Variant report

Variant	esv3341168
Chromosome Location	chr4:21455654-21460052
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR125-6	chr4:21454062-21463909	ucscGeneNc_uc003gqj_1

Extended variants
information (count: 181 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:181 , 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	rs187738578	chr4:21455674-21455675	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
2	rs139228447	chr4:21455675-21455676	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
3	rs73105834	chr4:21455709-21455710	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs79927079	chr4:21455716-21455717	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs537295014	chr4:21455758-21455759	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs192906746	chr4:21455759-21455760	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs568482982	chr4:21455765-21455766	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs184188622	chr4:21455774-21455775	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs554270543	chr4:21455800-21455801	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
10	rs13128830	chr4:21455808-21455809	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs572301308	chr4:21455809-21455810	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs527258736	chr4:21455814-21455815	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs539662942	chr4:21455815-21455816	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs11934595	chr4:21455835-21455836	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs576335201	chr4:21455838-21455839	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs542520368	chr4:21455844-21455845	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs139983167	chr4:21455854-21455855	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs13129400	chr4:21455861-21455862	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs377602266	chr4:21455865-21455866	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs1460485	chr4:21455877-21455878	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs143552824	chr4:21455888-21455889	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
22	rs533029806	chr4:21455920-21455921	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs76495396	chr4:21455986-21455987	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs563432150	chr4:21455990-21455991	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs1460486	chr4:21455993-21455994	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs549307010	chr4:21456017-21456018	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs358573	chr4:21456023-21456024	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs77811473	chr4:21456030-21456031	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs547441908	chr4:21456048-21456049	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs146797848	chr4:21456065-21456066	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs73249590	chr4:21456067-21456068	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
32	rs557942017	chr4:21456169-21456170	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
33	rs532816742	chr4:21456224-21456225	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs537223535	chr4:21456244-21456245	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs556057120	chr4:21456253-21456254	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs12510093	chr4:21456256-21456257	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
37	rs541041701	chr4:21456281-21456282	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
38	rs73105836	chr4:21456386-21456387	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs549719349	chr4:21456397-21456398	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs188913801	chr4:21456426-21456427	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs181654041	chr4:21456496-21456497	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs545165269	chr4:21456500-21456501	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
43	rs563370148	chr4:21456547-21456548	Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
44	rs358572	chr4:21456567-21456568	Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs368071825	chr4:21456615-21456616	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
46	rs532027470	chr4:21456620-21456621	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
47	rs10025716	chr4:21456622-21456623	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs76024853	chr4:21456630-21456631	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
49	rs142895913	chr4:21456633-21456634	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
50	rs531629222	chr4:21456674-21456675	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
Oral squamous cell carcinoma	17134496	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21858162	CNVD
small cell lung cancer	20016488	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Breast cancer	17133270	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	16608533	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Olfactory neuroblastoma	18408657	CNVD
Burkitt''s lymphoma	20823134	CNVD
Burkitt''s lymphoma	19759907	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	16774939	CNVD
Breast cancer	22522925	CNVD
Breast cancer	22737080	CNVD
Pancreatic cancer	17952125	CNVD
Cancer	22183965	CNVD
Gastric cancer	16891809	CNVD

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21448400-21465600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr4:21452200-21456200	Enhancers	NHEK	skin
3	chr4:21452400-21456200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:21453400-21455800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:21454000-21455800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:21455800-21456000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:21456600-21456800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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