Variant report

Variant	nsv526787
Chromosome Location	chr9:17436801-17440278
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SH3GL2-1	chr9:17435732-17437445	NONHSAT130302

Extended variants
information (count: 143 )
Associated
traits (count: 85 )

Variant overlapped rSNPs/rCNVs (count:143 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7870334	chr9:17436801-17436802	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs543877103	chr9:17436815-17436816	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs192462144	chr9:17436824-17436825	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs182373563	chr9:17436854-17436855	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs564789896	chr9:17436898-17436899	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs116881602	chr9:17436903-17436904	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs540201497	chr9:17436910-17436911	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs561378024	chr9:17436933-17436934	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs528921587	chr9:17436939-17436940	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs16935636	chr9:17436950-17436951	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs75335729	chr9:17436967-17436968	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs187869197	chr9:17436980-17436981	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs146632346	chr9:17437006-17437007	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs551335133	chr9:17437021-17437022	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs560042690	chr9:17437054-17437055	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs530427246	chr9:17437061-17437062	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs140203587	chr9:17437113-17437114	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs527625672	chr9:17437139-17437140	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs192608710	chr9:17437183-17437184	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs568491020	chr9:17437194-17437195	Weak transcription ZNF genes & repeats Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs535907222	chr9:17437236-17437237	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs372768241	chr9:17437269-17437270	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs114445080	chr9:17437285-17437286	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs540017657	chr9:17437312-17437313	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs558095618	chr9:17437313-17437314	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs13297697	chr9:17437321-17437322	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs548670231	chr9:17437460-17437461	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs573465102	chr9:17437463-17437464	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs540584045	chr9:17437472-17437473	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs377372960	chr9:17437482-17437483	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs62559050	chr9:17437483-17437484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs115882762	chr9:17437484-17437485	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs573305182	chr9:17437493-17437494	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs143797105	chr9:17437504-17437505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs567276579	chr9:17437523-17437524	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs550930670	chr9:17437547-17437548	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs114371978	chr9:17437548-17437549	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs559155987	chr9:17437562-17437563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs369185370	chr9:17437669-17437670	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs184045971	chr9:17437695-17437696	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs151301312	chr9:17437696-17437697	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs187143285	chr9:17437697-17437698	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs549834474	chr9:17437699-17437700	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs1372705	chr9:17437735-17437736	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs140477753	chr9:17437752-17437753	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs553558552	chr9:17437753-17437754	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs529298401	chr9:17437790-17437791	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs150433419	chr9:17437855-17437856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs551039648	chr9:17437883-17437884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs145167718	chr9:17437894-17437895	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:85)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
abnormal development	18461090	CNVD
Oral squamous cell carcinoma	17134496	CNVD
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
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
Pleomorphic xanthoastrocytoma	20730472	CNVD
microdeletion syndrome	16199537	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Cancer	20164919	CNVD
Chronic myeloid leukemia	21384125	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
Oral cancer	21386901	CNVD
lymphocytic leukemia	21291569	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21858162	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
low-grade B-cell lymphoma tumor	18367492	CNVD
Myelofibrosis	22110671	CNVD
Glycine encephalopathy	21572526	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Non-small cell lung cancer	19010865	CNVD
Myoepithelioma	18604193	CNVD
Breast cancer	22522925	CNVD
Autism	20858261	CNVD
Epilepsy	20858261	CNVD
Mental retardation	20858261	CNVD
Breast cancer	21364760	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17368400-17457800	Weak transcription	Pancreas	Pancrea
2	chr9:17396200-17440000	Weak transcription	Adipose Nuclei	Adipose
3	chr9:17408000-17437200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:17411800-17439800	Weak transcription	Left Ventricle	heart
5	chr9:17411800-17481000	Weak transcription	Aorta	Aorta
6	chr9:17412200-17440200	Weak transcription	Fetal Stomach	stomach
7	chr9:17412200-17443600	Weak transcription	Ovary	ovary
8	chr9:17425400-17449600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:17426400-17466800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr9:17428600-17440200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr9:17431000-17453400	Weak transcription	Fetal Lung	lung
12	chr9:17434000-17437200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:17434000-17453600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr9:17434000-17453600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:17435400-17437000	Weak transcription	Gastric	stomach
16	chr9:17435800-17437400	Enhancers	Liver	Liver
17	chr9:17436000-17447200	Weak transcription	Lung	lung
18	chr9:17436000-17448600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:17436000-17448800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:17437000-17437200	ZNF genes & repeats	Gastric	stomach
21	chr9:17438600-17439200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr9:17439000-17439400	Enhancers	NHDF-Ad	bronchial
23	chr9:17439400-17466800	Weak transcription	NHDF-Ad	bronchial
24	chr9:17439800-17440400	ZNF genes & repeats	Left Ventricle	heart
25	chr9:17440000-17441200	ZNF genes & repeats	Adipose Nuclei	Adipose
26	chr9:17440200-17440600	ZNF genes & repeats	Fetal Stomach	stomach
27	chr9:17440200-17441200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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