25087816	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr9:25087433-25087828	MCF10A-Er-Src	breast:	n/a	n/a
10	MAFK	chr9:25090843-25091032	H1-hESC	embryonic stem cell:	n/a	chr9:25090846-25090857
11	POLR2A	chr9:25089051-25089101	A549	lung:	n/a	n/a
12	POLR2A	chr9:25085382-25085403	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr9:25089029-25089045	A549	lung:	n/a	n/a
14	STAT3	chr9:25087514-25087763	MCF10A-Er-Src	breast:	n/a	n/a
15	STAT3	chr9:25087497-25087824	MCF10A-Er-Src	breast:	n/a	n/a
16	STAT3	chr9:25090477-25090677	MCF10A-Er-Src	breast:	n/a	chr9:25090595-25090603
17	STAT3	chr9:25089874-25089982	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr9:25091705-25091765	MCF10A-Er-Src	breast:	n/a	chr9:25091724-25091731

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IZUMO3-1	chr9:25088809-25089149	NONHSAT130498

Variant related genes	Relation type
RN7SKP120	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 142 )

Variant overlapped rSNPs/rCNVs (count:120 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs369918796	chr9:25088813-25088814	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs10966725	chr9:25088818-25088819	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs541809910	chr9:25088832-25088833	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs192830847	chr9:25088848-25088849	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs536464809	chr9:25088864-25088865	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs184407831	chr9:25088871-25088872	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs188040343	chr9:25088912-25088913	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs564298851	chr9:25088948-25088949	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs112498578	chr9:25088967-25088968	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs540334644	chr9:25089001-25089002	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs144617579	chr9:25089006-25089007	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs528980758	chr9:25089024-25089025	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs548745083	chr9:25089026-25089027	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs568498047	chr9:25089037-25089038	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs531137886	chr9:25089039-25089040	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs552512122	chr9:25089099-25089100	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
17	rs373050926	chr9:25089105-25089106	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
18	rs147887264	chr9:25089141-25089142	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs148132702	chr9:25089773-25089774	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs74501193	chr9:25089802-25089803	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs576336558	chr9:25089825-25089826	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs531301578	chr9:25089841-25089842	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs549468180	chr9:25089854-25089855	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs569284854	chr9:25089859-25089860	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs78568398	chr9:25089860-25089861	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs78039935	chr9:25089861-25089862	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs373990885	chr9:25089862-25089863	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs538725656	chr9:25089872-25089873	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs558182742	chr9:25089913-25089914	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs564497501	chr9:25089918-25089919	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs534079164	chr9:25089922-25089923	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs553713934	chr9:25089923-25089924	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs150253450	chr9:25089986-25089987	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs3126947	chr9:25090015-25090016	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs137970069	chr9:25090065-25090066	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs78898367	chr9:25090091-25090092	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs566047422	chr9:25090098-25090099	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs375340867	chr9:25090104-25090105	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs570732435	chr9:25090123-25090124	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs544651283	chr9:25090131-25090132	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs564526835	chr9:25090136-25090137	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs10966726	chr9:25090139-25090140	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs535993571	chr9:25090528-25090529	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs555936377	chr9:25090536-25090537	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs575771781	chr9:25090571-25090572	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs74477671	chr9:25090587-25090588	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs564563684	chr9:25090590-25090591	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs78991164	chr9:25090601-25090602	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs540583735	chr9:25090603-25090604	Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs12553393	chr9:25090615-25090616	Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:142)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic myeloid leukemia	21384125	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Metanephric adenoma	20802469	CNVD
Developmental delay	21147756	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	22183965	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Non-small cell lung cancer	19010865	CNVD
Myoepithelioma	18604193	CNVD
Cancer	22183965	CNVD
Myelofibrosis	22110671	CNVD
Ewing''s sarcoma	22429812	CNVD
Neuroblastoma	21899760	CNVD
Glioblastoma multiforme	19435819	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Glioblastoma multiforme	22291905	CNVD
Lung cancer	21911935	CNVD
Primary central nervous system lymphoma	21088137	CNVD
head and neck squamous cell carcinoma	21798897	CNVD
Cancer	21253487	CNVD
Glioblastoma multiforme	22286061	CNVD
Intracranial ependymoma	16609018	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Glioblastoma multiforme	21922591	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Urothelial cell carcinoma	18451213	CNVD
Glioma	17123091	CNVD
Mental retardation	17124404	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Leukemia	19602459	CNVD
Acute monocytic leukemia	16498392	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Leukemia	18688285	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Acute myeloid leukemia	19651601	CNVD
Coronary Disease	20032323	CNVD
Squamous cell cancer	20885788	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	21732550	CNVD
Gastric cancer	22539939	CNVD
Cancer	21183584	CNVD
T-cell lymphomas	19863542	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Metastatic melanoma	18483359	CNVD
Non-small cell lung cancer	20864512	CNVD
Cervical cancer	21062161	CNVD
Acute myeloid leukemia	16864856	CNVD
Glioblastoma	17090523	CNVD
Lung cancer	16773561	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Colorectal cancer	16774939	CNVD
Bladder cancer	19088036	CNVD
Colorectal cancer	16272173	CNVD
Melanoma	16977458	CNVD
Glioblastoma multiforme	17369134	CNVD
Chagasic megaesophagus	20163722	CNVD
Melanoma	19566914	CNVD
Squamous cell cancer	19047905	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung cancer	19525976	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Melanoma	17363583	CNVD
Adenoid cystic carcinoma	18332873	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Acute myeloid leukemia	21251322	CNVD
Oral cancer	21386901	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21364760	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Lung cancer	21569311	CNVD
Pancreatic cancer	21811587	CNVD

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:25090600-25091000	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr9:25090600-25091000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr9:25091000-25091400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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