Variant report

Variant	nsv613891
Chromosome Location	chr9:25253996-25301050
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:25261310..25262090-chr9:25716255..25716920,2	MCF-7	breast:
2	chr9:25292451..25293431-chr9:25673511..25674229,2	MCF-7	breast:
3	chr9:25267661..25270080-chr9:25677540..25679201,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TUSC1-1	chr9:25290336-25290489	NONHSAT130499
2	lnc-TUSC1-1	chr9:25288488-25288555	NONHSAT130499

Variant related genes	Relation type
ENSG00000198680	chromatin interactions

Extended variants
information (count: 1131 )
Associated
traits (count: 146 )

Variant overlapped rSNPs/rCNVs (count:1131 , 50 per page) page: 1 2 3 4 5 6 7 ... 23

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1372870	chr9:25253996-25253997	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs192876241	chr9:25254060-25254061	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs540779180	chr9:25254125-25254126	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs368190466	chr9:25254143-25254144	Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs560693744	chr9:25254145-25254146	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs574183036	chr9:25254150-25254151	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs144078368	chr9:25254230-25254231	Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs563270976	chr9:25254245-25254246	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs531980092	chr9:25254270-25254271	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs183111275	chr9:25254347-25254348	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs552061586	chr9:25254363-25254364	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs150700351	chr9:25254390-25254391	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs111400353	chr9:25254405-25254406	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs548001887	chr9:25254415-25254416	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs149836314	chr9:25254443-25254444	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs546065068	chr9:25254473-25254474	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs2383500	chr9:25254483-25254484	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs2383501	chr9:25254484-25254485	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs68165298	chr9:25254505-25254506	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs377498221	chr9:25254506-25254507	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs57761907	chr9:25254513-25254514	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs1662231	chr9:25254515-25254516	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs546209190	chr9:25254518-25254519	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs117920933	chr9:25254520-25254521	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs147264988	chr9:25254531-25254532	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs372022384	chr9:25254532-25254533	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs3059275	chr9:25254540-25254541	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs73642317	chr9:25254554-25254555	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs375688305	chr9:25254559-25254560	Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs538613543	chr9:25254573-25254574	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs139868507	chr9:25254588-25254589	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs565634808	chr9:25254664-25254665	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs115346117	chr9:25254674-25254675	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs143137901	chr9:25254685-25254686	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs116031231	chr9:25254690-25254691	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs543522468	chr9:25254725-25254726	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs556743044	chr9:25254742-25254743	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs576778983	chr9:25254832-25254833	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs372792671	chr9:25254909-25254910	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs73642318	chr9:25254912-25254913	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs375871266	chr9:25254937-25254938	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs75979480	chr9:25254958-25254959	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs73642319	chr9:25254965-25254966	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs541674479	chr9:25254972-25254973	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs561489766	chr9:25255001-25255002	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs374150293	chr9:25255016-25255017	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs550256548	chr9:25255017-25255018	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs184760958	chr9:25255020-25255021	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs532584248	chr9:25255024-25255025	Enhancers Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs552141076	chr9:25255043-25255044	Enhancers Active TSS	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
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
Lung cancer	21569311	CNVD
Pancreatic cancer	21811587	CNVD
early-passage human iPS cells	21368824	CNVD
Cancer	21215367	CNVD
Chordoma	21215367	CNVD
Bipolar disorder	19114987	CNVD
Non-small cell lung cancer	16651412	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:25253200-25254000	Enhancers	Fetal Brain Female	brain
2	chr9:25253400-25255800	Enhancers	Fetal Brain Male	brain
3	chr9:25254000-25254600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr9:25255000-25255400	Active TSS	HSMM	muscle
5	chr9:25259000-25260200	Enhancers	Fetal Kidney	kidney
6	chr9:25260200-25265000	Weak transcription	Fetal Kidney	kidney
7	chr9:25265000-25268000	Active TSS	Fetal Kidney	kidney
8	chr9:25266800-25267200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
9	chr9:25283600-25283800	Enhancers	Fetal Lung	lung
10	chr9:25283800-25284600	Weak transcription	Fetal Lung	lung
11	chr9:25284600-25285400	Enhancers	Fetal Lung	lung
12	chr9:25286600-25288200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr9:25287800-25288200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr9:25288000-25288200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr9:25289200-25291200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:25291800-25292000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr9:25292000-25292400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr9:25292400-25295600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:25295400-25296200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr9:25295600-25296000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:25295600-25296000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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