Variant report

Variant	nsv879015
Chromosome Location	chr4:54596466-54665559
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:54601577..54603651-chr4:54607437..54610085,2	K562	blood:
2	chr4:54572624..54573264-chr4:54610618..54611257,2	MCF-7	breast:
3	chr4:54662024..54664830-chr4:54666037..54667800,2	K562	blood:
4	chr4:54619811..54622044-chr4:54627656..54629607,2	K562	blood:
5	chr4:54631461..54634039-chr4:54637339..54639127,3	K562	blood:
6	chr4:54619811..54622044-chr4:54627656..54629607,2	K562	blood:
7	chr4:54637798..54639736-chr4:54642892..54644483,2	K562	blood:
8	chr4:54631461..54634039-chr4:54637339..54639127,3	K562	blood:
9	chr4:54637798..54639736-chr4:54642892..54644483,2	K562	blood:
10	chr4:54581907..54583610-chr4:54615886..54618732,2	MCF-7	breast:
11	chr4:54601577..54603651-chr4:54607437..54610085,2	K562	blood:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GSX2-9	chr4:54596073-54598379	NONHSAT096406
2	lnc-GSX2-2	chr4:54602090-54603323	ENSG00000249341.1
3	lnc-GSX2-2	chr4:54599354-54600525	ENSG00000249341.1

No data

Extended variants
information (count: 2075 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:2075 , 50 per page) page: 1 2 3 4 5 6 7 ... 42

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2245157	chr4:54596466-54596467	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs564572553	chr4:54596485-54596486	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs560216537	chr4:54596504-54596505	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs372801208	chr4:54596526-54596527	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs578084167	chr4:54596534-54596535	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs114743963	chr4:54596554-54596555	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs374382103	chr4:54596583-54596584	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs2898979	chr4:54596608-54596609	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs563574530	chr4:54596628-54596629	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs181898195	chr4:54596655-54596656	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs187060276	chr4:54596666-54596667	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs10028338	chr4:54596689-54596690	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs529194418	chr4:54596709-54596710	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs373501921	chr4:54596730-54596731	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs376983781	chr4:54596767-54596768	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs78204588	chr4:54596768-54596769	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs138228489	chr4:54596771-54596772	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs6844085	chr4:54596795-54596796	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs35425917	chr4:54596797-54596798	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs35078008	chr4:54596818-54596819	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
21	rs570926145	chr4:54596822-54596823	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs377603099	chr4:54596837-54596838	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs375027569	chr4:54596859-54596860	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs574590373	chr4:54596865-54596866	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs575993860	chr4:54596868-54596869	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs561475954	chr4:54596869-54596870	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
27	rs1382083	chr4:54596877-54596878	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs551656656	chr4:54596882-54596883	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs575553230	chr4:54596895-54596896	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs2616411	chr4:54596896-54596897	Enhancers Weak transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
31	rs191129095	chr4:54596903-54596904	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs115718349	chr4:54596949-54596950	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs540228590	chr4:54596978-54596979	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs564824002	chr4:54596983-54596984	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
35	rs559856481	chr4:54596995-54596996	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
36	rs576766523	chr4:54597002-54597003	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs2590775	chr4:54597015-54597016	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs142732571	chr4:54597033-54597034	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
39	rs2590776	chr4:54597040-54597041	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs548341707	chr4:54597095-54597096	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs562068185	chr4:54597106-54597107	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs374607752	chr4:54597118-54597119	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs527931863	chr4:54597136-54597137	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
44	rs547778936	chr4:54597155-54597156	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
45	rs77823482	chr4:54597171-54597172	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
46	rs180990375	chr4:54597177-54597178	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
47	rs550323889	chr4:54597187-54597188	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
48	rs573339884	chr4:54597246-54597247	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
49	rs186031246	chr4:54597267-54597268	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
50	rs190410596	chr4:54597270-54597271	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a

Variant related diseases (count:102)

Disease	PMID	Source
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Cancer	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	19435819	CNVD
Multiple myeloma	16616336	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Ovarian neoplasms	16753589	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Glioblastoma multiforme	21569311	CNVD
Glioblastoma	17504929	CNVD
Glioblastoma	16823502	CNVD
Melanoma	16908931	CNVD
Glioblastoma	20031968	CNVD
Medulloblastoma	19270706	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Olfactory neuroblastoma	18408657	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Rhabdomyosarcoma	16790082	CNVD
Gastrointestinal stromal cancer	17438095	CNVD
Colorectal cancer	16272173	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	19115005	CNVD
Glioblastoma multiforme	21525872	CNVD
Wilms tumour	21544195	CNVD
Cancer	20164919	CNVD
Gastrointestinal stromal cancer	17527083	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17209131	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Glioblastoma multiforme	21138945	CNVD
Cancer	20164920	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:381 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54584000-54600000	Weak transcription	Osteobl	bone
2	chr4:54595600-54596600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:54596200-54596600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr4:54596200-54597400	Enhancers	Fetal Stomach	stomach
5	chr4:54596400-54597000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr4:54596400-54597400	Enhancers	NHDF-Ad	bronchial
7	chr4:54596600-54597000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr4:54596800-54597400	Enhancers	Placenta	Placenta
9	chr4:54597000-54599600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr4:54597000-54600200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr4:54597400-54598400	Weak transcription	NHDF-Ad	bronchial
12	chr4:54598400-54598600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:54598400-54599200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:54598400-54600600	Enhancers	NHDF-Ad	bronchial
15	chr4:54598400-54601000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:54598400-54601000	Enhancers	Monocytes-CD14+_RO01746	blood
17	chr4:54598400-54602600	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr4:54598600-54600000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr4:54598800-54599200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:54598800-54599600	Enhancers	Fetal Lung	lung
21	chr4:54599200-54600800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr4:54599400-54600600	Enhancers	NHLF	lung
23	chr4:54599600-54600600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:54600000-54600600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:54600000-54600600	Enhancers	Osteobl	bone
26	chr4:54600000-54600800	Enhancers	HUVEC	blood vessel
27	chr4:54600000-54601400	Enhancers	Colon Smooth Muscle	Colon
28	chr4:54600000-54603400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr4:54600200-54600800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:54600200-54602400	Enhancers	HSMM	muscle
31	chr4:54600400-54600600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr4:54600400-54600600	Enhancers	NH-A	brain
33	chr4:54600600-54600800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr4:54600600-54601000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:54600600-54601000	Enhancers	HSMMtube	muscle
36	chr4:54600600-54601200	Flanking Active TSS	NHDF-Ad	bronchial
37	chr4:54600600-54601200	Flanking Active TSS	NHLF	lung
38	chr4:54600600-54601200	Flanking Active TSS	Osteobl	bone
39	chr4:54600600-54601400	Flanking Active TSS	NH-A	brain
40	chr4:54600600-54601800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:54600600-54601800	Enhancers	HMEC	breast
42	chr4:54600600-54601800	Enhancers	NHEK	skin
43	chr4:54600800-54601000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr4:54600800-54601000	Bivalent Enhancer	Fetal Lung	lung
45	chr4:54600800-54601200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:54600800-54601200	Flanking Active TSS	HUVEC	blood vessel
47	chr4:54600800-54601400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr4:54600800-54601800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
49	chr4:54601000-54601200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr4:54601000-54601200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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