Variant report

Variant	nsv523675
Chromosome Location	chr9:6402856-6409874
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	ATF1	chr9:6408431-6408699	K562	blood:	n/a	n/a
2	ATF3	chr9:6408408-6408659	K562	blood:	n/a	n/a
3	BHLHE40	chr9:6408385-6408658	K562	blood:	n/a	n/a
4	BHLHE40	chr9:6408412-6408647	HepG2	liver:	n/a	n/a
5	CEBPB	chr9:6405496-6405697	K562	blood:	n/a	chr9:6405557-6405570 chr9:6405619-6405630 chr9:6405559-6405570
6	CEBPB	chr9:6405472-6405788	IMR90	lung:	n/a	chr9:6405557-6405570 chr9:6405619-6405630 chr9:6405559-6405570
7	CEBPB	chr9:6405490-6405703	HepG2	liver:	n/a	chr9:6405557-6405570 chr9:6405619-6405630 chr9:6405559-6405570
8	CEBPB	chr9:6405482-6405699	A549	lung:	n/a	chr9:6405557-6405570 chr9:6405619-6405630 chr9:6405559-6405570
9	EP300	chr9:6407788-6408153	HepG2	liver:	n/a	n/a
10	FOXA1	chr9:6407865-6408137	HepG2	liver:	n/a	n/a
11	FOXA1	chr9:6408841-6409087	HepG2	liver:	n/a	n/a
12	FOXA1	chr9:6407799-6408128	HepG2	liver:	n/a	n/a
13	FOXA1	chr9:6408816-6409163	HepG2	liver:	n/a	n/a
14	FOXA1	chr9:6408688-6409159	HepG2	liver:	n/a	n/a
15	FOXA2	chr9:6408756-6409244	A549	lung:	n/a	n/a
16	FOXA2	chr9:6408849-6409103	HepG2	liver:	n/a	n/a
17	HNF4A	chr9:6407709-6408158	HepG2	liver:	n/a	chr9:6407944-6407956 chr9:6407965-6407977 chr9:6407965-6407977 chr9:6407944-6407957 chr9:6407964-6407978 chr9:6407965-6407978 chr9:6407944-6407956 chr9:6407962-6407980 chr9:6407963-6407978 chr9:6407965-6407977 chr9:6407943-6407957 chr9:6407944-6407956
18	HNF4A	chr9:6407742-6408184	HepG2	liver:	n/a	chr9:6407944-6407956 chr9:6407965-6407977 chr9:6407965-6407977 chr9:6407944-6407957 chr9:6407964-6407978 chr9:6407965-6407978 chr9:6407944-6407956 chr9:6407962-6407980 chr9:6407963-6407978 chr9:6407965-6407977 chr9:6407943-6407957 chr9:6407944-6407956
19	HNF4G	chr9:6407741-6408116	HepG2	liver:	n/a	chr9:6407944-6407956 chr9:6407965-6407977 chr9:6407965-6407977 chr9:6407944-6407957 chr9:6407948-6407963 chr9:6407964-6407978 chr9:6407965-6407978 chr9:6407944-6407956 chr9:6407962-6407980 chr9:6407965-6407977 chr9:6407943-6407957 chr9:6407944-6407956
20	JUND	chr9:6408448-6408693	HepG2	liver:	n/a	n/a
21	JUND	chr9:6408404-6408687	K562	blood:	n/a	n/a
22	MAX	chr9:6408396-6408654	K562	blood:	n/a	n/a
23	MAX	chr9:6408375-6408688	HepG2	liver:	n/a	n/a
24	MAX	chr9:6408275-6408737	HepG2	liver:	n/a	n/a
25	MAX	chr9:6405334-6405844	NB4	blood:	n/a	n/a
26	MAZ	chr9:6402855-6402867	Hela-S3	cervix:	n/a	n/a
27	MYC	chr9:6405410-6405815	NB4	blood:	n/a	n/a
28	MYC	chr9:6408636-6408761	MCF10A-Er-Src	breast:	n/a	n/a
29	MYC	chr9:6408462-6408648	K562	blood:	n/a	n/a
30	RXRA	chr9:6407771-6408112	HepG2	liver:	n/a	chr9:6407969-6407978 chr9:6407963-6407977 chr9:6407942-6407956 chr9:6407948-6407957
31	USF1	chr9:6408415-6408624	HepG2	liver:	n/a	chr9:6408515-6408526 chr9:6408529-6408540
32	USF1	chr9:6408352-6408697	H1-hESC	embryonic stem cell:	n/a	chr9:6408515-6408526 chr9:6408529-6408540
33	USF1	chr9:6408382-6408631	K562	blood:	n/a	chr9:6408515-6408526 chr9:6408529-6408540
34	USF1	chr9:6408347-6408643	K562	blood:	n/a	chr9:6408515-6408526 chr9:6408529-6408540
35	USF1	chr9:6408348-6408654	HepG2	liver:	n/a	chr9:6408515-6408526 chr9:6408529-6408540
36	USF2	chr9:6408385-6408576	Hela-S3	cervix:	n/a	chr9:6408515-6408526 chr9:6408529-6408540
37	USF2	chr9:6408353-6408712	HepG2	liver:	n/a	chr9:6408515-6408526 chr9:6408529-6408540
38	USF2	chr9:6408418-6408587	K562	blood:	n/a	chr9:6408515-6408526 chr9:6408529-6408540

No.	Distal block	Cell Line	Cell type
1	chr9:6408551..6411662-chr9:6412630..6415165,4	MCF-7	breast:
2	chr9:6398344..6401128-chr9:6407574..6409551,2	K562	blood:
3	chr9:6408168..6410435-chr9:6411394..6414242,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf38-2	chr9:6408525-6408756	XLOC_007638
2	lnc-C9orf38-2	chr9:6408524-6408756	NONHSAT130128

Variant related genes	Relation type
UHRF2	TF binding region
ENSG00000147854	chromatin interactions

Extended variants
information (count: 263 )
Associated
traits (count: 108 )

Variant overlapped rSNPs/rCNVs (count:263 , 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	rs147252529	chr9:6404613-6404614	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs546517312	chr9:6404617-6404618	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs547615991	chr9:6404678-6404679	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs78724546	chr9:6404693-6404694	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs146364006	chr9:6404701-6404702	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs552061390	chr9:6404719-6404720	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs569904691	chr9:6404723-6404724	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs537500317	chr9:6404741-6404742	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs549482417	chr9:6404776-6404777	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs559788166	chr9:6404789-6404790	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs528456744	chr9:6404825-6404826	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs10739096	chr9:6404888-6404889	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs535144097	chr9:6404891-6404892	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs188494651	chr9:6404914-6404915	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs572213117	chr9:6404937-6404938	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs181430116	chr9:6404942-6404943	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs554079811	chr9:6404946-6404947	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs183753728	chr9:6404952-6404953	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs558076031	chr9:6404958-6404959	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs189278272	chr9:6404980-6404981	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs543441548	chr9:6405045-6405046	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs561427118	chr9:6405067-6405068	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs573376459	chr9:6405074-6405075	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs118007873	chr9:6405082-6405083	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs559480284	chr9:6405095-6405096	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs577089095	chr9:6405133-6405134	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs546010412	chr9:6405164-6405165	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs556291644	chr9:6405172-6405173	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs139727488	chr9:6405173-6405174	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs545375246	chr9:6405188-6405189	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs564050983	chr9:6405243-6405244	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs530790272	chr9:6405245-6405246	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs373177763	chr9:6405259-6405260	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs77107844	chr9:6405307-6405308	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs528553781	chr9:6405309-6405310	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs547117755	chr9:6405316-6405317	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs565732476	chr9:6405365-6405366	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs539656549	chr9:6405430-6405431	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs557750265	chr9:6405445-6405446	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs569965063	chr9:6405495-6405496	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs368173894	chr9:6405498-6405499	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs536973930	chr9:6405500-6405501	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs554909388	chr9:6405505-6405506	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs7854026	chr9:6405525-6405526	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs548718896	chr9:6405565-6405566	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs7873206	chr9:6405568-6405569	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
47	rs373236736	chr9:6405600-6405601	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs527711717	chr9:6405610-6405611	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs578103672	chr9:6405648-6405649	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs545618192	chr9:6405671-6405672	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:108)

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
Prostate cancer	18632612	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21364760	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
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
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ovarian cancer	21781307	CNVD
Pancreatic cancer	17952125	CNVD
T-cell lymphomas	22341440	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6404600-6406200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr9:6405200-6405400	Enhancers	Thymus	Thymus
3	chr9:6405200-6405800	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr9:6405400-6412200	Weak transcription	Thymus	Thymus
5	chr9:6405800-6410600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr9:6406000-6406200	Weak transcription	HepG2	liver
7	chr9:6406000-6407000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr9:6406200-6407800	Enhancers	HepG2	liver
9	chr9:6407000-6411800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr9:6407800-6408000	Flanking Active TSS	HepG2	liver
11	chr9:6408000-6408400	Enhancers	HepG2	liver
12	chr9:6408200-6408800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:6408200-6412200	Weak transcription	Primary T cells from cord blood	blood
14	chr9:6408400-6408800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr9:6408400-6408800	Enhancers	Pancreas	Pancrea
16	chr9:6408400-6408800	Enhancers	K562	blood
17	chr9:6408400-6409000	Flanking Active TSS	HepG2	liver
18	chr9:6408400-6409800	Enhancers	Liver	Liver
19	chr9:6408600-6408800	Enhancers	NHEK	skin
20	chr9:6408800-6411800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:6408800-6412200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr9:6408800-6412400	Weak transcription	Pancreas	Pancrea
23	chr9:6409000-6409800	Enhancers	HepG2	liver
24	chr9:6409000-6412200	Weak transcription	NHEK	skin
25	chr9:6409800-6412400	Weak transcription	Liver	Liver

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