Variant report

Variant	esv999856
Chromosome Location	chr9:73313422-73355386
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	chr9:73320209-73320318	LNCaP	prostate:	n/a	n/a
2	CTCF	chr9:73351044-73351099	Lung_OC	lung:	n/a	n/a
3	CTCF	chr9:73348804-73348820	LNCaP	prostate:	n/a	n/a
4	CTCF	chr9:73327826-73327940	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
5	CTCF	chr9:73343196-73343258	GM20000	blood:	n/a	n/a
6	CTCF	chr9:73349090-73349180	LNCaP	prostate:	n/a	n/a
7	CTCF	chr9:73337632-73337648	GM10248	blood:	n/a	n/a
8	CTCF	chr9:73313782-73313837	Spleen_OC	spleen:	n/a	n/a
9	CTCF	chr9:73327847-73327912	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
10	CTCF	chr9:73327817-73327936	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
11	CTCF	chr9:73320426-73320489	GM10248	blood:	n/a	n/a
12	CTCF	chr9:73345802-73345917	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
13	CTCF	chr9:73345828-73345899	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
14	CTCF	chr9:73345832-73345884	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
15	CTCF	chr9:73327804-73327871	HepG2	liver:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
16	CTCF	chr9:73345821-73345929	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
17	CTCF	chr9:73327863-73327919	MCF-7	breast:	n/a	n/a
18	CTCF	chr9:73354392-73354442	Spleen_OC	spleen:	n/a	n/a
19	FOXA1	chr9:73321627-73322034	HepG2	liver:	n/a	n/a
20	FOXA1	chr9:73339620-73340027	HepG2	liver:	n/a	n/a
21	GATA3	chr9:73314295-73314820	MCF-7	breast:	n/a	n/a
22	NR2F2	chr9:73314340-73314813	MCF-7	breast:	n/a	n/a
23	POLR2A	chr9:73348727-73348755	Gliobla	brain:	n/a	n/a
24	POLR2A	chr9:73315965-73316508	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr9:73348789-73348850	Gliobla	brain:	n/a	n/a
26	POLR2A	chr9:73315790-73315922	MCF10A-Er-Src	breast:	n/a	n/a
27	POLR2A	chr9:73316018-73316418	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr9:73344048-73344183	GM12878	blood:	n/a	n/a
29	POLR2A	chr9:73326055-73326197	GM12878	blood:	n/a	n/a
30	POLR2A	chr9:73321725-73321807	GM12878	blood:	n/a	n/a
31	SP1	chr9:73321652-73321958	HepG2	liver:	n/a	n/a
32	SP1	chr9:73339645-73339951	HepG2	liver:	n/a	n/a
33	SPI1	chr9:73317035-73317217	GM12878	blood:	n/a	chr9:73317133-73317146 chr9:73317134-73317147 chr9:73317135-73317144
34	SPI1	chr9:73335028-73335210	GM12878	blood:	n/a	chr9:73335127-73335140 chr9:73335128-73335137 chr9:73335126-73335139
35	TEAD4	chr9:73327608-73327837	H1-hESC	embryonic stem cell:	n/a	n/a

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

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

Extended variants
information (count: 249 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:249 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs550924588	chr9:73313462-73313463	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs567935817	chr9:73313480-73313481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs369934829	chr9:73313488-73313489	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs6560148	chr9:73313490-73313491	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs185798418	chr9:73313524-73313525	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs566830429	chr9:73313529-73313530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs533943357	chr9:73313546-73313547	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs10124821	chr9:73313550-73313551	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs566136823	chr9:73313576-73313577	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs573886264	chr9:73313577-73313578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs538023667	chr9:73313584-73313585	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs555987502	chr9:73313593-73313594	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs577310088	chr9:73313607-73313608	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs571600993	chr9:73313614-73313615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs559820876	chr9:73313634-73313635	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs570954495	chr9:73313647-73313648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs34929700	chr9:73313649-73313650	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs150685992	chr9:73313659-73313660	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs562393337	chr9:73313715-73313716	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs10115414	chr9:73313719-73313720	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs551152976	chr9:73313868-73313869	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs144807178	chr9:73313922-73313923	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs147386631	chr9:73313929-73313930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs113016177	chr9:73313942-73313943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs1160741	chr9:73313963-73313964	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs566993334	chr9:73313995-73313996	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs1160742	chr9:73314011-73314012	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs189774309	chr9:73314027-73314028	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs373566393	chr9:73314065-73314066	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs555965650	chr9:73314135-73314136	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs549136976	chr9:73314161-73314162	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs567548526	chr9:73314207-73314208	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs115711936	chr9:73314214-73314215	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs575924332	chr9:73314231-73314232	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs182450496	chr9:73314293-73314294	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs577368323	chr9:73314303-73314304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs544823453	chr9:73314315-73314316	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs139557523	chr9:73314342-73314343	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs553415289	chr9:73314344-73314345	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs186429201	chr9:73314403-73314404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs542588904	chr9:73314405-73314406	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs34892479	chr9:73314431-73314432	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs17055711	chr9:73314438-73314439	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs191792499	chr9:73314459-73314460	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs74609634	chr9:73314463-73314464	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs563179328	chr9:73314480-73314481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs377005714	chr9:73314482-73314483	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs533538906	chr9:73314504-73314505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs145080384	chr9:73314560-73314561	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs10116217	chr9:73314609-73314610	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	mRNA abundance

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:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73309000-73317200	Weak transcription	Fetal Kidney	kidney
2	chr9:73309800-73316400	Weak transcription	Fetal Brain Male	brain
3	chr9:73312600-73315600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:73314600-73316600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:73315400-73316800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:73315600-73316400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:73315600-73316800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr9:73315800-73316600	Enhancers	Fetal Heart	heart
9	chr9:73316200-73316600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:73316400-73316600	Enhancers	Fetal Brain Male	brain
11	chr9:73316600-73316800	Weak transcription	Fetal Brain Male	brain
12	chr9:73352800-73367600	Weak transcription	Fetal Kidney	kidney

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