Variant report

Variant	nsv1032945
Chromosome Location	chr9:24512538-24572818
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	CEBPB	chr9:24542908-24543131	HepG2	liver:	n/a	chr9:24542993-24543004
2	CEBPB	chr9:24562320-24562452	A549	lung:	n/a	n/a
3	CEBPB	chr9:24565572-24565772	A549	lung:	n/a	n/a
4	CEBPB	chr9:24556332-24556354	H1-hESC	embryonic stem cell:	n/a	n/a
5	CEBPB	chr9:24556226-24556465	HepG2	liver:	n/a	chr9:24556345-24556356
6	CTCF	chr9:24535287-24535360	Kidney_OC	kidney:	n/a	n/a
7	E2F4	chr9:24551652-24551844	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr9:24519573-24519904	MCF10A-Er-Src	breast:	n/a	chr9:24519736-24519743 chr9:24519735-24519744 chr9:24519734-24519743 chr9:24519735-24519743
9	FOS	chr9:24516577-24516760	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr9:24519598-24519904	MCF10A-Er-Src	breast:	n/a	chr9:24519736-24519743 chr9:24519735-24519744 chr9:24519734-24519743 chr9:24519735-24519743
11	FOS	chr9:24519580-24519902	MCF10A-Er-Src	breast:	n/a	chr9:24519736-24519743 chr9:24519735-24519744 chr9:24519734-24519743 chr9:24519735-24519743
12	FOS	chr9:24519572-24519886	MCF10A-Er-Src	breast:	n/a	chr9:24519736-24519743 chr9:24519735-24519744 chr9:24519734-24519743 chr9:24519735-24519743
13	FOS	chr9:24519517-24519764	HUVEC	blood vessel:	n/a	chr9:24519736-24519743 chr9:24519735-24519744 chr9:24519734-24519743 chr9:24519735-24519743
14	FOXA1	chr9:24552571-24552842	T-47D	breast:	n/a	chr9:24552747-24552762
15	GATA3	chr9:24552518-24552837	T-47D	breast:	n/a	n/a
16	GATA3	chr9:24512686-24513051	SK-N-SH	brain:	n/a	n/a
17	GATA3	chr9:24518810-24519003	SH-SY5Y	brain:	n/a	n/a
18	GATA3	chr9:24552520-24552785	T-47D	breast:	n/a	n/a
19	GATA3	chr9:24533058-24533642	SK-N-SH	brain:	n/a	n/a
20	IRF3	chr9:24550167-24550195	GM12878	blood:	n/a	n/a
21	JUND	chr9:24519647-24519737	H1-hESC	embryonic stem cell:	n/a	n/a
22	JUND	chr9:24519575-24519842	HepG2	liver:	n/a	chr9:24519736-24519743 chr9:24519735-24519744 chr9:24519734-24519743 chr9:24519733-24519744 chr9:24519735-24519743
23	MAFF	chr9:24518557-24518910	HepG2	liver:	n/a	chr9:24518722-24518740
24	MAFF	chr9:24570021-24570192	HepG2	liver:	n/a	chr9:24570084-24570102
25	MAFK	chr9:24526008-24526183	HepG2	liver:	n/a	chr9:24526085-24526101
26	MAFK	chr9:24538547-24538747	HepG2	liver:	n/a	n/a
27	MAFK	chr9:24518563-24518938	H1-hESC	embryonic stem cell:	n/a	chr9:24518724-24518739
28	MAFK	chr9:24518550-24518916	IMR90	lung:	n/a	chr9:24518724-24518739
29	MAFK	chr9:24569940-24570203	HepG2	liver:	n/a	chr9:24570085-24570100
30	MAFK	chr9:24562618-24562852	HepG2	liver:	n/a	n/a
31	MAFK	chr9:24569959-24570239	HepG2	liver:	n/a	chr9:24570085-24570100
32	MAFK	chr9:24518562-24518904	HepG2	liver:	n/a	chr9:24518724-24518739
33	MAFK	chr9:24518640-24518877	Hela-S3	cervix:	n/a	chr9:24518724-24518739
34	MAFK	chr9:24569988-24570124	H1-hESC	embryonic stem cell:	n/a	chr9:24570085-24570100
35	MAFK	chr9:24518551-24518919	HepG2	liver:	n/a	chr9:24518724-24518739
36	MAFK	chr9:24538553-24538753	IMR90	lung:	n/a	n/a
37	MAZ	chr9:24518084-24518113	HepG2	liver:	n/a	n/a
38	MYC	chr9:24534452-24534652	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr9:24513288-24513417	MCF10A-Er-Src	breast:	n/a	n/a
40	POLR2A	chr9:24515940-24516306	H1-neurons	neurons:	n/a	n/a
41	POLR2A	chr9:24527379-24527415	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr9:24522739-24522803	MCF10A-Er-Src	breast:	n/a	n/a
43	POLR2A	chr9:24526697-24526972	H1-neurons	neurons:	n/a	n/a
44	POLR2A	chr9:24518684-24518778	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr9:24569765-24569957	MCF10A-Er-Src	breast:	n/a	n/a
46	POLR2A	chr9:24569889-24570054	MCF10A-Er-Src	breast:	n/a	n/a
47	POLR2A	chr9:24570190-24570359	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr9:24556741-24556742	MCF10A-Er-Src	breast:	n/a	n/a
49	POLR2A	chr9:24519383-24519453	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr9:24550518-24550668	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DMRTA1-7	chr9:24545856-24546127	XLOC_007304
2	lnc-DMRTA1-7	chr9:24545996-24546127	ENSG00000269957.1
3	lnc-DMRTA1-7	chr9:24551961-24552127	ENSG00000269957.1
4	lnc-DMRTA1-7	chr9:24561754-24561848	XLOC_007304
5	lnc-DMRTA1-7	chr9:24545423-24545526	XLOC_007304
6	lnc-DMRTA1-7	chr9:24552919-24553237	ENSG00000269957.1
7	lnc-DMRTA1-7	chr9:24545422-24546127	XLOC_007304
8	lnc-DMRTA1-7	chr9:24561754-24561848	ENSG00000269957.1
9	lnc-DMRTA1-7	chr9:24551961-24552127	ENSG00000269957.1
10	lnc-DMRTA1-7	chr9:24551961-24552156	XLOC_007304
11	lnc-DMRTA1-7	chr9:24545856-24546127	XLOC_007304
12	lnc-DMRTA1-7	chr9:24561325-24561428	XLOC_007304
13	lnc-DMRTA1-7	chr9:24545400-24545526	XLOC_007304
14	lnc-DMRTA1-7	chr9:24561754-24561848	XLOC_007304
15	lnc-DMRTA1-7	chr9:24551961-24552127	XLOC_007304
16	lnc-DMRTA1-7	chr9:24545422-24546127	XLOC_007304
17	lnc-DMRTA1-7	chr9:24552919-24553082	XLOC_007304
18	lnc-DMRTA1-7	chr9:24545950-24546127	ENSG00000269957.1
19	lnc-DMRTA1-7	chr9:24561754-24561848	XLOC_007304

Variant related genes	Relation type
IZUMO3	TF binding region
ENSG00000269957	TF binding region
LEPROTL1	miRNA target sites
ZDHHC17	miRNA target sites
MAP3K3	miRNA target sites
FRS2	miRNA target sites

Extended variants
information (count: 364 )
Associated
traits (count: 146 )

Variant overlapped rSNPs/rCNVs (count:364 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs544700043	chr9:24520401-24520402	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs564286586	chr9:24520442-24520443	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs35082908	chr9:24520450-24520451	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs183988846	chr9:24520474-24520475	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs540526705	chr9:24520540-24520541	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs560150800	chr9:24520573-24520574	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs376167241	chr9:24520574-24520575	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs16908415	chr9:24520633-24520634	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs548616372	chr9:24520650-24520651	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs535743696	chr9:24520652-24520653	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs562124743	chr9:24520657-24520658	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs557339307	chr9:24520665-24520666	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs531340357	chr9:24520691-24520692	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs28528362	chr9:24520725-24520726	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs575533025	chr9:24520726-24520727	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs188637012	chr9:24520826-24520827	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs540430802	chr9:24520879-24520880	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs112723865	chr9:24520890-24520891	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs368666215	chr9:24520894-24520895	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs567097995	chr9:24520912-24520913	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs147269812	chr9:24520940-24520941	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs546305918	chr9:24520953-24520954	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs575673551	chr9:24520988-24520989	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs139932367	chr9:24520989-24520990	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs558233683	chr9:24521014-24521015	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs577781279	chr9:24521020-24521021	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs564237771	chr9:24521023-24521024	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs540097784	chr9:24521036-24521037	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs560294111	chr9:24521058-24521059	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs192248471	chr9:24521067-24521068	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs542499891	chr9:24521156-24521157	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs149405110	chr9:24521204-24521205	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs531180064	chr9:24521249-24521250	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs551065684	chr9:24521294-24521295	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs184379781	chr9:24521331-24521332	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs564082888	chr9:24521391-24521392	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs546906151	chr9:24521396-24521397	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs16908420	chr9:24522412-24522413	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs188722560	chr9:24522431-24522432	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs115501402	chr9:24522442-24522443	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs529801417	chr9:24522479-24522480	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs116643738	chr9:24522501-24522502	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs532080348	chr9:24522502-24522503	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs373707389	chr9:24522515-24522516	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs552018340	chr9:24522524-24522525	Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs565159189	chr9:24522533-24522534	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs150957710	chr9:24522534-24522535	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs547584995	chr9:24522535-24522536	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs186085879	chr9:24522556-24522557	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs536325895	chr9:24522582-24522583	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:146)

Disease	PMID	Source
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	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
Oral squamous cell carcinoma	17134496	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
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	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
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic myeloid leukemia	21384125	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Renal cell carcinoma	21668985	CNVD
Myelodysplastic syndrome	21251322	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	18803288	CNVD
Metanephric adenoma	20802469	CNVD
Developmental delay	21147756	CNVD
Pilocytic astrocytoma	18670637	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	22183965	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Non-small cell lung cancer	19010865	CNVD
Myoepithelioma	18604193	CNVD
Cancer	22183965	CNVD
Myelofibrosis	22110671	CNVD
Ewing''s sarcoma	22429812	CNVD
Neuroblastoma	21899760	CNVD
Glioblastoma multiforme	19435819	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Cutaneous T-cell lymphoma	21881587	CNVD
Glioblastoma multiforme	22291905	CNVD
Lung cancer	21911935	CNVD
Primary central nervous system lymphoma	21088137	CNVD
head and neck squamous cell carcinoma	21798897	CNVD
Cancer	21253487	CNVD
Glioblastoma multiforme	22286061	CNVD
Intracranial ependymoma	16609018	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Glioblastoma multiforme	21922591	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Urothelial cell carcinoma	18451213	CNVD
Glioma	17123091	CNVD
Mental retardation	17124404	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Acute lymphoblastic leukemia	18768390	CNVD
Leukemia	19602459	CNVD
Acute monocytic leukemia	16498392	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Leukemia	18688285	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Acute myeloid leukemia	19651601	CNVD
Coronary Disease	20032323	CNVD
Squamous cell cancer	20885788	CNVD
Hirschsprung''s Disease	21712996	CNVD
Cancer	21732550	CNVD
Gastric cancer	22539939	CNVD
Cancer	21183584	CNVD
T-cell lymphomas	19863542	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Metastatic melanoma	18483359	CNVD
Non-small cell lung cancer	20864512	CNVD
Cervical cancer	21062161	CNVD
Acute myeloid leukemia	16864856	CNVD
Glioblastoma	17090523	CNVD
Lung cancer	16773561	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Colorectal cancer	16774939	CNVD
Bladder cancer	19088036	CNVD
Colorectal cancer	16272173	CNVD
Melanoma	16977458	CNVD
Glioblastoma multiforme	17369134	CNVD
Chagasic megaesophagus	20163722	CNVD
Melanoma	19566914	CNVD
Squamous cell cancer	19047905	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung cancer	19525976	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Melanoma	17363583	CNVD
Glioblastoma multiforme	19115005	CNVD
Adenoid cystic carcinoma	18332873	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Acute myeloid leukemia	21251322	CNVD
Oral cancer	21386901	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21364760	CNVD
Esophageal adenocarcinoma	18519675	CNVD
early-passage human iPS cells	21368824	CNVD
Renal cell carcinoma	21215367	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Lung cancer	21569311	CNVD

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:24520400-24521400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr9:24522400-24522800	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr9:24542200-24542800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:24545200-24545600	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr9:24545200-24546200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:24546200-24547200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr9:24547400-24547600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:24552600-24553000	Enhancers	Fetal Kidney	kidney
9	chr9:24553000-24553200	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr9:24571600-24571800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr9:24571800-24572200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:24571800-24580000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:24572200-24572600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:24572200-24573200	Enhancers	Adipose Nuclei	Adipose
15	chr9:24572600-24573400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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