Variant report

Variant	esv3388274
Chromosome Location	chr2:96625325-96630723
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPAT2-1	chr2:96626387-96626412	XLOC_002209

Variant related genes	Relation type
BACE1	miRNA target sites

Extended variants
information (count: 289 )
Associated
traits (count: 52 )

Variant overlapped rSNPs/rCNVs (count:289 , 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	rs373998914	chr2:96625332-96625333	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs576739505	chr2:96625340-96625341	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs543960455	chr2:96625343-96625344	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs139441194	chr2:96625374-96625375	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs556065283	chr2:96625379-96625380	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs376377799	chr2:96625408-96625409	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs370808510	chr2:96625412-96625413	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs572653445	chr2:96625447-96625448	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs541682145	chr2:96625458-96625459	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs559731930	chr2:96625460-96625461	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs531965031	chr2:96625476-96625477	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs201021829	chr2:96625480-96625481	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs545520851	chr2:96625481-96625482	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs201693353	chr2:96625495-96625496	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs367811440	chr2:96625520-96625521	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs372690966	chr2:96625543-96625544	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs7565503	chr2:96625553-96625554	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
18	rs201260323	chr2:96625565-96625566	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs202140691	chr2:96625644-96625645	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs193127596	chr2:96625677-96625678	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs548090187	chr2:96625704-96625705	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs568204184	chr2:96625709-96625710	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs372703164	chr2:96625717-96625718	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs200784078	chr2:96625732-96625733	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs72492195	chr2:96625808-96625809	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs202080259	chr2:96625843-96625844	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs200391539	chr2:96625869-96625870	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs527614202	chr2:96625874-96625875	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs547682891	chr2:96625895-96625896	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs372175311	chr2:96625899-96625900	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs201535750	chr2:96625922-96625923	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs539822351	chr2:96625929-96625930	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs72492196	chr2:96625944-96625945	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs113641616	chr2:96625951-96625952	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs185622960	chr2:96625990-96625991	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs556742563	chr2:96626006-96626007	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs182558072	chr2:96626026-96626027	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs535896382	chr2:96626029-96626030	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs7566050	chr2:96626030-96626031	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
40	rs187903817	chr2:96626063-96626064	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs71250566	chr2:96626094-96626095	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs71250565	chr2:96626125-96626126	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs576475343	chr2:96626147-96626148	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs545382090	chr2:96626158-96626159	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs71250564	chr2:96626189-96626190	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs144684773	chr2:96626191-96626192	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs576061719	chr2:96626251-96626252	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs541884118	chr2:96626265-96626266	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs561752247	chr2:96626282-96626283	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs4362598	chr2:96626292-96626293	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:52)

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
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD

Chromatin state (count:129 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96556200-96645000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr2:96556400-96628600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr2:96556400-96645000	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr2:96557400-96656800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:96574200-96629600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:96574600-96627600	Weak transcription	HSMM	muscle
7	chr2:96577800-96647800	Weak transcription	NHDF-Ad	bronchial
8	chr2:96577800-96651000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:96577800-96656600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:96578000-96645000	Weak transcription	NH-A	brain
11	chr2:96582800-96656400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:96585200-96649000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:96585600-96627400	Weak transcription	Left Ventricle	heart
14	chr2:96586000-96657200	Weak transcription	Ovary	ovary
15	chr2:96587800-96656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr2:96588200-96649000	Weak transcription	Fetal Intestine Large	intestine
17	chr2:96589000-96631200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:96589000-96645400	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr2:96593600-96645000	Weak transcription	Adipose Nuclei	Adipose
20	chr2:96600600-96657200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:96600800-96625600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr2:96600800-96645000	Weak transcription	Primary T cells from cord blood	blood
23	chr2:96605400-96644800	Weak transcription	Brain Anterior Caudate	brain
24	chr2:96605600-96655000	Weak transcription	HUVEC	blood vessel
25	chr2:96606000-96635000	Weak transcription	Fetal Intestine Small	intestine
26	chr2:96606400-96657200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:96607400-96644600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:96607400-96657200	Weak transcription	Brain Hippocampus Middle	brain
29	chr2:96608400-96635000	Weak transcription	Thymus	Thymus
30	chr2:96609000-96625800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:96610600-96645000	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:96610800-96629000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:96611000-96656600	Weak transcription	Osteobl	bone
34	chr2:96611400-96657200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr2:96611600-96625800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr2:96614400-96655800	Weak transcription	K562	blood
37	chr2:96614600-96627200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr2:96615000-96627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr2:96615200-96650000	Weak transcription	Brain Substantia Nigra	brain
40	chr2:96615600-96627200	Weak transcription	Spleen	Spleen
41	chr2:96616400-96627800	Weak transcription	HMEC	breast
42	chr2:96616400-96627800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:96616400-96643200	Weak transcription	Fetal Lung	lung
44	chr2:96616600-96645400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr2:96616800-96657200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr2:96617000-96627400	Weak transcription	Fetal Brain Female	brain
47	chr2:96617000-96627600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:96617000-96656600	Weak transcription	Fetal Stomach	stomach
49	chr2:96617000-96656800	Weak transcription	Fetal Muscle Leg	muscle
50	chr2:96617200-96627800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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