Variant report

Variant	esv3366133
Chromosome Location	chr2:96616138-96617224
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	chr2:96616497-96616527	XLOC_002209
2	lnc-GPAT2-1	chr2:96617096-96617156	XLOC_002209

Variant related genes	Relation type
BACE1	miRNA target sites

Extended variants
information (count: 92 )
Associated
traits (count: 49 )

Variant overlapped rSNPs/rCNVs (count:92 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs62154607	chr2:96616139-96616140	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs201045990	chr2:96616143-96616144	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs2107874	chr2:96616149-96616150	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs73958156	chr2:96616159-96616160	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs73958157	chr2:96616160-96616161	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs527996493	chr2:96616169-96616170	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs71219722	chr2:96616177-96616178	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs547745605	chr2:96616198-96616199	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs560110058	chr2:96616222-96616223	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs62154608	chr2:96616243-96616244	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs376246497	chr2:96616249-96616250	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs139114553	chr2:96616310-96616311	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs72545168	chr2:96616313-96616314	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs33961164	chr2:96616314-96616315	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs4110270	chr2:96616320-96616321	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs62154609	chr2:96616348-96616349	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs386648368	chr2:96616354-96616355	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs62154610	chr2:96616355-96616356	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs1852833	chr2:96616361-96616362	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs1636113	chr2:96616362-96616363	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs62154611	chr2:96616378-96616379	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs531998442	chr2:96616424-96616425	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs74960926	chr2:96616442-96616443	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
24	rs76503749	chr2:96616448-96616449	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs537691229	chr2:96616449-96616450	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs78218362	chr2:96616485-96616486	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs78179792	chr2:96616504-96616505	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
28	rs373114066	chr2:96616506-96616507	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
29	rs79603357	chr2:96616507-96616508	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	Overlapped CNVs	n/a
30	rs112676430	chr2:96616532-96616533	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs146478446	chr2:96616571-96616572	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
32	rs143490798	chr2:96616576-96616577	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs201649771	chr2:96616580-96616581	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs114583836	chr2:96616597-96616598	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs116630524	chr2:96616599-96616600	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs547993471	chr2:96616602-96616603	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs141967446	chr2:96616607-96616608	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs112338915	chr2:96616622-96616623	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs75283408	chr2:96616654-96616655	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs77249402	chr2:96616667-96616668	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs111409549	chr2:96616690-96616691	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs112782601	chr2:96616693-96616694	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs144289424	chr2:96616697-96616698	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs112595286	chr2:96616734-96616735	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs76572760	chr2:96616749-96616750	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs79038786	chr2:96616758-96616759	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs199561017	chr2:96616759-96616760	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs200292009	chr2:96616767-96616768	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs377099763	chr2:96616803-96616804	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs186812111	chr2:96616808-96616809	ZNF genes & repeats 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:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96502800-96616600	Weak transcription	Fetal Stomach	stomach
2	chr2:96556200-96645000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:96556400-96628600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:96556400-96645000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:96557400-96656800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:96574200-96629600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr2:96574600-96627600	Weak transcription	HSMM	muscle
8	chr2:96576800-96616200	Weak transcription	Brain Germinal Matrix	brain
9	chr2:96577800-96647800	Weak transcription	NHDF-Ad	bronchial
10	chr2:96577800-96651000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:96577800-96656600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:96578000-96645000	Weak transcription	NH-A	brain
13	chr2:96581400-96617000	Weak transcription	Pancreas	Pancrea
14	chr2:96582800-96656400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:96584000-96624600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:96584400-96621600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:96585200-96649000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:96585400-96616600	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:96585600-96627400	Weak transcription	Left Ventricle	heart
20	chr2:96586000-96657200	Weak transcription	Ovary	ovary
21	chr2:96587800-96656600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:96588200-96649000	Weak transcription	Fetal Intestine Large	intestine
23	chr2:96589000-96631200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:96589000-96645400	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:96591200-96616200	Weak transcription	Fetal Thymus	thymus
26	chr2:96593600-96616200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:96593600-96645000	Weak transcription	Adipose Nuclei	Adipose
28	chr2:96594400-96617600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:96594600-96623800	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr2:96600600-96657200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr2:96600800-96617600	Weak transcription	Fetal Brain Male	brain
32	chr2:96600800-96621400	Weak transcription	A549	lung
33	chr2:96600800-96625600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:96600800-96645000	Weak transcription	Primary T cells from cord blood	blood
35	chr2:96604200-96616800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr2:96605400-96644800	Weak transcription	Brain Anterior Caudate	brain
37	chr2:96605600-96655000	Weak transcription	HUVEC	blood vessel
38	chr2:96606000-96616200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:96606000-96635000	Weak transcription	Fetal Intestine Small	intestine
40	chr2:96606400-96657200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr2:96607400-96644600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:96607400-96657200	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:96608400-96635000	Weak transcription	Thymus	Thymus
44	chr2:96609000-96616200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:96609000-96625800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:96610600-96645000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:96610800-96616200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:96610800-96616400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr2:96610800-96629000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr2:96611000-96616200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links