Variant report

Variant	esv3500612
Chromosome Location	chr9:99901107-99904336
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: 108 )
Associated
traits (count: 74 )

Variant overlapped rSNPs/rCNVs (count:108 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs557592501	chr9:99901125-99901126	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs575683127	chr9:99901141-99901142	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs542091121	chr9:99901147-99901148	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs567123783	chr9:99901156-99901157	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs563348019	chr9:99901178-99901179	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs534494494	chr9:99901205-99901206	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs7033860	chr9:99901217-99901218	Strong transcription Weak transcription Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs545445318	chr9:99901255-99901256	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs144888495	chr9:99901301-99901302	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs532657259	chr9:99901325-99901326	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs187823227	chr9:99901330-99901331	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs149045237	chr9:99901344-99901345	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs114819714	chr9:99901388-99901389	Strong transcription Weak transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs530211155	chr9:99901450-99901451	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs145152536	chr9:99901456-99901457	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs570019871	chr9:99901465-99901466	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs139035942	chr9:99901488-99901489	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs552242539	chr9:99901510-99901511	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs11787964	chr9:99901566-99901567	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs115976722	chr9:99901577-99901578	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs192502511	chr9:99901585-99901586	Strong transcription Weak transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs114926801	chr9:99901618-99901619	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs574811940	chr9:99901666-99901667	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs535627478	chr9:99901695-99901696	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs557131660	chr9:99901705-99901706	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs184703767	chr9:99901896-99901897	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs368640088	chr9:99902010-99902011	Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs202142751	chr9:99902031-99902032	Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs188589217	chr9:99902039-99902040	Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs56058615	chr9:99902045-99902046	Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs114275218	chr9:99902061-99902062	Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs191956234	chr9:99902086-99902087	Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs530343347	chr9:99902096-99902097	Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs541991893	chr9:99902109-99902110	Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs563910277	chr9:99902125-99902126	Strong transcription Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs569978772	chr9:99902278-99902279	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs200090729	chr9:99902282-99902283	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs376952444	chr9:99902284-99902285	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs140726711	chr9:99902297-99902298	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs145768589	chr9:99902308-99902309	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs570902733	chr9:99902325-99902326	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs148142190	chr9:99902354-99902355	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs547049055	chr9:99902378-99902379	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs141886435	chr9:99902382-99902383	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs150652688	chr9:99902387-99902388	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs556841044	chr9:99902399-99902400	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs569027435	chr9:99902466-99902467	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs184420179	chr9:99902505-99902506	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs557815017	chr9:99902519-99902520	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs10817163	chr9:99902524-99902525	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance

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:28 , 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	chr9:99894600-99901400	Weak transcription	Pancreas	Pancrea
3	chr9:99895800-99902000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr9:99897800-99902600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr9:99897800-99907600	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr9:99898000-99902200	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr9:99898400-99908600	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:99898800-99908000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr9:99900200-99902400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:99900400-99901600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
11	chr9:99900400-99902800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
12	chr9:99900600-99908800	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr9:99901000-99901400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr9:99901000-99901600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr9:99901000-99921000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr9:99901400-99901600	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr9:99901400-99901600	Enhancers	Pancreas	Pancrea
18	chr9:99901600-99904400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:99901600-99907200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:99901600-99907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr9:99901600-99907600	Weak transcription	Pancreas	Pancrea
22	chr9:99902200-99908800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr9:99902400-99904200	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr9:99902600-99903400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:99902800-99904600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:99903200-99904600	Enhancers	HepG2	liver
27	chr9:99903400-99908200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr9:99904200-99908200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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