Variant report

Variant	nsv1040886
Chromosome Location	chr9:105246682-105296385
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	ATF2	chr9:105261656-105262092	GM12878	blood:	n/a	n/a
2	BCL3	chr9:105269329-105269562	GM12878	blood:	n/a	n/a
3	CEBPB	chr9:105262491-105262578	HepG2	liver:	n/a	chr9:105262492-105262505 chr9:105262565-105262576
4	CEBPB	chr9:105262431-105262639	A549	lung:	n/a	chr9:105262492-105262505 chr9:105262565-105262576
5	CEBPB	chr9:105261239-105261567	HepG2	liver:	n/a	chr9:105261388-105261399
6	CEBPB	chr9:105279460-105279660	HepG2	liver:	n/a	chr9:105279595-105279606
7	CEBPB	chr9:105276520-105276565	H1-hESC	embryonic stem cell:	n/a	n/a
8	CEBPB	chr9:105262536-105262576	K562	blood:	n/a	chr9:105262565-105262576
9	CEBPB	chr9:105276356-105276810	HepG2	liver:	n/a	chr9:105276688-105276699
10	CTCF	chr9:105260600-105260750	GM12865	blood:	n/a	n/a
11	CTCF	chr9:105286240-105286390	HA-sp	spinal cord:	n/a	n/a
12	CTCF	chr9:105285054-105285112	GM13976	blood:	n/a	n/a
13	CTCF	chr9:105262615-105262763	Kidney_OC	kidney:	n/a	n/a
14	CTCF	chr9:105262618-105262763	GM10248	blood:	n/a	n/a
15	E2F4	chr9:105271317-105271526	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F4	chr9:105274368-105274670	MCF10A-Er-Src	breast:	n/a	n/a
17	EBF1	chr9:105258789-105258983	GM12878	blood:	n/a	chr9:105258894-105258907 chr9:105258896-105258905 chr9:105258895-105258905
18	EBF1	chr9:105258745-105258988	GM12878	blood:	n/a	chr9:105258894-105258907 chr9:105258896-105258905 chr9:105258895-105258905
19	EP300	chr9:105274331-105274530	K562	blood:	n/a	n/a
20	EP300	chr9:105269527-105269796	GM12878	blood:	n/a	n/a
21	FOS	chr9:105283481-105283628	MCF10A-Er-Src	breast:	n/a	chr9:105283552-105283560 chr9:105283553-105283560
22	FOS	chr9:105293944-105294271	MCF10A-Er-Src	breast:	n/a	n/a
23	FOS	chr9:105293932-105294248	MCF10A-Er-Src	breast:	n/a	n/a
24	FOS	chr9:105293979-105294265	MCF10A-Er-Src	breast:	n/a	n/a
25	FOS	chr9:105252715-105252971	MCF10A-Er-Src	breast:	n/a	n/a
26	FOS	chr9:105293978-105294251	MCF10A-Er-Src	breast:	n/a	n/a
27	FOS	chr9:105261429-105261433	MCF10A-Er-Src	breast:	n/a	n/a
28	FOS	chr9:105283523-105283587	MCF10A-Er-Src	breast:	n/a	chr9:105283552-105283560 chr9:105283553-105283560
29	FOXM1	chr9:105261633-105262116	GM12878	blood:	n/a	n/a
30	HDAC2	chr9:105289067-105289340	H1-hESC	embryonic stem cell:	n/a	n/a
31	JUN	chr9:105293970-105294245	HepG2	liver:	n/a	n/a
32	JUND	chr9:105293934-105294246	HepG2	liver:	n/a	chr9:105294088-105294099
33	JUND	chr9:105267342-105267605	HepG2	liver:	n/a	n/a
34	MAFF	chr9:105259629-105259945	HepG2	liver:	n/a	chr9:105259793-105259811
35	MAFF	chr9:105275019-105275210	HepG2	liver:	n/a	n/a
36	MAFK	chr9:105268099-105268373	HepG2	liver:	n/a	chr9:105268219-105268230 chr9:105268219-105268230
37	MAFK	chr9:105275044-105275247	HepG2	liver:	n/a	n/a
38	MAFK	chr9:105274976-105275255	HepG2	liver:	n/a	n/a
39	MAFK	chr9:105259658-105259931	HepG2	liver:	n/a	chr9:105259794-105259808 chr9:105259795-105259806 chr9:105259796-105259807 chr9:105259795-105259811 chr9:105259795-105259806
40	MAFK	chr9:105272506-105272693	HepG2	liver:	n/a	n/a
41	MAFK	chr9:105259662-105259887	IMR90	lung:	n/a	chr9:105259794-105259808 chr9:105259795-105259806 chr9:105259796-105259807 chr9:105259795-105259811 chr9:105259795-105259806
42	MAFK	chr9:105261908-105261916	HepG2	liver:	n/a	n/a
43	MEF2A	chr9:105269324-105269757	GM12878	blood:	n/a	n/a
44	MTA3	chr9:105261759-105262142	GM12878	blood:	n/a	n/a
45	NFIC	chr9:105261456-105262136	GM12878	blood:	n/a	n/a
46	NFIC	chr9:105269243-105269858	GM12878	blood:	n/a	n/a
47	NFYB	chr9:105248704-105249004	K562	blood:	n/a	n/a
48	PML	chr9:105261616-105262169	GM12878	blood:	n/a	chr9:105261996-105262004
49	POLR2A	chr9:105296329-105296337	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr9:105273610-105273758	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:105274189..105276621-chr9:105279783..105281855,2	K562	blood:
2	chr9:105240394..105242498-chr9:105264587..105266535,2	MCF-7	breast:
3	chr9:105274189..105276621-chr9:105279783..105281855,2	K562	blood:
4	chr9:105240078..105241695-chr9:105245746..105248744,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf107-3	chr9:105281918-105281990	ENSG00000204250.3
2	lnc-C9orf107-3	chr9:105281919-105281990	NR_103830
3	lnc-C9orf107-4	chr9:105277486-105280590	NONHSAT133766

Variant related genes	Relation type
ENSG00000235901	TF binding region
LINC00587	TF binding region

Extended variants
information (count: 502 )
Associated
traits (count: 64 )

Variant overlapped rSNPs/rCNVs (count:502 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2068258	chr9:105246682-105246683	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs570138998	chr9:105246713-105246714	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs73659411	chr9:105246776-105246777	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs182815489	chr9:105246807-105246808	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs566109332	chr9:105246902-105246903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs58320076	chr9:105246914-105246915	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs185150351	chr9:105246932-105246933	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs537301103	chr9:105246975-105246976	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs7862593	chr9:105247000-105247001	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs118187318	chr9:105247011-105247012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs537622527	chr9:105247016-105247017	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs10990131	chr9:105247097-105247098	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs576489507	chr9:105247111-105247112	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs545496595	chr9:105247119-105247120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs375983063	chr9:105247288-105247289	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs552546377	chr9:105247291-105247292	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs112675019	chr9:105247292-105247293	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs73510672	chr9:105247312-105247313	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs376756706	chr9:105247360-105247361	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs138815682	chr9:105247399-105247400	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs191029484	chr9:105247446-105247447	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs76567623	chr9:105247451-105247452	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs376818160	chr9:105247461-105247462	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs143776694	chr9:105247508-105247509	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs556501337	chr9:105247526-105247527	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs574898998	chr9:105247532-105247533	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs552742187	chr9:105247607-105247608	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs565917304	chr9:105247625-105247626	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs183718622	chr9:105247641-105247642	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs548313181	chr9:105247747-105247748	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs73510673	chr9:105247763-105247764	Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs537356525	chr9:105247784-105247785	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs557085190	chr9:105247816-105247817	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs570757055	chr9:105247834-105247835	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs528448803	chr9:105247863-105247864	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs113208274	chr9:105247867-105247868	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs561667258	chr9:105247901-105247902	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs2162065	chr9:105247907-105247908	Weak transcription Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs542330967	chr9:105247946-105247947	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs572729010	chr9:105247950-105247951	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs189108331	chr9:105247952-105247953	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs555086486	chr9:105247954-105247955	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs575457228	chr9:105247958-105247959	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs150467909	chr9:105247962-105247963	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs545228113	chr9:105248013-105248014	Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs564261784	chr9:105248019-105248020	Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs533194259	chr9:105248057-105248058	Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs386736944	chr9:105248075-105248076	Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs546294961	chr9:105248150-105248151	Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs559769140	chr9:105248152-105248153	Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:64)

Disease	PMID	Source
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
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
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
small cell lung cancer	20016488	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Fukuyama congenital muscular dystrophy	21572526	CNVD
Testicular germ cell tumor	18059402	CNVD
Mantle cell lymphoma	19029149	CNVD
Intracranial aneurysm	16715129	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:105245600-105246800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:105246400-105247800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:105246800-105247200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr9:105247200-105247400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:105247200-105247400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:105247400-105247600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:105247400-105248000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr9:105247600-105249000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:105247800-105248800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:105260200-105260600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr9:105268800-105269800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:105269000-105269400	Enhancers	Fetal Heart	heart
13	chr9:105269000-105269800	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr9:105269400-105269800	Enhancers	Fetal Kidney	kidney
15	chr9:105269400-105269800	Active TSS	GM12878-XiMat	blood
16	chr9:105276200-105276800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr9:105276400-105276800	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr9:105276600-105277000	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr9:105276800-105277200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr9:105276800-105277400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr9:105277000-105277400	Enhancers	Fetal Brain Male	brain
22	chr9:105277200-105277400	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr9:105277400-105277800	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr9:105280200-105281000	Enhancers	Liver	Liver
25	chr9:105280600-105280800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr9:105280800-105281000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr9:105281000-105283400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr9:105281800-105282000	ZNF genes & repeats	Left Ventricle	heart
29	chr9:105283400-105283600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:105283400-105283600	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr9:105283600-105284000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:105283600-105284000	Enhancers	Muscle Satellite Cultured Cells	--
33	chr9:105283600-105284000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr9:105284000-105284200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr9:105295800-105296200	Enhancers	Pancreatic Islets	Pancreatic Islet

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