Variant report

Variant	nsv520912
Chromosome Location	chr9:11254070-11308992
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	BRCA1	chr9:11272473-11272479	Hela-S3	cervix:	n/a	n/a
2	CBX3	chr9:11269115-11269340	K562	blood:	n/a	n/a
3	CEBPB	chr9:11258134-11258408	HepG2	liver:	n/a	chr9:11258233-11258244
4	CEBPB	chr9:11258090-11258374	MCF-7	breast:	n/a	chr9:11258233-11258244
5	CEBPB	chr9:11258095-11258408	IMR90	lung:	n/a	chr9:11258233-11258244
6	CEBPB	chr9:11267017-11267301	K562	blood:	n/a	chr9:11267135-11267146
7	CEBPB	chr9:11258112-11258312	K562	blood:	n/a	chr9:11258233-11258244
8	CEBPB	chr9:11266996-11267317	IMR90	lung:	n/a	chr9:11267135-11267146
9	CEBPB	chr9:11257560-11257807	HepG2	liver:	n/a	n/a
10	CEBPB	chr9:11267004-11267299	HepG2	liver:	n/a	chr9:11267135-11267146
11	CEBPB	chr9:11258136-11258368	H1-hESC	embryonic stem cell:	n/a	chr9:11258233-11258244
12	CEBPB	chr9:11294410-11294610	HepG2	liver:	n/a	n/a
13	CEBPB	chr9:11258112-11258370	A549	lung:	n/a	chr9:11258233-11258244
14	CTCF	chr9:11291462-11291489	GM10248	blood:	n/a	n/a
15	CTCF	chr9:11267628-11267697	Lung_OC	lung:	n/a	n/a
16	CTCF	chr9:11292504-11292560	GM13976	blood:	n/a	n/a
17	CTCF	chr9:11266011-11266069	Kidney_OC	kidney:	n/a	n/a
18	CTCF	chr9:11256206-11256235	GM10266	blood:	n/a	n/a
19	CTCF	chr9:11256655-11256708	GM13976	blood:	n/a	n/a
20	CTCF	chr9:11300853-11300916	Pancreas_OC	pancreas:	n/a	n/a
21	CTCF	chr9:11293769-11293802	Kidney_OC	kidney:	n/a	n/a
22	CTCF	chr9:11293809-11293811	Kidney_OC	kidney:	n/a	n/a
23	CTCF	chr9:11266027-11266077	LNCaP	prostate:	n/a	n/a
24	CTCF	chr9:11273460-11273610	GM12866	blood:	n/a	n/a
25	E2F4	chr9:11283208-11283408	MCF10A-Er-Src	breast:	n/a	n/a
26	E2F4	chr9:11274565-11274765	MCF10A-Er-Src	breast:	n/a	n/a
27	E2F4	chr9:11272521-11272714	MCF10A-Er-Src	breast:	n/a	n/a
28	EP300	chr9:11269259-11269265	K562	blood:	n/a	n/a
29	FOS	chr9:11298684-11298876	MCF10A-Er-Src	breast:	n/a	n/a
30	FOXP2	chr9:11264566-11264802	SK-N-MC	brain:	n/a	n/a
31	GABPA	chr9:11300066-11300142	HepG2	liver:	n/a	n/a
32	GABPA	chr9:11300064-11300154	HepG2	liver:	n/a	n/a
33	GATA3	chr9:11257913-11258463	MCF-7	breast:	n/a	n/a
34	JUND	chr9:11298708-11298978	HepG2	liver:	n/a	chr9:11298832-11298843
35	KAP1	chr9:11307549-11307915	HEK293	kidney:	n/a	n/a
36	KAP1	chr9:11268945-11269640	K562	blood:	n/a	n/a
37	KAP1	chr9:11268917-11269615	HEK293	kidney:	n/a	n/a
38	MAFK	chr9:11305411-11305640	HepG2	liver:	n/a	n/a
39	MAFK	chr9:11305407-11305602	IMR90	lung:	n/a	n/a
40	MAFK	chr9:11277023-11277138	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr9:11276668-11276729	HepG2	liver:	n/a	n/a
42	MYC	chr9:11261363-11261502	GM12878	blood:	n/a	n/a
43	POLR2A	chr9:11289170-11289286	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr9:11296267-11296421	A549	lung:	n/a	n/a
45	POLR2A	chr9:11296464-11296547	MCF-7	breast:	n/a	n/a
46	POLR2A	chr9:11296483-11296484	MCF-7	breast:	n/a	n/a
47	POLR2A	chr9:11281812-11281827	Gliobla	brain:	n/a	n/a
48	POLR2A	chr9:11265081-11265138	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr9:11273100-11273121	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr9:11264401-11264962	SK-N-MC	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTPRD-9	chr9:11265314-11265536	NONHSAT130211
2	lnc-TYRP1-2	chr9:11277792-11277964	XLOC_007281
3	lnc-PTPRD-9	chr9:11266253-11266314	NONHSAT130211
4	lnc-PTPRD-4	chr9:11275314-11275536	XLOC_007646
5	lnc-TYRP1-2	chr9:11277589-11277655	XLOC_007281
6	lnc-PTPRD-4	chr9:11276253-11276314	XLOC_007646

Variant related genes	Relation type
ENSG00000230365	TF binding region

Extended variants
information (count: 605 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:605 , 50 per page) page: 1 2 3 4 5 6 7 ... 13

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs10959669	chr9:11254204-11254205	Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs189334409	chr9:11254228-11254229	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
3	rs571892201	chr9:11254267-11254268	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
4	rs536909656	chr9:11254274-11254275	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
5	rs1158666	chr9:11254279-11254280	Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs10959670	chr9:11254284-11254285	Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs542198057	chr9:11254290-11254291	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs180713025	chr9:11254297-11254298	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
9	rs186356799	chr9:11254298-11254299	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
10	rs140227642	chr9:11254304-11254305	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
11	rs10115315	chr9:11254334-11254335	Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs10115316	chr9:11254344-11254345	Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs551038643	chr9:11254349-11254350	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs558881051	chr9:11254371-11254372	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs12003565	chr9:11254373-11254374	Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs140909310	chr9:11254418-11254419	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs530073656	chr9:11254428-11254429	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs577231047	chr9:11254432-11254433	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs191307044	chr9:11254477-11254478	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs566995331	chr9:11254478-11254479	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs539103299	chr9:11254513-11254514	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs372535635	chr9:11254557-11254558	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs375413017	chr9:11254581-11254582	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs571397481	chr9:11254586-11254587	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs181146106	chr9:11254619-11254620	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs557006664	chr9:11254628-11254629	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
27	rs185979701	chr9:11254642-11254643	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
28	rs12351724	chr9:11254673-11254674	Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs28875890	chr9:11254678-11254679	Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs572611907	chr9:11254700-11254701	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
31	rs73408926	chr9:11254714-11254715	Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs569850377	chr9:11254717-11254718	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
33	rs532480141	chr9:11254732-11254733	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
34	rs573568750	chr9:11254741-11254742	Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs570106589	chr9:11257423-11257424	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs548533972	chr9:11257430-11257431	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs529444141	chr9:11257441-11257442	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs139866794	chr9:11257444-11257445	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs10959672	chr9:11257448-11257449	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	disease
40	rs534717287	chr9:11257476-11257477	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs114744247	chr9:11257501-11257502	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs571722060	chr9:11257508-11257509	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs537101283	chr9:11257529-11257530	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs557423764	chr9:11257571-11257572	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs534603005	chr9:11257590-11257591	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs192156511	chr9:11257617-11257618	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs11496219	chr9:11257638-11257639	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs183802049	chr9:11257642-11257643	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs111503732	chr9:11257657-11257658	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs186189602	chr9:11257670-11257671	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:102)

Disease	PMID	Source
abnormal development	18461090	CNVD
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
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
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	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
Barrett''s syndrome	19417022	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Bipolar disorder	19114987	CNVD
Schizophrenia	23813976	CNVD

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:11254200-11254800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
2	chr9:11257400-11258600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr9:11257600-11258000	Enhancers	Fetal Heart	heart
4	chr9:11258000-11258400	Flanking Active TSS	Fetal Heart	heart
5	chr9:11258200-11258600	Enhancers	Placenta Amnion	Placenta Amnion
6	chr9:11258200-11258800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:11258200-11258800	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr9:11258400-11259000	Enhancers	Fetal Heart	heart
9	chr9:11258800-11259800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr9:11259200-11260200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr9:11259400-11259800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr9:11259800-11260000	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr9:11268800-11269600	ZNF genes & repeats	Adipose Nuclei	Adipose
14	chr9:11280400-11281000	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr9:11280600-11281000	Enhancers	Fetal Brain Female	brain
16	chr9:11280800-11281200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:11295400-11297000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:11296400-11296600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:11296600-11300800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr9:11297000-11297400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:11300800-11301000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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