Variant report

Variant	nsv961623
Chromosome Location	chr2:96557042-96560529
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	chr2:96559198-96559313	ucscGeneNc_uc002swd_1
2	lnc-GPAT2-5	chr2:96557405-96557647	ucscGeneNc_uc002swd_1

Extended variants
information (count: 191 )
Associated
traits (count: 49 )

Variant overlapped rSNPs/rCNVs (count:191 , 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	rs186055523	chr2:96557055-96557056	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs540523632	chr2:96557059-96557060	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs560329935	chr2:96557060-96557061	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs556936990	chr2:96557151-96557152	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs150005456	chr2:96557184-96557185	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs563021497	chr2:96557201-96557202	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs531647086	chr2:96557213-96557214	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs548384602	chr2:96557215-96557216	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs568308298	chr2:96557223-96557224	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs189201244	chr2:96557230-96557231	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs547665203	chr2:96557250-96557251	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs566376675	chr2:96557258-96557259	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs181766879	chr2:96557319-96557320	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs575028856	chr2:96557322-96557323	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs558236758	chr2:96557330-96557331	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs532730717	chr2:96557339-96557340	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs537898694	chr2:96557340-96557341	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs554843944	chr2:96557371-96557372	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs574679470	chr2:96557377-96557378	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs540560318	chr2:96557379-96557380	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs554051604	chr2:96557397-96557398	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs577035671	chr2:96557461-96557462	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
23	rs546181873	chr2:96557474-96557475	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
24	rs562698973	chr2:96557475-96557476	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
25	rs186496927	chr2:96557493-96557494	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
26	rs551110238	chr2:96557509-96557510	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
27	rs541920464	chr2:96557511-96557512	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
28	rs561975574	chr2:96557626-96557627	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
29	rs569882198	chr2:96557627-96557628	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
30	rs527866043	chr2:96557639-96557640	Weak transcription Strong transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
31	rs536953489	chr2:96557667-96557668	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs547637888	chr2:96557707-96557708	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs571143741	chr2:96557714-96557715	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs145367784	chr2:96557739-96557740	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs552157894	chr2:96557746-96557747	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs568860183	chr2:96557747-96557748	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs368092612	chr2:96557758-96557759	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs554682197	chr2:96557769-96557770	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs567513044	chr2:96557772-96557773	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs534000957	chr2:96557775-96557776	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs553640478	chr2:96557780-96557781	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs577077694	chr2:96557791-96557792	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs190491297	chr2:96557812-96557813	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs182977952	chr2:96557844-96557845	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs186879954	chr2:96557854-96557855	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs541955565	chr2:96557868-96557869	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs148775961	chr2:96557876-96557877	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs527750870	chr2:96557894-96557895	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs143764178	chr2:96557922-96557923	Strong transcription Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs564479992	chr2:96557929-96557930	Strong transcription Weak transcription Enhancers	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:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96502600-96561400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:96502800-96585000	Weak transcription	Left Ventricle	heart
3	chr2:96502800-96616600	Weak transcription	Fetal Stomach	stomach
4	chr2:96503000-96563600	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:96506600-96562000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:96526800-96557600	Weak transcription	NHDF-Ad	bronchial
7	chr2:96528600-96560000	Weak transcription	Fetal Intestine Large	intestine
8	chr2:96531200-96557800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:96533000-96558000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:96536000-96576800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr2:96541000-96582000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:96541000-96595400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr2:96541200-96559800	Weak transcription	HMEC	breast
14	chr2:96541600-96595200	Weak transcription	Fetal Brain Male	brain
15	chr2:96542400-96557200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:96542600-96558400	Weak transcription	Brain Substantia Nigra	brain
17	chr2:96543800-96596200	Weak transcription	K562	blood
18	chr2:96544600-96561800	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:96544800-96557200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr2:96545000-96559600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr2:96545000-96576400	Weak transcription	Brain Germinal Matrix	brain
22	chr2:96546000-96577400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:96546400-96559800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:96546800-96562200	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:96547000-96586400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:96547200-96558200	Weak transcription	HepG2	liver
27	chr2:96547400-96557200	Weak transcription	Aorta	Aorta
28	chr2:96547600-96575800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:96547800-96560200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:96548000-96563000	Weak transcription	Right Ventricle	heart
31	chr2:96548200-96557400	Weak transcription	NHEK	skin
32	chr2:96548200-96564200	Weak transcription	A549	lung
33	chr2:96548600-96558200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:96548600-96559800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:96549600-96563000	Weak transcription	Liver	Liver
36	chr2:96549800-96557400	Weak transcription	Osteobl	bone
37	chr2:96549800-96557600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr2:96549800-96558600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:96549800-96576400	Weak transcription	Thymus	Thymus
40	chr2:96549800-96576600	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr2:96549800-96579600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr2:96549800-96580200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr2:96549800-96588600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:96549800-96590600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr2:96550000-96562000	Weak transcription	Placenta	Placenta
46	chr2:96551400-96600800	Weak transcription	Brain Angular Gyrus	brain
47	chr2:96551800-96588600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:96552400-96576200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr2:96552400-96595400	Weak transcription	Fetal Kidney	kidney
50	chr2:96553400-96558400	Strong transcription	Fetal Thymus	thymus

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