Variant report

Variant	nsv893647
Chromosome Location	chr9:105046926-105124832
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	chr9:105116776-105117104	HepG2	liver:	n/a	chr9:105117017-105117030 chr9:105117019-105117028 chr9:105117019-105117028 chr9:105117019-105117028 chr9:105117019-105117028 chr9:105117019-105117030 chr9:105116943-105116954
2	CEBPB	chr9:105053338-105053531	A549	lung:	n/a	chr9:105053392-105053403
3	CEBPB	chr9:105123166-105123481	HepG2	liver:	n/a	chr9:105123302-105123313
4	CEBPB	chr9:105053288-105053488	HepG2	liver:	n/a	chr9:105053392-105053403
5	CEBPB	chr9:105116836-105117075	A549	lung:	n/a	chr9:105117017-105117030 chr9:105117019-105117028 chr9:105117019-105117028 chr9:105117019-105117028 chr9:105117019-105117028 chr9:105117019-105117030 chr9:105116943-105116954
6	CTCF	chr9:105090926-105090959	Lung_OC	lung:	n/a	n/a
7	CTCF	chr9:105071620-105071770	WERI-Rb-1	eye:	n/a	n/a
8	CTCF	chr9:105065960-105066110	GM12869	blood:	n/a	n/a
9	CTCF	chr9:105068383-105068442	GM20000	blood:	n/a	n/a
10	CTCF	chr9:105074979-105075026	ProgFib	skin:	n/a	n/a
11	CTCF	chr9:105118166-105118279	GM10266	blood:	n/a	n/a
12	CTCF	chr9:105071620-105071770	HEK293	kidney:	n/a	n/a
13	CTCF	chr9:105118420-105118570	GM12875	blood:	n/a	n/a
14	E2F4	chr9:105120475-105120705	MCF10A-Er-Src	breast:	n/a	n/a
15	E2F4	chr9:105056777-105056954	MCF10A-Er-Src	breast:	n/a	n/a
16	E2F4	chr9:105047302-105047493	MCF10A-Er-Src	breast:	n/a	n/a
17	EP300	chr9:105093487-105093883	MCF-7	breast:	n/a	n/a
18	EP300	chr9:105118272-105118630	T-47D	breast:	n/a	n/a
19	ESR1	chr9:105115237-105115532	ECC-1	luminal epithelium:	n/a	n/a
20	ESR1	chr9:105115297-105115524	T-47D	breast:	n/a	n/a
21	ESR1	chr9:105115194-105115511	ECC-1	luminal epithelium:	n/a	n/a
22	FOS	chr9:105116370-105116669	MCF10A-Er-Src	breast:	n/a	chr9:105116508-105116518 chr9:105116505-105116516 chr9:105116507-105116519 chr9:105116508-105116518
23	FOS	chr9:105116355-105116670	MCF10A-Er-Src	breast:	n/a	chr9:105116508-105116518 chr9:105116505-105116516 chr9:105116507-105116519 chr9:105116508-105116518
24	FOS	chr9:105116361-105116612	MCF10A-Er-Src	breast:	n/a	chr9:105116508-105116518 chr9:105116505-105116516 chr9:105116507-105116519 chr9:105116508-105116518
25	FOS	chr9:105116355-105116665	MCF10A-Er-Src	breast:	n/a	chr9:105116508-105116518 chr9:105116505-105116516 chr9:105116507-105116519 chr9:105116508-105116518
26	FOXA1	chr9:105118345-105118553	T-47D	breast:	n/a	n/a
27	FOXA1	chr9:105099766-105100078	HepG2	liver:	n/a	n/a
28	FOXA2	chr9:105099771-105100305	A549	lung:	n/a	n/a
29	GATA2	chr9:105118268-105118640	SH-SY5Y	brain:	n/a	n/a
30	GATA3	chr9:105118211-105118729	T-47D	breast:	n/a	n/a
31	GATA3	chr9:105093476-105093919	MCF-7	breast:	n/a	n/a
32	GATA3	chr9:105118191-105118769	T-47D	breast:	n/a	n/a
33	JUN	chr9:105054402-105054602	K562	blood:	n/a	n/a
34	JUN	chr9:105116377-105116598	HepG2	liver:	n/a	chr9:105116508-105116518 chr9:105116505-105116516 chr9:105116483-105116496 chr9:105116507-105116519 chr9:105116508-105116518
35	JUND	chr9:105116342-105116667	HepG2	liver:	n/a	chr9:105116508-105116518 chr9:105116505-105116516 chr9:105116507-105116519 chr9:105116508-105116518
36	KAP1	chr9:105089680-105090160	K562	blood:	n/a	n/a
37	KAP1	chr9:105118263-105118714	HEK293	kidney:	n/a	n/a
38	MAFF	chr9:105070991-105071261	HepG2	liver:	n/a	chr9:105071117-105071135
39	MAFF	chr9:105123740-105124024	HepG2	liver:	n/a	n/a
40	MAFF	chr9:105098090-105098279	HepG2	liver:	n/a	chr9:105098189-105098207
41	MAFK	chr9:105063120-105063303	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAFK	chr9:105123770-105123975	IMR90	lung:	n/a	n/a
43	MAFK	chr9:105063870-105063877	HepG2	liver:	n/a	n/a
44	MAFK	chr9:105063775-105063983	HepG2	liver:	n/a	chr9:105063908-105063923
45	MAFK	chr9:105123701-105124077	HepG2	liver:	n/a	n/a
46	MAFK	chr9:105070968-105071273	HepG2	liver:	n/a	chr9:105071119-105071134
47	MAFK	chr9:105071020-105071270	HepG2	liver:	n/a	chr9:105071119-105071134
48	MAFK	chr9:105047678-105047750	HepG2	liver:	n/a	n/a
49	MAFK	chr9:105071008-105071300	IMR90	lung:	n/a	chr9:105071119-105071134
50	MAFK	chr9:105123660-105124069	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:106538363..106538863-chr9:105123307..105123875,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRIN3A-3	chr9:105066627-105066753	NONHSAT133756
2	lnc-GRIN3A-3	chr9:105078134-105078251	NONHSAT133764
3	lnc-GRIN3A-3	chr9:105078134-105078251	NONHSAT133756
4	lnc-GRIN3A-3	chr9:105066714-105066751	NONHSAT133764
5	lnc-GRIN3A-3	chr9:105122117-105122289	ucscGeneNc_uc004bbt_2
6	lnc-GRIN3A-3	chr9:105122117-105122289	NONHSAT133756
7	lnc-C9orf107-5	chr9:105055136-105055273	NONHSAT133761
8	lnc-GRIN3A-3	chr9:105079433-105079602	NONHSAT133756
9	lnc-GRIN3A-3	chr9:105117245-105117384	NONHSAT133756
10	lnc-GRIN3A-3	chr9:105079433-105079602	NONHSAT133764
11	lnc-GRIN3A-3	chr9:105066627-105066753	ucscGeneNc_uc004bbt_2
12	lnc-GRIN3A-3	chr9:105117245-105117384	NONHSAT133764
13	lnc-C9orf107-1	chr9:105053028-105053194	XLOC_007495
14	lnc-GRIN3A-3	chr9:105079433-105079602	ucscGeneNc_uc004bbt_2
15	lnc-GRIN3A-3	chr9:105078134-105078251	ucscGeneNc_uc004bbt_2
16	lnc-GRIN3A-3	chr9:105117245-105117384	ucscGeneNc_uc004bbt_2
17	lnc-C9orf107-1	chr9:105052402-105052947	XLOC_007495

Variant related genes	Relation type
ENSG00000222117	TF binding region

Extended variants
information (count: 265 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:265 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs371443067	chr9:105052413-105052414	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs188943570	chr9:105052476-105052477	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs41282165	chr9:105052554-105052555	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
4	rs41282167	chr9:105052574-105052575	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs541849613	chr9:105052622-105052623	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
6	rs150305607	chr9:105052627-105052628	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
7	rs575634946	chr9:105052634-105052635	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
8	rs41282169	chr9:105052647-105052648	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
9	rs137890671	chr9:105052679-105052680	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
10	rs532610007	chr9:105052713-105052714	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
11	rs552394243	chr9:105052749-105052750	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
12	rs559846716	chr9:105052756-105052757	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
13	rs543380913	chr9:105052823-105052824	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
14	rs528467418	chr9:105052854-105052855	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
15	rs548600962	chr9:105052903-105052904	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
16	rs2209061	chr9:105052923-105052924	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs41282171	chr9:105052929-105052930	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs191835774	chr9:105053029-105053030	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
19	rs13284366	chr9:105053031-105053032	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
20	rs35391678	chr9:105053074-105053075	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
21	rs41282173	chr9:105053149-105053150	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs555362971	chr9:105053180-105053181	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
23	rs575575322	chr9:105053184-105053185	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
24	rs139127191	chr9:105053193-105053194	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
25	rs557939057	chr9:105053278-105053279	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs577910671	chr9:105053292-105053293	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs540462962	chr9:105053293-105053294	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs559577691	chr9:105053301-105053302	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs528616797	chr9:105053303-105053304	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs117984550	chr9:105053307-105053308	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs561763924	chr9:105053316-105053317	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs184293819	chr9:105053322-105053323	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs549199347	chr9:105053342-105053343	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs575562687	chr9:105053402-105053403	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs531071792	chr9:105053405-105053406	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs144679667	chr9:105053477-105053478	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs537888385	chr9:105053740-105053741	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs7018663	chr9:105053752-105053753	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs559074413	chr9:105053764-105053765	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs532981743	chr9:105053772-105053773	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs578025621	chr9:105053851-105053852	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs13285460	chr9:105053927-105053928	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs551421397	chr9:105053931-105053932	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs377366126	chr9:105054343-105054344	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs528933538	chr9:105054407-105054408	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs549097183	chr9:105054419-105054420	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs73502701	chr9:105054450-105054451	Inactive region	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs537825501	chr9:105054486-105054487	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs372447952	chr9:105054548-105054549	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs578152815	chr9:105055218-105055219	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:66)

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
Acute lymphoblastic leukemia	18458336	CNVD
Mantle cell lymphoma	19029149	CNVD
Intracranial aneurysm	16715129	CNVD
Neuroblastoma	20406844	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:105070400-105070600	Enhancers	H1 Cell Line	embryonic stem cell
2	chr9:105071000-105072600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr9:105115000-105115400	Enhancers	Pancreatic Islets	Pancreatic Islet
4	chr9:105122800-105124000	Enhancers	Liver	Liver
5	chr9:105124000-105124800	Weak transcription	Liver	Liver
6	chr9:105124800-105125400	Enhancers	Liver	Liver

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