Variant report

Variant	esv2373290
Chromosome Location	chr2:96554410-96560234
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPAT2-5	chr2:96557405-96557647	ucscGeneNc_uc002swd_1
2	lnc-GPAT2-5	chr2:96559198-96559313	ucscGeneNc_uc002swd_1

Extended variants
information (count: 287 )
Associated
traits (count: 49 )

Variant overlapped rSNPs/rCNVs (count:287 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs532767436	chr2:96554411-96554412	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs201437130	chr2:96554448-96554449	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs558065549	chr2:96554452-96554453	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs199913234	chr2:96554487-96554488	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs563253002	chr2:96554494-96554495	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs201013185	chr2:96554556-96554557	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs202096438	chr2:96554571-96554572	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs200432088	chr2:96554577-96554578	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs569865943	chr2:96554607-96554608	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs141803341	chr2:96554609-96554610	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs190639783	chr2:96554690-96554691	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs534648849	chr2:96554700-96554701	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs376247594	chr2:96554739-96554740	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs571650349	chr2:96554822-96554823	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs113470069	chr2:96554827-96554828	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs11689832	chr2:96554851-96554852	Strong transcription Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs113228551	chr2:96554852-96554853	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs557299040	chr2:96554869-96554870	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs567767251	chr2:96554926-96554927	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs536706684	chr2:96554934-96554935	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs553645877	chr2:96554948-96554949	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs573470671	chr2:96555046-96555047	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs545710145	chr2:96555100-96555101	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs182563095	chr2:96555111-96555112	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs575857555	chr2:96555124-96555125	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs543072094	chr2:96555135-96555136	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs563248183	chr2:96555160-96555161	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs528964609	chr2:96555183-96555184	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs542303874	chr2:96555203-96555204	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs35351605	chr2:96555332-96555333	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs559151889	chr2:96555355-96555356	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs35278032	chr2:96555357-96555358	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs147225281	chr2:96555372-96555373	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs202097345	chr2:96555444-96555445	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs571476609	chr2:96555463-96555464	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs200418948	chr2:96555472-96555473	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs550709915	chr2:96555473-96555474	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs570240295	chr2:96555484-96555485	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs188323821	chr2:96555514-96555515	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs113160495	chr2:96555521-96555522	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs12471925	chr2:96555522-96555523	Strong transcription Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs542382911	chr2:96555552-96555553	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs17410885	chr2:96555578-96555579	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs567101290	chr2:96555601-96555602	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs537213116	chr2:96555635-96555636	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs199941227	chr2:96555640-96555641	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs538871609	chr2:96555643-96555644	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs201993112	chr2:96555655-96555656	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs559079805	chr2:96555660-96555661	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs372755684	chr2:96555721-96555722	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:49)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	17483303	CNVD
Medulloblastoma	20607354	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Seminomas	18059402	CNVD
Testicular germ cell tumor	18059402	CNVD
Myxofibrosarcoma	16751306	CNVD
Breast cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Lung cancer	18438408	CNVD
Mowat-Wilson syndrome	21572526	CNVD
Disorders of sex development	21048976	CNVD
epilepsy	18472482	CNVD
Ewing''s sarcoma	17952124	CNVD
Neuroblastoma	18574593	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
lymphocytic leukemia	21291569	CNVD
Breast cancer	21509527	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Epilepsy	22083797	CNVD

Chromatin state (count:190 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96502600-96561400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:96502800-96555200	Weak transcription	Ovary	ovary
3	chr2:96502800-96585000	Weak transcription	Left Ventricle	heart
4	chr2:96502800-96616600	Weak transcription	Fetal Stomach	stomach
5	chr2:96503000-96563600	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:96506600-96562000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:96521800-96555600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:96526600-96555200	Weak transcription	Fetal Muscle Leg	muscle
9	chr2:96526800-96555200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:96526800-96557600	Weak transcription	NHDF-Ad	bronchial
11	chr2:96528600-96555600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:96528600-96560000	Weak transcription	Fetal Intestine Large	intestine
13	chr2:96530600-96555200	Weak transcription	Fetal Brain Female	brain
14	chr2:96531200-96557800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:96533000-96558000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:96536000-96576800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr2:96541000-96555200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:96541000-96555800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:96541000-96582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:96541000-96595400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:96541200-96559800	Weak transcription	HMEC	breast
22	chr2:96541600-96595200	Weak transcription	Fetal Brain Male	brain
23	chr2:96542400-96557200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr2:96542600-96558400	Weak transcription	Brain Substantia Nigra	brain
25	chr2:96543000-96555200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:96543800-96596200	Weak transcription	K562	blood
27	chr2:96544000-96555800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr2:96544600-96561800	Weak transcription	Colon Smooth Muscle	Colon
29	chr2:96544800-96557200	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:96545000-96559600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr2:96545000-96576400	Weak transcription	Brain Germinal Matrix	brain
32	chr2:96546000-96555600	Weak transcription	Fetal Lung	lung
33	chr2:96546000-96577400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr2:96546400-96559800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:96546800-96562200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:96547000-96555800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:96547000-96586400	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr2:96547200-96555600	Weak transcription	Fetal Heart	heart
39	chr2:96547200-96555600	Weak transcription	NH-A	brain
40	chr2:96547200-96558200	Weak transcription	HepG2	liver
41	chr2:96547400-96557200	Weak transcription	Aorta	Aorta
42	chr2:96547600-96575800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:96547800-96560200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:96548000-96563000	Weak transcription	Right Ventricle	heart
45	chr2:96548200-96555600	Weak transcription	GM12878-XiMat	blood
46	chr2:96548200-96557400	Weak transcription	NHEK	skin
47	chr2:96548200-96564200	Weak transcription	A549	lung
48	chr2:96548600-96555600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:96548600-96556400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr2:96548600-96558200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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