Variant report

Variant	nsv613616
Chromosome Location	chr9:12922330-13018096
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:324)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:324 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr9:12954486-12954757	GM12878	blood:	n/a	chr9:12954660-12954671
2	CEBPB	chr9:12923707-12924077	IMR90	lung:	n/a	n/a
3	CEBPB	chr9:12993478-12993785	IMR90	lung:	n/a	n/a
4	CEBPB	chr9:12939987-12940115	A549	lung:	n/a	chr9:12940029-12940040
5	CEBPB	chr9:13017970-13018214	A549	lung:	n/a	n/a
6	CEBPB	chr9:12973769-12974074	IMR90	lung:	n/a	chr9:12973911-12973922
7	CEBPB	chr9:12939943-12940204	HepG2	liver:	n/a	chr9:12940029-12940040
8	CEBPB	chr9:13017938-13018130	HepG2	liver:	n/a	n/a
9	CEBPB	chr9:12933878-12934366	HCT-116	colon:	n/a	n/a
10	CEBPB	chr9:12961066-12961594	IMR90	lung:	n/a	chr9:12961125-12961136 chr9:12961125-12961138 chr9:12961125-12961138
11	CREB1	chr9:12923756-12923942	A549	lung:	n/a	n/a
12	CTCF	chr9:12972640-12972790	HMF	breast:	n/a	n/a
13	CTCF	chr9:12922280-12922430	NHEK	skin:	n/a	chr9:12922395-12922411
14	CTCF	chr9:12977080-12977230	NHEK	skin:	n/a	n/a
15	CTCF	chr9:12977120-12977270	MCF-7	breast:	n/a	n/a
16	CTCF	chr9:12977140-12977290	BE2_C	brain:	n/a	n/a
17	CTCF	chr9:12922360-12922510	AG09319	gingival:	n/a	chr9:12922395-12922411
18	CTCF	chr9:12972580-12972730	HCM	heart:	n/a	chr9:12972596-12972617
19	CTCF	chr9:12977020-12977170	GM12866	blood:	n/a	n/a
20	CTCF	chr9:12988360-12988510	HCPEpiC	choroid plexus:	n/a	n/a
21	CTCF	chr9:12977160-12977310	BJ	skin:	n/a	n/a
22	CTCF	chr9:12977133-12977217	MCF-7	breast:	n/a	n/a
23	CTCF	chr9:12972594-12972675	LNCaP	prostate:	n/a	chr9:12972596-12972617
24	CTCF	chr9:12922360-12922510	HEEpiC	esophagus:	n/a	chr9:12922395-12922411
25	CTCF	chr9:12922380-12922530	HMEC	breast:	n/a	chr9:12922395-12922411
26	CTCF	chr9:12922340-12922490	AG10803	skin:	n/a	chr9:12922395-12922411
27	CTCF	chr9:12922300-12922450	AG10803	skin:	n/a	chr9:12922395-12922411
28	CTCF	chr9:12922320-12922470	HFF	foreskin:	n/a	chr9:12922395-12922411
29	CTCF	chr9:12955680-12955830	GM12871	blood:	n/a	n/a
30	CTCF	chr9:12988340-12988490	AG10803	skin:	n/a	n/a
31	CTCF	chr9:12972627-12972677	MCF-7	breast:	n/a	n/a
32	CTCF	chr9:12988360-12988510	HFF	foreskin:	n/a	n/a
33	CTCF	chr9:12988346-12988658	MCF-7	breast:	n/a	chr9:12988636-12988644
34	CTCF	chr9:12977148-12977243	Hela-S3	cervix:	n/a	n/a
35	CTCF	chr9:12972640-12972790	HPF	lung:	n/a	n/a
36	CTCF	chr9:12988340-12988490	AG09319	gingival:	n/a	n/a
37	CTCF	chr9:12988424-12988474	MCF-7	breast:	n/a	n/a
38	CTCF	chr9:12922380-12922530	HCPEpiC	choroid plexus:	n/a	chr9:12922395-12922411
39	CTCF	chr9:12977100-12977250	HRPEpiC	eye:	n/a	n/a
40	CTCF	chr9:12972440-12972590	MCF-7	breast:	n/a	n/a
41	CTCF	chr9:12988240-12988390	HMEC	breast:	n/a	n/a
42	CTCF	chr9:12988380-12988530	HEEpiC	esophagus:	n/a	n/a
43	CTCF	chr9:12977144-12977227	Lung_OC	lung:	n/a	n/a
44	CTCF	chr9:12977080-12977230	BE2_C	brain:	n/a	n/a
45	CTCF	chr9:12922360-12922510	HFF-Myc	foreskin:	n/a	chr9:12922395-12922411
46	CTCF	chr9:12988440-12988590	AG09319	gingival:	n/a	n/a
47	CTCF	chr9:12972626-12972631	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr9:12988443-12988497	Hela-S3	cervix:	n/a	n/a
49	CTCF	chr9:12977100-12977250	A549	lung:	n/a	n/a
50	CTCF	chr9:12977140-12977290	HCT-116	colon:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:13013683..13015999-chr9:13017070..13019514,2	MCF-7	breast:
2	chr9:12964990..12966933-chr9:12968548..12971225,2	MCF-7	breast:
3	chr9:12955347..12957519-chr9:12959298..12960920,2	MCF-7	breast:
4	chr9:13008470..13010567-chr9:13018005..13020586,2	MCF-7	breast:
5	chr9:12964990..12966933-chr9:12968548..12971225,2	MCF-7	breast:
6	chr9:13008470..13010567-chr9:13018005..13020586,2	MCF-7	breast:
7	chr9:12922589..12925309-chr9:12932316..12933934,2	MCF-7	breast:
8	chr9:12776384..12777092-chr9:12988313..12988856,2	MCF-7	breast:
9	chr9:12922589..12925309-chr9:12932316..12933934,2	MCF-7	breast:
10	chr9:13013683..13015999-chr9:13017070..13019514,2	MCF-7	breast:
11	chr9:12723685..12724314-chr9:12988034..12988919,3	MCF-7	breast:
12	chr9:12719485..12720037-chr9:12987933..12988498,2	MCF-7	breast:
13	chr9:12774582..12776386-chr9:12976678..12978992,2	MCF-7	breast:
14	chr9:12955347..12957519-chr9:12959298..12960920,2	MCF-7	breast:
15	chr9:13002424..13004560-chr9:13006872..13008431,2	MCF-7	breast:
16	chr9:13002424..13004560-chr9:13006872..13008431,2	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MPDZ-6	chr9:12968103-12968512	NONHSAT130231
2	lnc-MPDZ-7	chr9:12950565-12950844	NONHSAT130230
3	lnc-MPDZ-7	chr9:12956371-12956378	NONHSAT130230
4	lnc-MPDZ-6	chr9:12951763-12951838	NONHSAT130231

No data

Variant related genes	Relation type
TDPX2	TF binding region
ENSG00000153714	chromatin interactions

Extended variants
information (count: 3759 )
Associated
traits (count: 103 )

Variant overlapped rSNPs/rCNVs (count:3759 , 50 per page) page: 1 2 3 4 5 6 7 ... 76

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2065423	chr9:12922330-12922331	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs116283700	chr9:12922339-12922340	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs375997421	chr9:12922340-12922341	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs540643669	chr9:12922347-12922348	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs551657948	chr9:12922350-12922351	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs78697719	chr9:12922397-12922398	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs533237552	chr9:12922408-12922409	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs199737156	chr9:12922414-12922415	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs569828598	chr9:12922447-12922448	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs373101327	chr9:12922473-12922474	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs181006012	chr9:12922487-12922488	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs548660581	chr9:12922498-12922499	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs114397966	chr9:12922512-12922513	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs368466001	chr9:12922533-12922534	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs138863644	chr9:12922535-12922536	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs371065882	chr9:12922629-12922630	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs547748954	chr9:12922641-12922642	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs570792338	chr9:12922674-12922675	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs540118657	chr9:12922689-12922690	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs571987577	chr9:12922702-12922703	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs556632615	chr9:12922732-12922733	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs576536061	chr9:12922773-12922774	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs142072761	chr9:12922783-12922784	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs555013378	chr9:12922796-12922797	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs185541907	chr9:12922840-12922841	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs189488572	chr9:12922861-12922862	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs375129060	chr9:12922878-12922879	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs115366408	chr9:12922882-12922883	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs577610556	chr9:12922901-12922902	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs543652838	chr9:12922914-12922915	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs563443884	chr9:12922918-12922919	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs111349901	chr9:12922940-12922941	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs181475676	chr9:12923003-12923004	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs145437415	chr9:12923006-12923007	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs28638037	chr9:12923011-12923012	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs547616560	chr9:12923020-12923021	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs570824050	chr9:12923039-12923040	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs539453977	chr9:12923045-12923046	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs550410836	chr9:12923051-12923052	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs138043982	chr9:12923074-12923075	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs535627989	chr9:12923075-12923076	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs567710430	chr9:12923092-12923093	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs572343302	chr9:12923100-12923101	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs534710543	chr9:12923115-12923116	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs186069538	chr9:12923138-12923139	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs577524913	chr9:12923157-12923158	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs190833155	chr9:12923177-12923178	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs35873446	chr9:12923187-12923188	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs573960862	chr9:12923192-12923193	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs542978448	chr9:12923212-12923213	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:103)

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
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
Melanoma	22183965	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21611746	CNVD
Chordoma	21215367	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	22522925	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD

Chromatin state (count:505 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:12916200-12922400	Weak transcription	Fetal Lung	lung
2	chr9:12917000-12922600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr9:12917000-12933600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr9:12917200-12922600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr9:12917200-12930000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:12917200-12934000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr9:12917400-12933600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:12921600-12922400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr9:12921600-12922800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr9:12921800-12922800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:12921800-12922800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:12922000-12923000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr9:12922000-12925400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:12922200-12922400	Enhancers	Colon Smooth Muscle	Colon
15	chr9:12922200-12922800	Enhancers	Duodenum Smooth Muscle	Duodenum
16	chr9:12922200-12924800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr9:12922200-12924800	Enhancers	Fetal Heart	heart
18	chr9:12922200-12925400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:12922200-12925400	Enhancers	NHDF-Ad	bronchial
20	chr9:12922400-12922600	Enhancers	Fetal Lung	lung
21	chr9:12922400-12922600	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:12922400-12923400	Weak transcription	Colon Smooth Muscle	Colon
23	chr9:12922400-12924000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:12922600-12922800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:12922600-12922800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr9:12922600-12923400	Weak transcription	Fetal Lung	lung
27	chr9:12922600-12924000	Enhancers	Fetal Stomach	stomach
28	chr9:12922600-12924200	Enhancers	Adipose Nuclei	Adipose
29	chr9:12922800-12923800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:12922800-12923800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr9:12922800-12931000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:12923000-12924800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr9:12923200-12923600	Enhancers	Fetal Brain Male	brain
34	chr9:12923200-12923600	Enhancers	Left Ventricle	heart
35	chr9:12923200-12924000	Enhancers	HSMMtube	muscle
36	chr9:12923200-12924200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:12923200-12924200	Enhancers	Aorta	Aorta
38	chr9:12923200-12924200	Enhancers	Right Atrium	heart
39	chr9:12923200-12924200	Enhancers	HMEC	breast
40	chr9:12923200-12924400	Enhancers	NHLF	lung
41	chr9:12923200-12924400	Enhancers	Osteobl	bone
42	chr9:12923200-12925400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:12923200-12925400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr9:12923400-12923800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr9:12923400-12924000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:12923400-12924000	Enhancers	Colon Smooth Muscle	Colon
47	chr9:12923400-12924000	Enhancers	Fetal Lung	lung
48	chr9:12923400-12924200	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr9:12923400-12924200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr9:12923400-12924200	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links