Variant report

Variant	nsv613329
Chromosome Location	chr9:9796116-9805134
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	E2F4	chr9:9796904-9797116	MCF10A-Er-Src	breast:	n/a	n/a
2	EP300	chr9:9798861-9798880	Hela-S3	cervix:	n/a	n/a
3	GATA3	chr9:9804049-9804244	SH-SY5Y	brain:	n/a	n/a
4	IRF1	chr9:9803600-9803610	K562	blood:	n/a	n/a
5	JUN	chr9:9796761-9797028	HepG2	liver:	n/a	chr9:9796897-9796910
6	JUND	chr9:9796725-9797083	HepG2	liver:	n/a	n/a
7	MAX	chr9:9800581-9800781	NB4	blood:	n/a	chr9:9800665-9800675
8	POLR2A	chr9:9804086-9804364	H1-neurons	neurons:	n/a	n/a
9	POLR2A	chr9:9804094-9804390	H1-neurons	neurons:	n/a	n/a
10	POLR2A	chr9:9804175-9804188	GM12878	blood:	n/a	n/a
11	POLR2A	chr9:9797634-9797646	A549	lung:	n/a	n/a
12	POLR2A	chr9:9798694-9798695	MCF10A-Er-Src	breast:	n/a	n/a
13	REST	chr9:9804107-9804495	H1-neurons	neurons:	n/a	n/a
14	REST	chr9:9803913-9804719	H1-neurons	neurons:	n/a	n/a
15	RFX5	chr9:9804151-9804169	K562	blood:	n/a	n/a
16	TCF7L2	chr9:9801345-9801886	HepG2	liver:	n/a	n/a
17	TEAD4	chr9:9800110-9800350	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM4C-10	chr9:9803717-9803784	ENSG00000230920
2	lnc-KDM4C-10	chr9:9800546-9800674	ENSG00000230920
3	lnc-KDM4C-10	chr9:9799423-9799608	ENSG00000230920

Variant related genes	Relation type
ENSG00000230920	TF binding region

Extended variants
information (count: 146 )
Associated
traits (count: 112 )

Variant overlapped rSNPs/rCNVs (count:146 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs538296221	chr9:9796726-9796727	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs143204881	chr9:9796735-9796736	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs568968322	chr9:9796761-9796762	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs556631328	chr9:9796791-9796792	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs138820666	chr9:9796794-9796795	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs554772985	chr9:9796795-9796796	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs142841324	chr9:9796813-9796814	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs147260766	chr9:9796821-9796822	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs554156255	chr9:9796823-9796824	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs567071963	chr9:9796889-9796890	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs535821722	chr9:9796892-9796893	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs76553457	chr9:9796898-9796899	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs140830787	chr9:9796993-9796994	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs377278419	chr9:9797004-9797005	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs141398171	chr9:9797011-9797012	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs542022066	chr9:9797015-9797016	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs10977986	chr9:9797029-9797030	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs561956096	chr9:9797041-9797042	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs10977987	chr9:9797049-9797050	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs527934405	chr9:9797063-9797064	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs547685452	chr9:9797098-9797099	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs547341219	chr9:9797107-9797108	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs141214159	chr9:9797112-9797113	Inactive region	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs189768587	chr9:9799417-9799418	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs371250465	chr9:9799424-9799425	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs567796661	chr9:9799438-9799439	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs113460807	chr9:9799439-9799440	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs181604476	chr9:9799451-9799452	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs561165813	chr9:9799461-9799462	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs2296171	chr9:9799476-9799477	Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs146153795	chr9:9799489-9799490	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs546682230	chr9:9799520-9799521	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs567135849	chr9:9799532-9799533	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs548752046	chr9:9799548-9799549	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs369292440	chr9:9799565-9799566	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs566486736	chr9:9799580-9799581	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs556915974	chr9:9799581-9799582	Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs571154182	chr9:9799631-9799632	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs537082520	chr9:9799671-9799672	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs556615965	chr9:9799674-9799675	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs573423242	chr9:9799682-9799683	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs542379316	chr9:9799704-9799705	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs185897458	chr9:9799729-9799730	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs573044380	chr9:9799732-9799733	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs12377440	chr9:9799740-9799741	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs538625168	chr9:9799751-9799752	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs74687645	chr9:9799760-9799761	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs569139599	chr9:9799772-9799773	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs142786251	chr9:9799773-9799774	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs567083640	chr9:9799793-9799794	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:112)

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
XY gonadal dysgenesis	20685758	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
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Lung cancer	20668451	CNVD
Schizophrenia	20838587	CNVD
Glioblastoma	18772890	CNVD
Glioblastoma multiforme	21390271	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	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
Lung adenocarcinoma	17982442	CNVD
Breast cancer	21611746	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:9799400-9799800	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr9:9799400-9799800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:9799400-9800800	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr9:9799400-9801400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr9:9799600-9799800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr9:9799800-9800600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:9799800-9800800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:9799800-9801000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr9:9800600-9801600	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr9:9800800-9801600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr9:9801000-9801600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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