Variant report

Variant	nsv499504
Chromosome Location	chr9:73316717-73352708
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	chr9:73345821-73345929	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
2	CTCF	chr9:73320209-73320318	LNCaP	prostate:	n/a	n/a
3	CTCF	chr9:73327826-73327940	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
4	CTCF	chr9:73351044-73351099	Lung_OC	lung:	n/a	n/a
5	CTCF	chr9:73327847-73327912	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
6	CTCF	chr9:73337632-73337648	GM10248	blood:	n/a	n/a
7	CTCF	chr9:73327863-73327919	MCF-7	breast:	n/a	n/a
8	CTCF	chr9:73348804-73348820	LNCaP	prostate:	n/a	n/a
9	CTCF	chr9:73345832-73345884	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
10	CTCF	chr9:73327817-73327936	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
11	CTCF	chr9:73343196-73343258	GM20000	blood:	n/a	n/a
12	CTCF	chr9:73345802-73345917	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
13	CTCF	chr9:73327804-73327871	HepG2	liver:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
14	CTCF	chr9:73345828-73345899	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
15	CTCF	chr9:73349090-73349180	LNCaP	prostate:	n/a	n/a
16	CTCF	chr9:73320426-73320489	GM10248	blood:	n/a	n/a
17	FOXA1	chr9:73339620-73340027	HepG2	liver:	n/a	n/a
18	FOXA1	chr9:73321627-73322034	HepG2	liver:	n/a	n/a
19	POLR2A	chr9:73321725-73321807	GM12878	blood:	n/a	n/a
20	POLR2A	chr9:73348727-73348755	Gliobla	brain:	n/a	n/a
21	POLR2A	chr9:73326055-73326197	GM12878	blood:	n/a	n/a
22	POLR2A	chr9:73344048-73344183	GM12878	blood:	n/a	n/a
23	POLR2A	chr9:73348789-73348850	Gliobla	brain:	n/a	n/a
24	SP1	chr9:73339645-73339951	HepG2	liver:	n/a	n/a
25	SP1	chr9:73321652-73321958	HepG2	liver:	n/a	n/a
26	SPI1	chr9:73335028-73335210	GM12878	blood:	n/a	chr9:73335127-73335140 chr9:73335128-73335137 chr9:73335126-73335139
27	SPI1	chr9:73317035-73317217	GM12878	blood:	n/a	chr9:73317133-73317146 chr9:73317134-73317147 chr9:73317135-73317144
28	TEAD4	chr9:73327608-73327837	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SMC5-2	chr9:73345622-73345772	ENSG00000223966.1
2	lnc-SMC5-1	chr9:73322963-73323148	ENSG00000232086.1
3	lnc-SMC5-2	chr9:73340956-73341141	ENSG00000223966.1
4	lnc-SMC5-1	chr9:73327629-73327779	ENSG00000232086.1

Variant related genes	Relation type
ENSG00000223966	TF binding region
ENSG00000232086	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs138162619	chr9:73316750-73316751	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs35201133	chr9:73316796-73316797	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs541451453	chr9:73316814-73316815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs530032045	chr9:73316849-73316850	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs372387293	chr9:73316866-73316867	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs563432063	chr9:73316888-73316889	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs530727919	chr9:73316898-73316899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs552272805	chr9:73316948-73316949	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs377149755	chr9:73317000-73317001	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs137940400	chr9:73317048-73317049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs62543355	chr9:73320486-73320487	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs62543765	chr9:73327766-73327767	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Melanoma	22183965	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute myeloid leukemia	20729466	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Oral cancer	21386901	CNVD
Epilepsy	22083797	CNVD
Glioblastoma multiforme	21750150	CNVD
Cancer	21183584	CNVD
Bipolar disorder	18458673	CNVD
Malignant melanoma	17260012	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73309000-73317200	Weak transcription	Fetal Kidney	kidney
2	chr9:73315400-73316800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:73315600-73316800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:73316600-73316800	Weak transcription	Fetal Brain Male	brain

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