Variant report

Variant	esv3364035
Chromosome Location	chr2:54673580-54676508
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54668438..54670233-chr2:54675850..54678657,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPTBN1-2	chr2:54673813-54673837	XLOC_001475
2	lnc-SPTBN1-2	chr2:54673812-54673837	NONHSAT070736

Extended variants
information (count: 120 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:120 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs375748080	chr2:54673595-54673596	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs563445442	chr2:54673599-54673600	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs576754993	chr2:54673601-54673602	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs539822387	chr2:54673604-54673605	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs187929726	chr2:54673679-54673680	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs138916523	chr2:54673705-54673706	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs547545322	chr2:54673764-54673765	Weak transcription Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs566929824	chr2:54673801-54673802	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs373704758	chr2:54673867-54673868	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs192455680	chr2:54673889-54673890	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs548487244	chr2:54673931-54673932	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs562124304	chr2:54673941-54673942	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs531159981	chr2:54673996-54673997	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs550791443	chr2:54674035-54674036	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs570962904	chr2:54674040-54674041	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs184364754	chr2:54674046-54674047	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs190566963	chr2:54674083-54674084	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs566891379	chr2:54674117-54674118	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs12617509	chr2:54674121-54674122	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs181892288	chr2:54674140-54674141	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs149481886	chr2:54674153-54674154	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs537293428	chr2:54674162-54674163	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs556888310	chr2:54674169-54674170	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs576481616	chr2:54674207-54674208	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs184560970	chr2:54674223-54674224	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs545514892	chr2:54674239-54674240	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs145957259	chr2:54674243-54674244	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs111473900	chr2:54674269-54674270	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs572539755	chr2:54674279-54674280	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs116216076	chr2:54674280-54674281	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs138594392	chr2:54674351-54674352	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs531000141	chr2:54674353-54674354	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs386646256	chr2:54674362-54674363	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs76655100	chr2:54674363-54674364	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs533433785	chr2:54674453-54674454	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs181338094	chr2:54674499-54674500	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs141503058	chr2:54674506-54674507	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs535898896	chr2:54674510-54674511	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs74653826	chr2:54674554-54674555	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs568305101	chr2:54674599-54674600	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs146188084	chr2:54674638-54674639	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs557090415	chr2:54674643-54674644	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs570327576	chr2:54674661-54674662	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs113764417	chr2:54674683-54674684	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs186503189	chr2:54674712-54674713	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs4671932	chr2:54674715-54674716	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs142716568	chr2:54674730-54674731	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs576623647	chr2:54674747-54674748	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs150560725	chr2:54674765-54674766	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs189769081	chr2:54674772-54674773	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21147756	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54668600-54682000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr2:54673200-54673600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr2:54673200-54673800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:54673200-54674000	Enhancers	Brain Angular Gyrus	brain
5	chr2:54673200-54674000	Enhancers	Brain Substantia Nigra	brain
6	chr2:54673200-54674000	Enhancers	Fetal Heart	heart
7	chr2:54673200-54674200	Enhancers	Brain Hippocampus Middle	brain
8	chr2:54673200-54674600	Enhancers	Brain Inferior Temporal Lobe	brain
9	chr2:54673400-54673600	Enhancers	Left Ventricle	heart
10	chr2:54673400-54673600	Enhancers	Lung	lung
11	chr2:54673400-54673800	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr2:54673400-54674000	Enhancers	Brain Anterior Caudate	brain
13	chr2:54673400-54674000	Enhancers	Fetal Muscle Leg	muscle
14	chr2:54673400-54674000	Enhancers	Fetal Thymus	thymus
15	chr2:54673400-54674000	Enhancers	Right Atrium	heart
16	chr2:54673400-54674000	Flanking Active TSS	HepG2	liver
17	chr2:54673400-54674200	Enhancers	Brain Cingulate Gyrus	brain
18	chr2:54673400-54674400	Enhancers	HSMMtube	muscle
19	chr2:54673600-54673800	Weak transcription	Lung	lung
20	chr2:54673800-54674200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr2:54674000-54675400	Enhancers	HepG2	liver
22	chr2:54674000-54678000	Weak transcription	Brain Angular Gyrus	brain
23	chr2:54674000-54678200	Weak transcription	Brain Anterior Caudate	brain
24	chr2:54674200-54678000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:54674200-54681400	Weak transcription	Brain Hippocampus Middle	brain
26	chr2:54674400-54674800	Weak transcription	HSMMtube	muscle
27	chr2:54674600-54678200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:54674800-54675400	Enhancers	HSMMtube	muscle
29	chr2:54675400-54681000	Weak transcription	HepG2	liver
30	chr2:54675400-54681800	Weak transcription	HSMMtube	muscle
31	chr2:54676000-54676200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:54676200-54677200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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