Variant report

Variant	nsv875949
Chromosome Location	chr2:231407663-231434272
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP110-1	chr2:231415763-231415816	ENSG00000235419.1
2	lnc-SP110-1	chr2:231415763-231415816	ENSG00000235419.1
3	lnc-SP100-1	chr2:231412423-231412717	NONHSAT077296

Extended variants
information (count: 1259 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:1259 , 50 per page) page: 1 2 3 4 5 6 7 ... 26

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs9288668	chr2:231407663-231407664	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs527245223	chr2:231407671-231407672	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs190190738	chr2:231407704-231407705	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs376930412	chr2:231407705-231407706	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs541374396	chr2:231407756-231407757	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs182464913	chr2:231407777-231407778	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs141779952	chr2:231407797-231407798	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs116132819	chr2:231407848-231407849	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs138446956	chr2:231407862-231407863	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs148802399	chr2:231407863-231407864	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs398105427	chr2:231407864-231407865	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs563519991	chr2:231407870-231407871	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs530566203	chr2:231407897-231407898	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs548661404	chr2:231407930-231407931	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs560611902	chr2:231407938-231407939	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs150580629	chr2:231407980-231407981	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs546549206	chr2:231407990-231407991	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs6749060	chr2:231408047-231408048	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs186794100	chr2:231408050-231408051	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
20	rs550527043	chr2:231408070-231408071	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
21	rs836238	chr2:231408095-231408096	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs139703657	chr2:231408115-231408116	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
23	rs6720796	chr2:231408137-231408138	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs192528771	chr2:231408157-231408158	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
25	rs113519122	chr2:231408178-231408179	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
26	rs149338202	chr2:231408187-231408188	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
27	rs578209237	chr2:231408258-231408259	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
28	rs836239	chr2:231408281-231408282	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs188441887	chr2:231408294-231408295	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
30	rs34311867	chr2:231408315-231408316	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
31	rs10202660	chr2:231408347-231408348	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs542768377	chr2:231408364-231408365	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
33	rs531734514	chr2:231408394-231408395	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
34	rs114944358	chr2:231408404-231408405	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
35	rs528155848	chr2:231408567-231408568	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
36	rs193056071	chr2:231408674-231408675	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
37	rs146336014	chr2:231408677-231408678	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
38	rs532346696	chr2:231408690-231408691	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs550884519	chr2:231408700-231408701	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs569497150	chr2:231408709-231408710	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs185076909	chr2:231408741-231408742	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs568398394	chr2:231408743-231408744	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs188677517	chr2:231408745-231408746	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs181160876	chr2:231408746-231408747	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs113837397	chr2:231408769-231408770	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs377721347	chr2:231408797-231408798	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs533912132	chr2:231408902-231408903	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs577961490	chr2:231408903-231408904	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs144430613	chr2:231408920-231408921	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs376403679	chr2:231408930-231408931	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16272173	CNVD
Ewing''s sarcoma	17952124	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
Colorectal cancer	16272173	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Cervical cancer	21062161	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Chordoma	18071362	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Cancer	22429812	CNVD
Bladder cancer	21909424	CNVD
Renal cell carcinoma	21668985	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Wilms tumour	21544195	CNVD
Esophageal adenocarcinoma	18519675	CNVD
prenatal diagnosis	22389664	CNVD
Myelofibrosis	22110671	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Mental retardation	20152051	CNVD
Cancer	21183584	CNVD
Albright''s disease	22277900	CNVD
Brachydactyly-Mental Retardation Syndrome	22470819	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Colorectal cancer	19359472	CNVD
Autism	18414403	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:157 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231371000-231409800	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:231390600-231408200	Weak transcription	Esophagus	oesophagus
3	chr2:231390800-231409200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr2:231401000-231430200	Weak transcription	Pancreas	Pancrea
5	chr2:231401400-231408600	Weak transcription	Colon Smooth Muscle	Colon
6	chr2:231401800-231409200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:231403200-231410200	Strong transcription	Primary B cells from cord blood	blood
8	chr2:231403600-231407800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:231403600-231408600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr2:231403800-231408800	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr2:231403800-231409600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:231404000-231408400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:231404000-231409000	Strong transcription	Primary T cells from cord blood	blood
14	chr2:231404000-231409000	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr2:231404000-231417200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:231404200-231409000	Strong transcription	Adipose Nuclei	Adipose
17	chr2:231404200-231409200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:231404200-231409400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:231404200-231409600	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:231404200-231410200	Strong transcription	Primary B cells from peripheral blood	blood
21	chr2:231404400-231408400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr2:231404400-231408400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr2:231404400-231409800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr2:231404400-231410000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr2:231404600-231409000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr2:231404600-231416400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr2:231404800-231408800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr2:231404800-231410800	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr2:231405000-231409800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr2:231405200-231408800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:231405400-231409800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:231405400-231411600	Weak transcription	Placenta	Placenta
33	chr2:231405400-231411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:231405600-231408400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:231405600-231408600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:231405600-231408800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr2:231405600-231409000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:231405600-231409000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr2:231405600-231410200	Strong transcription	Primary hematopoietic stem cells	blood
40	chr2:231405800-231415000	Weak transcription	Gastric	stomach
41	chr2:231406000-231408400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr2:231406000-231408600	Strong transcription	Liver	Liver
43	chr2:231406400-231409400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:231406400-231410200	Weak transcription	Thymus	Thymus
45	chr2:231406600-231408800	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr2:231406800-231407800	Flanking Active TSS	GM12878-XiMat	blood
47	chr2:231406800-231408200	Weak transcription	Ovary	ovary
48	chr2:231406800-231408200	Weak transcription	Spleen	Spleen
49	chr2:231406800-231408800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr2:231406800-231408800	Weak transcription	Lung	lung

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