Variant report

Variant	nsv969695
Chromosome Location	chr9:99924101-99925101
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTSL2-5	chr9:99924037-99924230	NONHSAT133483
2	lnc-CTSL2-4	chr9:99924037-99924248	ENSG00000159712.9
3	lnc-CTSL2-4	chr9:99924847-99925128	ENSG00000159712.9

Extended variants
information (count: 33 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs544025075	chr9:99924249-99924250	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs201020295	chr9:99924281-99924282	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs189070201	chr9:99924288-99924289	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs528683647	chr9:99924293-99924294	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs533059644	chr9:99924329-99924330	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs139727316	chr9:99924401-99924402	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs142848085	chr9:99924404-99924405	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs202101061	chr9:99924413-99924414	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs574167187	chr9:99924484-99924485	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs112204200	chr9:99924531-99924532	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs527313186	chr9:99924585-99924586	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs3953686	chr9:99924604-99924605	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs568783028	chr9:99924643-99924644	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs200177009	chr9:99924709-99924710	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs139995622	chr9:99924731-99924732	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs190625688	chr9:99924741-99924742	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs116864422	chr9:99924745-99924746	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs71500000	chr9:99924761-99924762	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs569212138	chr9:99924795-99924796	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs534788542	chr9:99924846-99924847	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs377567850	chr9:99924847-99924848	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs202121803	chr9:99924880-99924881	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs182919029	chr9:99924905-99924906	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs111380843	chr9:99924957-99924958	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs113529711	chr9:99924982-99924983	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs558015949	chr9:99924991-99924992	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs566843054	chr9:99924996-99924997	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs12555636	chr9:99925034-99925035	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs140017077	chr9:99925039-99925040	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs573603404	chr9:99925057-99925058	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs543964540	chr9:99925077-99925078	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs368920821	chr9:99925096-99925097	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs187685296	chr9:99925101-99925102	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:73)

Disease	PMID	Source
Chordoma	18071362	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
Renal cell carcinoma	18592004	CNVD
Developmental delay	19490664	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pleomorphic xanthoastrocytoma	20730472	CNVD
Medulloblastoma	21979893	CNVD
microdeletion syndrome	16199537	CNVD
Ovarian cancer	21720365	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20164919	CNVD
Urothelial carcinoma	21177765	CNVD
Renal cell carcinoma	21668985	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Cancer	16751803	CNVD
Myelofibrosis	22110671	CNVD
lymphocytic leukemia	21291569	CNVD
Leukemia	17361228	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Glioblastoma	16823260	CNVD
Leukemia	18688285	CNVD
Non-small cell lung cancer	21044232	CNVD
Brain cancer	20823417	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Astrocytoma	17387387	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Renal cell carcinoma	19461508	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Heart disease	21282601	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute myeloid leukemia	21251322	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	17603634	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral cancer	21386901	CNVD
Bipolar disorder	18458673	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Wilms tumour	21544195	CNVD
Prostate cancer	18632612	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Biliary cancer	19435499	CNVD
small cell lung cancer	20016488	CNVD
Intracranial aneurysm	16715129	CNVD
Cardiac fibroma	18329553	CNVD
Breast cancer	17133270	CNVD
Basal cell nevus syndrome	21572526	CNVD
Mental retardation	19951919	CNVD
Retinoblastoma	22278416	CNVD
9q22.3 microdeletion syndrome	22283845	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
overgrowth syndrome	16570072	CNVD
Neurodevelopmental disorder	22521361	CNVD
Nicotine dependence	17160897	CNVD
Mantle cell lymphoma	19029149	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99911600-99957600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:99913000-99924400	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr9:99913200-99924200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr9:99913400-99924600	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr9:99913400-99930800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr9:99913600-99924200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
7	chr9:99913600-99930800	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:99918000-99946800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr9:99921400-99948800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr9:99922000-99937800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr9:99922800-99926200	Weak transcription	Dnd41	blood
12	chr9:99923600-99932200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:99923600-99938000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:99923800-99927000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr9:99923800-99936200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr9:99924200-99925800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:99924200-99926600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:99924400-99926000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr9:99924600-99926000	Weak transcription	HUES48 Cell Line	embryonic stem cell

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