Variant report

Variant	nsv540041
Chromosome Location	chr9:11904248-12196202
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	BACH1	chr9:12170667-12170713	H1-hESC	embryonic stem cell:	n/a	n/a
2	BRCA1	chr9:12011400-12011402	GM12878	blood:	n/a	n/a
3	CBX3	chr9:12054451-12054644	K562	blood:	n/a	n/a
4	CEBPB	chr9:11959593-11959818	IMR90	lung:	n/a	chr9:11959657-11959668
5	CEBPB	chr9:12129071-12129335	HepG2	liver:	n/a	n/a
6	CEBPB	chr9:11959508-11959839	HepG2	liver:	n/a	chr9:11959657-11959668
7	CEBPB	chr9:12180768-12180970	IMR90	lung:	n/a	n/a
8	CEBPB	chr9:11933909-11934318	Hela-S3	cervix:	n/a	chr9:11934105-11934116 chr9:11934106-11934117 chr9:11934105-11934118
9	CEBPB	chr9:12193945-12194181	A549	lung:	n/a	chr9:12194071-12194082 chr9:12194071-12194084
10	CEBPB	chr9:11946375-11946610	HepG2	liver:	n/a	chr9:11946481-11946492
11	CEBPB	chr9:12012267-12012412	A549	lung:	n/a	n/a
12	CEBPB	chr9:11946400-11946627	IMR90	lung:	n/a	chr9:11946481-11946492
13	CEBPB	chr9:12119993-12120079	A549	lung:	n/a	chr9:12120059-12120068 chr9:12120057-12120070 chr9:12120057-12120068
14	CEBPB	chr9:12195471-12195788	IMR90	lung:	n/a	chr9:12195611-12195622
15	CEBPB	chr9:12195456-12195797	HepG2	liver:	n/a	chr9:12195611-12195622
16	CEBPB	chr9:11968320-11968531	HepG2	liver:	n/a	chr9:11968445-11968456 chr9:11968447-11968456 chr9:11968446-11968457 chr9:11968445-11968458
17	CEBPB	chr9:11934067-11934195	HepG2	liver:	n/a	chr9:11934105-11934116 chr9:11934106-11934117 chr9:11934105-11934118
18	CEBPB	chr9:11968269-11968582	A549	lung:	n/a	chr9:11968445-11968456 chr9:11968447-11968456 chr9:11968446-11968457 chr9:11968445-11968458
19	CEBPB	chr9:12195470-12195708	H1-hESC	embryonic stem cell:	n/a	chr9:12195611-12195622
20	CEBPB	chr9:11933929-11934303	IMR90	lung:	n/a	chr9:11934105-11934116 chr9:11934106-11934117 chr9:11934105-11934118
21	CEBPB	chr9:11959566-11959766	K562	blood:	n/a	chr9:11959657-11959668
22	CEBPB	chr9:11933995-11934266	ECC-1	luminal epithelium:	n/a	chr9:11934105-11934116 chr9:11934106-11934117 chr9:11934105-11934118
23	CEBPB	chr9:12195488-12195695	K562	blood:	n/a	chr9:12195611-12195622
24	CTCF	chr9:12101680-12101830	GM12869	blood:	n/a	n/a
25	CTCF	chr9:12180880-12181030	GM12878	blood:	n/a	n/a
26	CTCF	chr9:11944302-11944336	GM13977	blood:	n/a	n/a
27	CTCF	chr9:12041004-12041085	GM20000	blood:	n/a	n/a
28	CTCF	chr9:11952660-11952810	AG09319	gingival:	n/a	n/a
29	CTCF	chr9:12045540-12045690	HPF	lung:	n/a	n/a
30	CTCF	chr9:12195560-12195710	AoAF	blood vessel:	n/a	n/a
31	CTCF	chr9:12041600-12041634	GM20000	blood:	n/a	n/a
32	CTCF	chr9:12148949-12149036	Fibrobl	skin:	n/a	n/a
33	CTCF	chr9:11906644-11906673	GM13976	blood:	n/a	n/a
34	CTCF	chr9:12092280-12092430	WERI-Rb-1	eye:	n/a	n/a
35	CTCF	chr9:12195520-12195670	HMF	breast:	n/a	n/a
36	CTCF	chr9:12195560-12195710	HEK293	kidney:	n/a	n/a
37	CTCF	chr9:12092304-12092357	MCF-7	breast:	n/a	n/a
38	CTCF	chr9:12115897-12115954	GM10248	blood:	n/a	n/a
39	CTCF	chr9:12055107-12055140	GM13976	blood:	n/a	n/a
40	CTCF	chr9:12053853-12053871	GM20000	blood:	n/a	n/a
41	CTCF	chr9:12078782-12078864	LNCaP	prostate:	n/a	n/a
42	CTCF	chr9:12195560-12195710	HMF	breast:	n/a	n/a
43	CTCF	chr9:12195600-12195750	HCPEpiC	choroid plexus:	n/a	n/a
44	CTCF	chr9:12100160-12100310	NB4	blood:	n/a	n/a
45	CTCF	chr9:12142395-12142451	LNCaP	prostate:	n/a	n/a
46	CTCF	chr9:12092315-12092389	MCF-7	breast:	n/a	n/a
47	CTCF	chr9:11997160-11997310	HEK293	kidney:	n/a	n/a
48	CTCF	chr9:12180880-12181030	HEK293	kidney:	n/a	n/a
49	CTCF	chr9:12076206-12076321	GM10266	blood:	n/a	n/a
50	CTCF	chr9:12195600-12195750	NHEK	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:12182493..12185046-chr9:12186407..12189303,2	K562	blood:
2	chr18:21570976..21573123-chr9:12145530..12147030,2	MCF-7	breast:
3	chr9:12094328..12096426-chr9:12096756..12098736,2	K562	blood:
4	chr9:12094328..12096426-chr9:12096756..12098736,2	K562	blood:
5	chr9:12182493..12185046-chr9:12186407..12189303,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MPDZ-9	chr9:12136273-12136401	NONHSAT130219
2	lnc-MPDZ-2	chr9:12159117-12159147	XLOC_007648
3	lnc-MPDZ-2	chr9:12116821-12116865	XLOC_007648
4	lnc-MPDZ-9	chr9:12088660-12089015	NONHSAT130219
5	lnc-MPDZ-2	chr9:12116821-12116865	XLOC_007648
6	lnc-MPDZ-2	chr9:12098660-12099015	XLOC_007648
7	lnc-MPDZ-2	chr9:12098714-12099015	XLOC_007648
8	lnc-MPDZ-2	chr9:12146273-12146401	XLOC_007648
9	lnc-MPDZ-9	chr9:12106821-12106865	NONHSAT130219
10	lnc-MPDZ-2	chr9:12139007-12139044	XLOC_007648
11	lnc-MPDZ-9	chr9:12149117-12149147	NONHSAT130219

Variant related genes	Relation type
ENSG00000224935	TF binding region
ENSG00000168234	chromatin interactions

Extended variants
information (count: 3827 )
Associated
traits (count: 106 )

Variant overlapped rSNPs/rCNVs (count:3827 , 50 per page) page: 1 2 3 4 5 6 7 ... 77

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs397764706	chr9:11904249-11904250	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs544515662	chr9:11904255-11904256	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs554530949	chr9:11904256-11904257	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs376418721	chr9:11904261-11904262	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs192292258	chr9:11904299-11904300	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs540081262	chr9:11904319-11904320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs560384333	chr9:11904322-11904323	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs577024780	chr9:11904347-11904348	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs545870634	chr9:11904408-11904409	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs116763521	chr9:11904412-11904413	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs144304132	chr9:11904439-11904440	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs562274180	chr9:11904451-11904452	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs527985079	chr9:11904463-11904464	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs148748208	chr9:11904476-11904477	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs114799317	chr9:11904483-11904484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs537776548	chr9:11904512-11904513	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs371366573	chr9:11904562-11904563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs182407883	chr9:11904621-11904622	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs371857477	chr9:11904637-11904638	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs186742324	chr9:11904643-11904644	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs4741190	chr9:11904677-11904678	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs142012548	chr9:11904683-11904684	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs146302712	chr9:11904698-11904699	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs371466886	chr9:11904709-11904710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs577087445	chr9:11904740-11904741	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs376691247	chr9:11904770-11904771	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs545932078	chr9:11904786-11904787	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs537673797	chr9:11904831-11904832	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs555493875	chr9:11904837-11904838	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs66815991	chr9:11904845-11904846	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs576066079	chr9:11904869-11904870	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs536718519	chr9:11904874-11904875	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs200156112	chr9:11904876-11904877	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs73396673	chr9:11904896-11904897	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs540897442	chr9:11904899-11904900	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs561716129	chr9:11904925-11904926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs527985541	chr9:11904935-11904936	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs10809645	chr9:11904937-11904938	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs189721552	chr9:11904941-11904942	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs114125278	chr9:11904966-11904967	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs376115420	chr9:11904986-11904987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs538444226	chr9:11905017-11905018	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs182758283	chr9:11905032-11905033	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs112872774	chr9:11905058-11905059	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs73396675	chr9:11905109-11905110	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs10960357	chr9:11905164-11905165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs535939743	chr9:11905176-11905177	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs549147272	chr9:11905224-11905225	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs564420165	chr9:11905227-11905228	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs116530373	chr9:11905229-11905230	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:106)

Disease	PMID	Source
Disorders of sex development	21048976	CNVD
Honadal dysgenesis	21048976	CNVD
Medulloblastoma	21979893	CNVD
Lung cancer	16740712	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
abnormal development	18461090	CNVD
Glioblastoma multiforme	21080181	CNVD
Breast cancer	16608533	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Cervical cancer	21063398	CNVD
Retinoblastoma	22278416	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Melanoma	18172304	CNVD
Biliary cancer	19435499	CNVD
Gastric cancer	21586687	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myopathy	18421352	CNVD
Neuroblastoma	18664255	CNVD
Acute lymphoblastic leukemia	18957548	CNVD
Myeloproliferative neoplasm	17564968	CNVD
Malignant meningioma	17937814	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Oligodendroglial tumors	17285580	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Cancer	20164920	CNVD
Developmental delay	21147756	CNVD
small cell lung cancer	21764851	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioma	17123091	CNVD
Lung cancer	16773561	CNVD
Colorectal cancer	16272173	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Gastric cancer	16891809	CNVD
Mental retardation	17847001	CNVD
Cutaneous squamous cell carcinomas	17420988	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21611746	CNVD
Melanoma	22183965	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Type 2 diabetes	21526130	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Schizophrenia	20967226	CNVD
early-passage human iPS cells	21368824	CNVD
Williams Syndrome	20824207	CNVD
Schizophrenia	23813976	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:11901600-11911400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:11912400-11912600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:11914800-11915000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:11914800-11915600	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr9:11914800-11916600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr9:11914800-11916600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr9:11915000-11915600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr9:11915000-11916000	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr9:11915000-11916400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr9:11915000-11916400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:11915600-11915800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr9:11915600-11915800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr9:11915600-11915800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:11915600-11916000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:11915800-11916000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr9:11915800-11916000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr9:11916000-11916200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr9:11916000-11916200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr9:11916000-11916200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr9:11916200-11916400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr9:11916200-11916400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr9:11916200-11916400	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr9:11931000-11931400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:11931200-11932000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr9:11931400-11933400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:11932000-11933400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr9:11933400-11934600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:11933400-11934600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr9:11933600-11934800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:11933800-11934600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:11934000-11934400	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr9:11946400-11947400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr9:11947000-11947800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:11966600-11967200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:11966800-11967200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:11966800-11967200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr9:11966800-11967400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:11968800-11969000	Enhancers	Pancreas	Pancrea
39	chr9:11972800-11973200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr9:11975000-11975200	Enhancers	Pancreatic Islets	Pancreatic Islet
41	chr9:11975600-11976200	Enhancers	Fetal Brain Male	brain
42	chr9:11976000-11976200	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr9:11977400-11977600	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr9:11991400-11994000	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr9:11991800-11992200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:11991800-11992200	Enhancers	Fetal Heart	heart
47	chr9:11991800-11993400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:11992400-11993200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr9:11993000-11993800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr9:11995800-11996600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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