Variant report

Variant	nsv524645
Chromosome Location	chr9:6650885-6664901
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:223)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:7)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:223 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr9:6664541-6665413	HepG2	liver:	n/a	n/a
2	ATF2	chr9:6654995-6655416	GM12878	blood:	n/a	n/a
3	ATF2	chr9:6654912-6655463	GM12878	blood:	n/a	n/a
4	ATF3	chr9:6664294-6664873	A549	lung:	n/a	n/a
5	ATF3	chr9:6664488-6664934	A549	lung:	n/a	n/a
6	BATF	chr9:6656332-6656632	GM12878	blood:	n/a	n/a
7	BATF	chr9:6655058-6655371	GM12878	blood:	n/a	n/a
8	BCL11A	chr9:6655034-6655412	GM12878	blood:	n/a	n/a
9	BCL3	chr9:6664480-6665034	A549	lung:	n/a	n/a
10	BCL3	chr9:6664426-6665297	A549	lung:	n/a	chr9:6665033-6665042
11	BCLAF1	chr9:6654844-6655458	GM12878	blood:	n/a	n/a
12	BHLHE40	chr9:6654915-6655315	GM12878	blood:	n/a	n/a
13	BHLHE40	chr9:6664329-6665171	HepG2	liver:	n/a	n/a
14	BRCA1	chr9:6664464-6664732	HepG2	liver:	n/a	n/a
15	BRCA1	chr9:6664596-6664874	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr9:6664574-6665059	Hela-S3	cervix:	n/a	n/a
17	CEBPB	chr9:6662560-6662584	K562	blood:	n/a	n/a
18	CEBPB	chr9:6664492-6665376	HepG2	liver:	n/a	n/a
19	CEBPB	chr9:6664643-6664861	HepG2	liver:	n/a	n/a
20	CEBPB	chr9:6664587-6665287	HepG2	liver:	n/a	n/a
21	CEBPB	chr9:6664576-6665291	HepG2	liver:	n/a	n/a
22	CEBPB	chr9:6664453-6665284	A549	lung:	n/a	n/a
23	CEBPB	chr9:6654850-6655851	GM12878	blood:	n/a	n/a
24	CEBPB	chr9:6657074-6657184	K562	blood:	n/a	n/a
25	CEBPB	chr9:6658601-6659127	A549	lung:	n/a	chr9:6658871-6658882
26	CEBPB	chr9:6664533-6665234	MCF-7	breast:	n/a	n/a
27	CEBPB	chr9:6652027-6652178	A549	lung:	n/a	n/a
28	CEBPB	chr9:6658728-6659036	K562	blood:	n/a	chr9:6658871-6658882
29	CEBPB	chr9:6658722-6659320	MCF-7	breast:	n/a	chr9:6658871-6658882
30	CEBPB	chr9:6664583-6664967	MCF-7	breast:	n/a	n/a
31	CEBPB	chr9:6658721-6659242	A549	lung:	n/a	chr9:6658871-6658882
32	CEBPB	chr9:6664551-6665250	A549	lung:	n/a	n/a
33	CEBPB	chr9:6658749-6659061	IMR90	lung:	n/a	chr9:6658871-6658882
34	CEBPB	chr9:6662460-6662719	HepG2	liver:	n/a	chr9:6662551-6662562
35	CEBPB	chr9:6664875-6665208	HepG2	liver:	n/a	n/a
36	CEBPB	chr9:6658750-6659166	HepG2	liver:	n/a	chr9:6658871-6658882
37	CEBPB	chr9:6664589-6665192	A549	lung:	n/a	n/a
38	CEBPD	chr9:6664675-6665149	HepG2	liver:	n/a	n/a
39	CEBPD	chr9:6664550-6665175	HepG2	liver:	n/a	n/a
40	CEBPZ	chr9:6664872-6665103	HepG2	liver:	n/a	n/a
41	CHD2	chr9:6664463-6664849	HepG2	liver:	n/a	n/a
42	CHD2	chr9:6664515-6664915	Hela-S3	cervix:	n/a	n/a
43	CREB1	chr9:6664317-6665332	HepG2	liver:	n/a	n/a
44	CREB1	chr9:6654862-6655412	GM12878	blood:	n/a	n/a
45	CREB1	chr9:6664431-6664819	A549	lung:	n/a	n/a
46	CREB1	chr9:6664582-6664891	A549	lung:	n/a	n/a
47	CREB1	chr9:6664175-6665459	HepG2	liver:	n/a	n/a
48	CTCF	chr9:6658352-6658408	GM10266	blood:	n/a	n/a
49	CTCF	chr9:6653401-6653444	GM10248	blood:	n/a	n/a
50	CTCF	chr9:6664073-6664092	GM20000	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:6656639..6659482-chr9:6662780..6664665,3	MCF-7	breast:
2	chr9:6656639..6659482-chr9:6662780..6664665,3	MCF-7	breast:
3	chr9:6641084..6643158-chr9:6652442..6654682,2	MCF-7	breast:
4	chr9:6652273..6654630-chr9:6673766..6675385,2	MCF-7	breast:
5	chr9:6662765..6664429-chr9:6666367..6668579,2	MCF-7	breast:
6	chr9:6643546..6649129-chr9:6652921..6657149,5	MCF-7	breast:
7	chr9:6663029..6667664-chr9:6679639..6683357,9	MCF-7	breast:
8	chr9:6654607..6656764-chr9:6663214..6664911,2	K562	blood:
9	chr9:6585232..6587306-chr9:6664888..6666750,2	MCF-7	breast:
10	chr9:6663663..6666675-chr9:6715678..6718421,3	MCF-7	breast:
11	chr9:6654607..6656764-chr9:6663214..6664911,2	K562	blood:

(count:7 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM4C-14	chr9:6661783-6661845	NONHSAT130146
2	lnc-KDM4C-13	chr9:6663156-6663366	NONHSAT130148
3	lnc-KDM4C-14	chr9:6661291-6661345	NONHSAT130146
4	lnc-KDM4C-13	chr9:6662424-6662810	NONHSAT130148
5	lnc-KDM4C-13	chr9:6663657-6663792	NONHSAT130148
6	lnc-KDM4C-14	chr9:6660407-6661044	NONHSAT130146
7	lnc-KDM4C-14	chr9:6661651-6661936	NONHSAT130147

No data

Variant related genes	Relation type
RN7SL123P	TF binding region
ENSG00000229057	TF binding region
ENSG00000236924	chromatin interactions
ENSG00000232946	chromatin interactions
ENSG00000178445	chromatin interactions
ENSG00000225489	chromatin interactions

Extended variants
information (count: 855 )
Associated
traits (count: 107 )

Variant overlapped rSNPs/rCNVs (count:855 , 50 per page) page: 1 2 3 4 5 6 7 ... 18

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2988418	chr9:6650885-6650886	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs191505070	chr9:6650899-6650900	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs118156352	chr9:6650902-6650903	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs184122358	chr9:6650938-6650939	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs577055059	chr9:6650951-6650952	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs142837237	chr9:6650952-6650953	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs188141088	chr9:6650962-6650963	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs574896589	chr9:6650981-6650982	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs542526983	chr9:6650991-6650992	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs2988419	chr9:6650993-6650994	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs78487821	chr9:6650998-6650999	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs376823974	chr9:6651005-6651006	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs113558270	chr9:6651007-6651008	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs545828144	chr9:6651053-6651054	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs76692342	chr9:6651069-6651070	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs111516823	chr9:6651073-6651074	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs531878013	chr9:6651080-6651081	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs549958834	chr9:6651085-6651086	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs569041641	chr9:6651100-6651101	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs529814117	chr9:6651139-6651140	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs536104015	chr9:6651188-6651189	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs150817051	chr9:6651190-6651191	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs534073596	chr9:6651201-6651202	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs577502760	chr9:6651213-6651214	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs111441664	chr9:6651223-6651224	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs376402865	chr9:6651224-6651225	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs60959086	chr9:6651246-6651247	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs572731762	chr9:6651250-6651251	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs558636219	chr9:6651252-6651253	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs531241221	chr9:6651262-6651263	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs115340978	chr9:6651264-6651265	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs537958177	chr9:6651292-6651293	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs149586247	chr9:6651293-6651294	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs575000991	chr9:6651307-6651308	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs542085785	chr9:6651308-6651309	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs7853864	chr9:6651319-6651320	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs572445706	chr9:6651336-6651337	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs114869387	chr9:6651396-6651397	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs564141390	chr9:6651411-6651412	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs191389273	chr9:6651413-6651414	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs1138718	chr9:6651474-6651475	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs4742235	chr9:6651494-6651495	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs543910053	chr9:6651500-6651501	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs185621111	chr9:6651521-6651522	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs113669927	chr9:6651527-6651528	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs547146278	chr9:6651550-6651551	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs2578284	chr9:6651552-6651553	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs10975713	chr9:6651564-6651565	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs527589658	chr9:6651577-6651578	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs182479866	chr9:6651579-6651580	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:107)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Intracranial aneurysm	16715129	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Disorders of sex development	22290220	CNVD
Glioblastoma multiforme	21080181	CNVD
Sudden cardiac death	19188705	CNVD
Non-small cell lung cancer	21829676	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	21952639	CNVD
Disorders of sex development	21048976	CNVD
Neuroblastoma	18923191	CNVD
Intellectual disability	22102821	CNVD
abnormal development	18461090	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
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
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Developmental delay	21147756	CNVD
Lung cancer	18438408	CNVD
XY gonadal dysgenesis	20685758	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelodysplastic syndrome	21251322	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Hepatocellular carcinoma	18803288	CNVD
Breast cancer	21364760	CNVD
Metastatic melanoma	18483359	CNVD
Glioblastoma	19074898	CNVD
Malignant melanoma	19074898	CNVD
Prostate cancer	16573809	CNVD
Metanephric adenoma	20802469	CNVD
Medulloblastoma	16783165	CNVD
Dyslexia	22102821	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Schizophrenia	21346763	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
early-passage human iPS cells	21368824	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6646600-6656800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:6646800-6657000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:6647000-6656600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr9:6647600-6654600	Weak transcription	GM12878-XiMat	blood
5	chr9:6648000-6656600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr9:6648200-6653800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:6648200-6670400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr9:6648400-6658200	Weak transcription	A549	lung
9	chr9:6648400-6669400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:6648400-6680400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:6648600-6652800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr9:6648600-6653600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr9:6648600-6656600	Weak transcription	Liver	Liver
14	chr9:6648600-6677600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr9:6648600-6680400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr9:6648800-6680400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr9:6649600-6651600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr9:6649800-6652600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr9:6649800-6656600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:6649800-6664200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:6650000-6657000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr9:6650000-6658400	Weak transcription	HepG2	liver
23	chr9:6651600-6652800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:6652600-6654200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
25	chr9:6652800-6653200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:6652800-6654000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:6653200-6656800	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr9:6653600-6654000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr9:6654000-6656600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:6654000-6669400	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr9:6654200-6656600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:6654600-6654800	Enhancers	GM12878-XiMat	blood
33	chr9:6654800-6655200	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr9:6654800-6655400	Enhancers	Primary B cells from peripheral blood	blood
35	chr9:6654800-6655600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr9:6654800-6655600	Enhancers	Fetal Thymus	thymus
37	chr9:6654800-6655800	Enhancers	Dnd41	blood
38	chr9:6654800-6656000	Flanking Active TSS	GM12878-XiMat	blood
39	chr9:6655000-6655200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr9:6655000-6655200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:6655000-6655200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
42	chr9:6655000-6655200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr9:6655000-6655800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
44	chr9:6656000-6656400	Enhancers	GM12878-XiMat	blood
45	chr9:6656400-6656600	Flanking Active TSS	GM12878-XiMat	blood
46	chr9:6656600-6656800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
47	chr9:6656600-6656800	Enhancers	GM12878-XiMat	blood
48	chr9:6656600-6657200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr9:6656600-6657200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr9:6656600-6657400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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