Variant report

Variant	nsv613579
Chromosome Location	chr9:12095022-12267967
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	BATF	chr9:12230772-12231081	GM12878	blood:	n/a	n/a
3	CEBPB	chr9:12195471-12195788	IMR90	lung:	n/a	chr9:12195611-12195622
4	CEBPB	chr9:12195470-12195708	H1-hESC	embryonic stem cell:	n/a	chr9:12195611-12195622
5	CEBPB	chr9:12180768-12180970	IMR90	lung:	n/a	n/a
6	CEBPB	chr9:12119993-12120079	A549	lung:	n/a	chr9:12120059-12120068 chr9:12120057-12120070 chr9:12120057-12120068
7	CEBPB	chr9:12129071-12129335	HepG2	liver:	n/a	n/a
8	CEBPB	chr9:12195456-12195797	HepG2	liver:	n/a	chr9:12195611-12195622
9	CEBPB	chr9:12208833-12209071	HepG2	liver:	n/a	chr9:12208898-12208909 chr9:12208899-12208908 chr9:12208897-12208910
10	CEBPB	chr9:12195488-12195695	K562	blood:	n/a	chr9:12195611-12195622
11	CEBPB	chr9:12193945-12194181	A549	lung:	n/a	chr9:12194071-12194082 chr9:12194071-12194084
12	CTCF	chr9:12215488-12215552	GM13977	blood:	n/a	n/a
13	CTCF	chr9:12195600-12195750	NHEK	skin:	n/a	n/a
14	CTCF	chr9:12264400-12264550	HFF	foreskin:	n/a	n/a
15	CTCF	chr9:12210667-12210803	GM10248	blood:	n/a	n/a
16	CTCF	chr9:12180880-12181030	HEK293	kidney:	n/a	n/a
17	CTCF	chr9:12195560-12195710	HMF	breast:	n/a	n/a
18	CTCF	chr9:12142395-12142451	LNCaP	prostate:	n/a	n/a
19	CTCF	chr9:12219074-12219108	GM10248	blood:	n/a	n/a
20	CTCF	chr9:12195560-12195710	AoAF	blood vessel:	n/a	n/a
21	CTCF	chr9:12100160-12100310	NB4	blood:	n/a	n/a
22	CTCF	chr9:12219290-12219372	GM13976	blood:	n/a	n/a
23	CTCF	chr9:12195600-12195750	HCPEpiC	choroid plexus:	n/a	n/a
24	CTCF	chr9:12210677-12210803	Kidney_OC	kidney:	n/a	n/a
25	CTCF	chr9:12195560-12195710	HEK293	kidney:	n/a	n/a
26	CTCF	chr9:12115897-12115954	GM10248	blood:	n/a	n/a
27	CTCF	chr9:12230966-12231007	Kidney_OC	kidney:	n/a	n/a
28	CTCF	chr9:12101680-12101830	GM12869	blood:	n/a	n/a
29	CTCF	chr9:12148949-12149036	Fibrobl	skin:	n/a	n/a
30	CTCF	chr9:12180880-12181030	GM12878	blood:	n/a	n/a
31	CTCF	chr9:12195520-12195670	HMF	breast:	n/a	n/a
32	CTCF	chr9:12231143-12231170	GM20000	blood:	n/a	n/a
33	CTCF	chr9:12224065-12224152	GM13976	blood:	n/a	n/a
34	CUX1	chr9:12116986-12116993	GM12878	blood:	n/a	n/a
35	CUX1	chr9:12230853-12230855	GM12878	blood:	n/a	n/a
36	E2F4	chr9:12145578-12145647	MCF10A-Er-Src	breast:	n/a	n/a
37	E2F4	chr9:12208242-12208320	MCF10A-Er-Src	breast:	n/a	n/a
38	E2F4	chr9:12185683-12185754	MCF10A-Er-Src	breast:	n/a	n/a
39	E2F4	chr9:12150860-12151087	MCF10A-Er-Src	breast:	n/a	n/a
40	E2F4	chr9:12129041-12129241	MCF10A-Er-Src	breast:	n/a	n/a
41	E2F4	chr9:12155208-12155412	MCF10A-Er-Src	breast:	n/a	n/a
42	E2F6	chr9:12246607-12246944	H1-hESC	embryonic stem cell:	n/a	n/a
43	FAM48A	chr9:12117068-12117206	GM12878	blood:	n/a	n/a
44	FOS	chr9:12185838-12186217	MCF10A-Er-Src	breast:	n/a	chr9:12186008-12186019
45	FOS	chr9:12183392-12183690	MCF10A-Er-Src	breast:	n/a	chr9:12183552-12183561 chr9:12183551-12183560
46	FOS	chr9:12183409-12183596	MCF10A-Er-Src	breast:	n/a	chr9:12183552-12183561 chr9:12183551-12183560
47	FOS	chr9:12228774-12228990	MCF10A-Er-Src	breast:	n/a	chr9:12228868-12228879 chr9:12228870-12228877 chr9:12228872-12228881 chr9:12228873-12228880 chr9:12228870-12228882 chr9:12228871-12228881 chr9:12228872-12228880
48	FOS	chr9:12185825-12186238	MCF10A-Er-Src	breast:	n/a	chr9:12186008-12186019
49	FOS	chr9:12124939-12125159	MCF10A-Er-Src	breast:	n/a	n/a
50	FOS	chr9:12185825-12186224	MCF10A-Er-Src	breast:	n/a	chr9:12186008-12186019

No.	Distal block	Cell Line	Cell type
1	chr9:12182493..12185046-chr9:12186407..12189303,2	K562	blood:
2	chr9:12182493..12185046-chr9:12186407..12189303,2	K562	blood:
3	chr18:21570976..21573123-chr9:12145530..12147030,2	MCF-7	breast:
4	chr16:89002000..89004763-chr9:12244429..12246932,2	MCF-7	breast:
5	chr9:12094328..12096426-chr9:12096756..12098736,2	K562	blood:
6	chr9:12094328..12096426-chr9:12096756..12098736,2	K562	blood:

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

Variant related genes	Relation type
ENSG00000224935	TF binding region
ENSG00000168234	chromatin interactions
ENSG00000261226	chromatin interactions

Extended variants
information (count: 2702 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:2702 , 50 per page) page: 1 2 3 4 5 6 7 ... 55

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10738261	chr9:12095022-12095023	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs547037839	chr9:12095045-12095046	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs78548463	chr9:12095059-12095060	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs532397212	chr9:12095069-12095070	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs139117120	chr9:12095091-12095092	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs558711339	chr9:12095113-12095114	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs573625042	chr9:12095121-12095122	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs575373954	chr9:12095126-12095127	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs12552484	chr9:12095135-12095136	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs537944534	chr9:12095145-12095146	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs555007018	chr9:12095152-12095153	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs574757051	chr9:12095182-12095183	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs542319368	chr9:12095209-12095210	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs144048229	chr9:12095218-12095219	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs559417041	chr9:12095224-12095225	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs573161169	chr9:12095267-12095268	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs146440582	chr9:12095284-12095285	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs140824788	chr9:12095333-12095334	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs10733240	chr9:12095364-12095365	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs550412139	chr9:12095366-12095367	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs73645858	chr9:12095377-12095378	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs529676763	chr9:12095397-12095398	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs546551299	chr9:12095435-12095436	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs576775628	chr9:12095485-12095486	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs138260937	chr9:12095486-12095487	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs531278267	chr9:12095487-12095488	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs566858228	chr9:12095531-12095532	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs75890041	chr9:12095537-12095538	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs143126890	chr9:12095565-12095566	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs569118605	chr9:12095585-12095586	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs538016905	chr9:12095641-12095642	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs554787984	chr9:12095652-12095653	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs145658133	chr9:12095653-12095654	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs533976330	chr9:12095662-12095663	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs7854342	chr9:12095671-12095672	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs573222607	chr9:12095718-12095719	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs77107402	chr9:12095726-12095727	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs541661071	chr9:12095757-12095758	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs372261627	chr9:12095780-12095781	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs377164025	chr9:12095816-12095817	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs148896613	chr9:12095838-12095839	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs544364130	chr9:12095863-12095864	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs560845747	chr9:12095886-12095887	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs529780171	chr9:12095909-12095910	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs546319661	chr9:12095933-12095934	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs559713881	chr9:12095950-12095951	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs564705437	chr9:12095951-12095952	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs552468532	chr9:12095962-12095963	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs188769387	chr9:12095982-12095983	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs148031610	chr9:12095991-12095992	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:102)

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

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12091200-12096400	Enhancers	Placenta Amnion	Placenta Amnion
2	chr9:12092600-12096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:12096200-12096400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:12096400-12101600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:12101600-12102200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:12101600-12102400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:12101800-12102800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:12102400-12104200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:12104200-12104400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr9:12135800-12137400	Enhancers	Fetal Heart	heart
11	chr9:12137600-12138400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr9:12137800-12138200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:12139800-12142600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
14	chr9:12142400-12144000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:12155400-12156200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr9:12156200-12161400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr9:12161400-12167200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr9:12161600-12164800	Enhancers	Brain Germinal Matrix	brain
19	chr9:12162200-12162400	Active TSS	Brain Anterior Caudate	brain
20	chr9:12162200-12162600	Active TSS	Brain Angular Gyrus	brain
21	chr9:12162200-12162800	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr9:12162200-12163200	Enhancers	Fetal Brain Female	brain
23	chr9:12162400-12162600	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr9:12162400-12162600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:12162400-12162800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:12162400-12163000	Enhancers	Brain Hippocampus Middle	brain
27	chr9:12162600-12162800	Enhancers	Brain Anterior Caudate	brain
28	chr9:12162600-12163000	Enhancers	Brain Angular Gyrus	brain
29	chr9:12162600-12163400	Enhancers	Fetal Brain Male	brain
30	chr9:12162800-12166400	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr9:12162800-12166600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:12163200-12164000	Weak transcription	Fetal Brain Female	brain
33	chr9:12164000-12164200	Enhancers	Fetal Brain Female	brain
34	chr9:12164200-12166200	Weak transcription	Fetal Brain Female	brain
35	chr9:12165800-12166400	Enhancers	Brain Substantia Nigra	brain
36	chr9:12166200-12166400	Enhancers	Fetal Brain Female	brain
37	chr9:12166400-12167000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr9:12166600-12167000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:12191600-12192000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr9:12191600-12192000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr9:12191800-12192000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr9:12192000-12200800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr9:12200400-12200600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr9:12200400-12200800	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr9:12200400-12202000	Enhancers	Placenta Amnion	Placenta Amnion
46	chr9:12200600-12201000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr9:12200800-12201200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr9:12201200-12204400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr9:12204400-12204800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr9:12212600-12213000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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