Variant report

Variant	esv3376072
Chromosome Location	chr9:99899231-99905329
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTSL2-6	chr9:99901930-99902236	NONHSAT133476

Extended variants
information (count: 200 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:200 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4743059	chr9:99899313-99899314	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs537445720	chr9:99899344-99899345	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs539260094	chr9:99899414-99899415	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs200726288	chr9:99899437-99899438	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs542675717	chr9:99899438-99899439	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs145800307	chr9:99899439-99899440	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs551523861	chr9:99899440-99899441	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs34533733	chr9:99899463-99899464	Weak transcription Strong transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs190471522	chr9:99899549-99899550	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs554568325	chr9:99899562-99899563	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs183087550	chr9:99899566-99899567	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs57932357	chr9:99899568-99899569	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs543363944	chr9:99899614-99899615	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs565226167	chr9:99899670-99899671	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs532205713	chr9:99899750-99899751	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs541248738	chr9:99899756-99899757	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs144373763	chr9:99899769-99899770	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs567656077	chr9:99899830-99899831	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs548179444	chr9:99899835-99899836	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs118125845	chr9:99899869-99899870	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs535388135	chr9:99899879-99899880	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs550196179	chr9:99899882-99899883	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs571952133	chr9:99899905-99899906	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs541720328	chr9:99899935-99899936	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs554376490	chr9:99899939-99899940	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs370545616	chr9:99900048-99900049	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs374888694	chr9:99900055-99900056	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs187780950	chr9:99900100-99900101	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs192442004	chr9:99900360-99900361	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs554504893	chr9:99900429-99900430	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs576020174	chr9:99900435-99900436	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs543846525	chr9:99900473-99900474	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs71499988	chr9:99900498-99900499	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs558551510	chr9:99900512-99900513	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs71499989	chr9:99900517-99900518	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs71499990	chr9:99900533-99900534	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs71499991	chr9:99900540-99900541	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs58111876	chr9:99900549-99900550	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs540833840	chr9:99900555-99900556	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs559610178	chr9:99900578-99900579	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs151200999	chr9:99900579-99900580	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs541954338	chr9:99900583-99900584	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs563412209	chr9:99900623-99900624	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs530418653	chr9:99900656-99900657	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs73549990	chr9:99900668-99900669	Strong transcription Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs142679396	chr9:99900685-99900686	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs377122680	chr9:99900694-99900695	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs565420961	chr9:99900705-99900706	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs545550964	chr9:99900734-99900735	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs73654657	chr9:99900754-99900755	Strong transcription Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:74)

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
Breast cancer	22522925	CNVD

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:99889400-99908200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:99894400-99900400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:99894600-99901400	Weak transcription	Pancreas	Pancrea
4	chr9:99895600-99901000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:99895800-99900800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr9:99895800-99902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:99897200-99899800	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr9:99897800-99902600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:99897800-99907600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:99898000-99902200	Strong transcription	H9 Cell Line	embryonic stem cell
11	chr9:99898400-99908600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr9:99898800-99899400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
13	chr9:99898800-99908000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr9:99899000-99900200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:99899400-99899600	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr9:99899600-99900400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:99899800-99900600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:99900200-99902400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr9:99900400-99901000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr9:99900400-99901600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:99900400-99902800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:99900600-99908800	Strong transcription	H1 Cell Line	embryonic stem cell
23	chr9:99900800-99901000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr9:99901000-99901400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:99901000-99901600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr9:99901000-99921000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr9:99901400-99901600	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:99901400-99901600	Enhancers	Pancreas	Pancrea
29	chr9:99901600-99904400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr9:99901600-99907200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr9:99901600-99907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:99901600-99907600	Weak transcription	Pancreas	Pancrea
33	chr9:99902200-99908800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr9:99902400-99904200	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:99902600-99903400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr9:99902800-99904600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr9:99903200-99904600	Enhancers	HepG2	liver
38	chr9:99903400-99908200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:99904200-99908200	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr9:99904400-99904600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr9:99904600-99904800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:99904600-99907600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
43	chr9:99904600-99909400	Weak transcription	HepG2	liver
44	chr9:99904800-99905800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:99905000-99905400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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