Variant report

Variant	nsv6556
Chromosome Location	chr9:73304158-73363098
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	chr9:73361709-73361869	IMR90	lung:	n/a	chr9:73361819-73361832 chr9:73361819-73361830 chr9:73361821-73361832 chr9:73361821-73361830
2	CEBPB	chr9:73357619-73357834	HepG2	liver:	n/a	chr9:73357693-73357704
3	CEBPB	chr9:73357563-73357733	IMR90	lung:	n/a	chr9:73357693-73357704
4	CEBPB	chr9:73361705-73361987	MCF-7	breast:	n/a	chr9:73361819-73361832 chr9:73361819-73361830 chr9:73361821-73361832 chr9:73361821-73361830
5	CEBPB	chr9:73361662-73361969	HepG2	liver:	n/a	chr9:73361819-73361832 chr9:73361819-73361830 chr9:73361821-73361832 chr9:73361821-73361830
6	CEBPB	chr9:73357607-73357810	A549	lung:	n/a	chr9:73357693-73357704
7	CEBPB	chr9:73361667-73361979	Hela-S3	cervix:	n/a	chr9:73361819-73361832 chr9:73361819-73361830 chr9:73361821-73361832 chr9:73361821-73361830
8	CTCF	chr9:73345828-73345899	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
9	CTCF	chr9:73354392-73354442	Spleen_OC	spleen:	n/a	n/a
10	CTCF	chr9:73320426-73320489	GM10248	blood:	n/a	n/a
11	CTCF	chr9:73320209-73320318	LNCaP	prostate:	n/a	n/a
12	CTCF	chr9:73345832-73345884	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
13	CTCF	chr9:73345821-73345929	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
14	CTCF	chr9:73337632-73337648	GM10248	blood:	n/a	n/a
15	CTCF	chr9:73343196-73343258	GM20000	blood:	n/a	n/a
16	CTCF	chr9:73327804-73327871	HepG2	liver:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
17	CTCF	chr9:73313782-73313837	Spleen_OC	spleen:	n/a	n/a
18	CTCF	chr9:73348804-73348820	LNCaP	prostate:	n/a	n/a
19	CTCF	chr9:73349090-73349180	LNCaP	prostate:	n/a	n/a
20	CTCF	chr9:73311820-73311970	GM12868	blood:	n/a	n/a
21	CTCF	chr9:73345802-73345917	MCF-7	breast:	n/a	chr9:73345846-73345859 chr9:73345844-73345862
22	CTCF	chr9:73351044-73351099	Lung_OC	lung:	n/a	n/a
23	CTCF	chr9:73327817-73327936	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
24	CTCF	chr9:73327826-73327940	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
25	CTCF	chr9:73327847-73327912	MCF-7	breast:	n/a	chr9:73327853-73327866 chr9:73327851-73327869
26	CTCF	chr9:73310400-73310550	GM12869	blood:	n/a	n/a
27	CTCF	chr9:73327863-73327919	MCF-7	breast:	n/a	n/a
28	ELK1	chr9:73310712-73310747	Hela-S3	cervix:	n/a	n/a
29	FOS	chr9:73362324-73362459	MCF10A-Er-Src	breast:	n/a	n/a
30	FOXA1	chr9:73339620-73340027	HepG2	liver:	n/a	n/a
31	FOXA1	chr9:73321627-73322034	HepG2	liver:	n/a	n/a
32	FOXP2	chr9:73361700-73361944	SK-N-MC	brain:	n/a	n/a
33	GATA3	chr9:73314295-73314820	MCF-7	breast:	n/a	n/a
34	IRF3	chr9:73312254-73312270	GM12878	blood:	n/a	n/a
35	KAP1	chr9:73360570-73362908	U2OS	brain:	n/a	n/a
36	KAP1	chr9:73360846-73362894	HEK293	kidney:	n/a	n/a
37	MAFF	chr9:73359288-73359474	HepG2	liver:	n/a	n/a
38	MAFK	chr9:73359225-73359468	HepG2	liver:	n/a	n/a
39	MAFK	chr9:73359245-73359499	HepG2	liver:	n/a	n/a
40	MYC	chr9:73307020-73307034	MCF10A-Er-Src	breast:	n/a	n/a
41	MYC	chr9:73361724-73361916	MCF10A-Er-Src	breast:	n/a	n/a
42	MYC	chr9:73362227-73362474	MCF10A-Er-Src	breast:	n/a	n/a
43	NR2F2	chr9:73314340-73314813	MCF-7	breast:	n/a	n/a
44	POLR2A	chr9:73326055-73326197	GM12878	blood:	n/a	n/a
45	POLR2A	chr9:73348789-73348850	Gliobla	brain:	n/a	n/a
46	POLR2A	chr9:73315965-73316508	H1-neurons	neurons:	n/a	n/a
47	POLR2A	chr9:73315790-73315922	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr9:73359657-73359697	GM12878	blood:	n/a	n/a
49	POLR2A	chr9:73348727-73348755	Gliobla	brain:	n/a	n/a
50	POLR2A	chr9:73321725-73321807	GM12878	blood:	n/a	n/a

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

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

Extended variants
information (count: 908 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:908 , 50 per page) page: 1 2 3 4 5 6 7 ... 19

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs554339438	chr9:73304184-73304185	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs575872761	chr9:73304206-73304207	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs546149914	chr9:73304334-73304335	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs150326946	chr9:73304337-73304338	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs576881616	chr9:73304349-73304350	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs367981291	chr9:73304358-73304359	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs559419665	chr9:73304369-73304370	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs137974288	chr9:73304382-73304383	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs78762741	chr9:73304397-73304398	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs11394146	chr9:73304437-73304438	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs200810137	chr9:73304445-73304446	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs397942298	chr9:73304447-73304448	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs561579314	chr9:73304452-73304453	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs562967742	chr9:73304460-73304461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs181134608	chr9:73304504-73304505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs117243900	chr9:73304519-73304520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs565344227	chr9:73304598-73304599	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs149040306	chr9:73304635-73304636	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs10121703	chr9:73304681-73304682	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs571620130	chr9:73304689-73304690	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs184852874	chr9:73304704-73304705	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs536131817	chr9:73304709-73304710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs145763432	chr9:73304721-73304722	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs569617118	chr9:73304732-73304733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs138969287	chr9:73304760-73304761	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs115143663	chr9:73304768-73304769	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs142904734	chr9:73304778-73304779	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs534468336	chr9:73304795-73304796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs146998032	chr9:73304895-73304896	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs148040078	chr9:73304899-73304900	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs1410374	chr9:73304950-73304951	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs141717671	chr9:73304963-73304964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs150861161	chr9:73304964-73304965	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs551459106	chr9:73304988-73304989	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs571311437	chr9:73305118-73305119	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs114541673	chr9:73305150-73305151	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs377201690	chr9:73305187-73305188	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs12351403	chr9:73305198-73305199	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs372103946	chr9:73305202-73305203	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs139296554	chr9:73305347-73305348	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs181010898	chr9:73305359-73305360	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs569917921	chr9:73305366-73305367	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs560430791	chr9:73305434-73305435	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs142814634	chr9:73305435-73305436	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs552346426	chr9:73305453-73305454	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs11279694	chr9:73305459-73305460	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs570598467	chr9:73305465-73305466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs201210972	chr9:73305466-73305467	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs202002162	chr9:73305468-73305469	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs544757331	chr9:73305480-73305481	Weak transcription	n/a	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:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:73295800-73310400	Weak transcription	Pancreas	Pancrea
2	chr9:73302200-73306200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr9:73305600-73306000	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr9:73305800-73311800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:73306000-73306400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:73306400-73306600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr9:73306400-73306600	Enhancers	Pancreatic Islets	Pancreatic Islet
8	chr9:73306600-73311000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr9:73308600-73309000	Enhancers	Fetal Heart	heart
10	chr9:73308600-73309200	Enhancers	Adipose Nuclei	Adipose
11	chr9:73308600-73309800	Enhancers	Fetal Brain Male	brain
12	chr9:73308800-73309000	Enhancers	Fetal Kidney	kidney
13	chr9:73308800-73309200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:73309000-73317200	Weak transcription	Fetal Kidney	kidney
15	chr9:73309800-73310200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr9:73309800-73316400	Weak transcription	Fetal Brain Male	brain
17	chr9:73310200-73310600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:73310400-73310600	Enhancers	Pancreas	Pancrea
19	chr9:73310600-73312000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr9:73310600-73312800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:73310800-73312600	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr9:73311000-73312800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr9:73311200-73312600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:73311200-73312800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr9:73311400-73312800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr9:73311800-73312200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr9:73311800-73312600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr9:73311800-73312800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:73312000-73312400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr9:73312000-73312600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr9:73312400-73312600	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr9:73312600-73315600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr9:73314600-73316600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr9:73315400-73316800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:73315600-73316400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:73315600-73316800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr9:73315800-73316600	Enhancers	Fetal Heart	heart
38	chr9:73316200-73316600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr9:73316400-73316600	Enhancers	Fetal Brain Male	brain
40	chr9:73316600-73316800	Weak transcription	Fetal Brain Male	brain
41	chr9:73352800-73367600	Weak transcription	Fetal Kidney	kidney
42	chr9:73355400-73356000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
43	chr9:73355600-73357400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr9:73356000-73364800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:73356600-73368800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr9:73356800-73376000	Weak transcription	Pancreatic Islets	Pancreatic Islet
47	chr9:73357400-73358600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:73357800-73362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:73358600-73365400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:73361000-73362800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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