Variant report

Variant	nsv969696
Chromosome Location	chr9:99928429-99933157
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTSL2-4	chr9:99932889-99933018	ENSG00000159712.9

Extended variants
information (count: 159 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:159 , 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	rs530006447	chr9:99928447-99928448	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs60362425	chr9:99928521-99928522	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs530930217	chr9:99928568-99928569	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs549317260	chr9:99928573-99928574	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs182021599	chr9:99928589-99928590	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs569727711	chr9:99928665-99928666	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs148831439	chr9:99928697-99928698	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs57733770	chr9:99928778-99928779	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs57476701	chr9:99928779-99928780	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs534276059	chr9:99928810-99928811	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs552560768	chr9:99928822-99928823	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs184033133	chr9:99928868-99928869	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs537017060	chr9:99928877-99928878	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs551764042	chr9:99928946-99928947	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs536547663	chr9:99928955-99928956	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs555273061	chr9:99928980-99928981	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs112754699	chr9:99929026-99929027	Weak transcription Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs576545533	chr9:99929091-99929092	Weak transcription Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs186615554	chr9:99929116-99929117	Weak transcription Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs570163741	chr9:99929219-99929220	Weak transcription Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs10980912	chr9:99929223-99929224	Weak transcription Strong transcription Flanking Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs558754123	chr9:99929233-99929234	Weak transcription Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs189887837	chr9:99929330-99929331	Weak transcription Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs373114477	chr9:99929354-99929355	Weak transcription Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs535372958	chr9:99929385-99929386	Weak transcription Strong transcription Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs541577927	chr9:99929428-99929429	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs113347080	chr9:99929482-99929483	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs112223332	chr9:99929523-99929524	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs559779104	chr9:99929550-99929551	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs11792723	chr9:99929605-99929606	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs200998397	chr9:99929610-99929611	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs542127847	chr9:99929619-99929620	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs571843594	chr9:99929639-99929640	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs202120818	chr9:99929647-99929648	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs11795173	chr9:99929677-99929678	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs11792736	chr9:99929690-99929691	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs4452918	chr9:99929723-99929724	Weak transcription Strong transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs563987201	chr9:99929735-99929736	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs528166100	chr9:99929765-99929766	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs546337270	chr9:99929773-99929774	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs536660722	chr9:99929775-99929776	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs567697171	chr9:99929881-99929882	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs535115914	chr9:99929905-99929906	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs548567040	chr9:99929926-99929927	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs570348741	chr9:99929942-99929943	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs537207175	chr9:99929956-99929957	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs141449259	chr9:99930018-99930019	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs12338046	chr9:99930034-99930035	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs565590500	chr9:99930047-99930048	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs113136363	chr9:99930098-99930099	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	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:47 , 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	chr9:99913400-99930800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr9:99913600-99930800	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:99918000-99946800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:99921400-99948800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr9:99922000-99937800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:99923600-99932200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr9:99923600-99938000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr9:99923800-99936200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:99925800-99930200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr9:99926000-99933000	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr9:99926000-99933000	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr9:99926200-99929000	Enhancers	Dnd41	blood
14	chr9:99927400-99930200	Weak transcription	K562	blood
15	chr9:99927400-99934400	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr9:99927600-99929000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr9:99929000-99929400	Flanking Active TSS	Dnd41	blood
18	chr9:99929000-99930800	Enhancers	GM12878-XiMat	blood
19	chr9:99929000-99931400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr9:99929400-99932000	Enhancers	Dnd41	blood
21	chr9:99930200-99930400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:99930200-99930400	Enhancers	K562	blood
23	chr9:99930200-99930600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:99930200-99930600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr9:99930200-99930800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:99930200-99930800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr9:99930200-99930800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:99930200-99931000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:99930400-99930800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr9:99930400-99930800	Weak transcription	K562	blood
31	chr9:99930400-99931000	Enhancers	NHEK	skin
32	chr9:99930600-99931000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr9:99930600-99931000	Enhancers	HMEC	breast
34	chr9:99930800-99931200	Enhancers	K562	blood
35	chr9:99930800-99931800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr9:99930800-99932200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
37	chr9:99931000-99931800	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr9:99931400-99936200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr9:99931800-99932200	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr9:99931800-99932800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr9:99932200-99932800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr9:99932200-99933400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:99932200-99936600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr9:99932800-99936400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr9:99932800-99947200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr9:99933000-99934400	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:99933000-99936000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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