Variant report

Variant	esv15357
Chromosome Location	chr4:54591392-54603209
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54601577..54603651-chr4:54607437..54610085,2	K562	blood:

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

Extended variants
information (count: 490 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:490 , 50 per page) page: 1 2 3 4 5 6 7 ... 10

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs571325841	chr4:54591395-54591396	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs386674448	chr4:54591399-54591400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs2616408	chr4:54591400-54591401	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs183218606	chr4:54591402-54591403	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs539314010	chr4:54591404-54591405	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs556413056	chr4:54591407-54591408	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs186084931	chr4:54591409-54591410	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs4339272	chr4:54591434-54591435	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs541402262	chr4:54591444-54591445	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs561480064	chr4:54591472-54591473	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs538827223	chr4:54591475-54591476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs190611442	chr4:54591479-54591480	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs78427250	chr4:54591506-54591507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs564472259	chr4:54591534-54591535	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs533684798	chr4:54591555-54591556	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs543810370	chr4:54591562-54591563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs183342315	chr4:54591576-54591577	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs529342225	chr4:54591644-54591645	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs138923568	chr4:54591653-54591654	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs187882461	chr4:54591673-54591674	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs528549719	chr4:54591712-54591713	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs62323723	chr4:54591727-54591728	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs142066527	chr4:54591733-54591734	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs138194308	chr4:54591744-54591745	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs556213065	chr4:54591756-54591757	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs201155131	chr4:54591765-54591766	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs199703553	chr4:54591785-54591786	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs569598694	chr4:54591808-54591809	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs535096531	chr4:54591810-54591811	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs554911357	chr4:54591854-54591855	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs571808804	chr4:54591891-54591892	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs555834676	chr4:54591907-54591908	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs540727238	chr4:54591909-54591910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs574101815	chr4:54591920-54591921	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs191708164	chr4:54591925-54591926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs578132633	chr4:54591948-54591949	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs541140173	chr4:54591965-54591966	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs183163291	chr4:54591970-54591971	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs563990477	chr4:54591978-54591979	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs529586844	chr4:54592003-54592004	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs367673500	chr4:54592029-54592030	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs543047653	chr4:54592116-54592117	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs559744517	chr4:54592121-54592122	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs187492390	chr4:54592139-54592140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs528487157	chr4:54592149-54592150	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs371512916	chr4:54592181-54592182	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs376901837	chr4:54592186-54592187	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs571691445	chr4:54592204-54592205	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs533013829	chr4:54592211-54592212	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs549913937	chr4:54592213-54592214	Weak transcription	n/a	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:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54584000-54600000	Weak transcription	Osteobl	bone
2	chr4:54591000-54591800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr4:54595600-54596600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr4:54596000-54596400	Bivalent Enhancer	Fetal Lung	lung
5	chr4:54596200-54596600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr4:54596200-54597400	Enhancers	Fetal Stomach	stomach
7	chr4:54596400-54597000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr4:54596400-54597400	Enhancers	NHDF-Ad	bronchial
9	chr4:54596600-54597000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr4:54596800-54597400	Enhancers	Placenta	Placenta
11	chr4:54597000-54599600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:54597000-54600200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:54597400-54598400	Weak transcription	NHDF-Ad	bronchial
14	chr4:54598400-54598600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr4:54598400-54599200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr4:54598400-54600600	Enhancers	NHDF-Ad	bronchial
17	chr4:54598400-54601000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:54598400-54601000	Enhancers	Monocytes-CD14+_RO01746	blood
19	chr4:54598400-54602600	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr4:54598600-54600000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:54598800-54599200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:54598800-54599600	Enhancers	Fetal Lung	lung
23	chr4:54599200-54600800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr4:54599400-54600600	Enhancers	NHLF	lung
25	chr4:54599600-54600600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:54600000-54600600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:54600000-54600600	Enhancers	Osteobl	bone
28	chr4:54600000-54600800	Enhancers	HUVEC	blood vessel
29	chr4:54600000-54601400	Enhancers	Colon Smooth Muscle	Colon
30	chr4:54600000-54603400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:54600200-54600800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:54600200-54602400	Enhancers	HSMM	muscle
33	chr4:54600400-54600600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr4:54600400-54600600	Enhancers	NH-A	brain
35	chr4:54600600-54600800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:54600600-54601000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:54600600-54601000	Enhancers	HSMMtube	muscle
38	chr4:54600600-54601200	Flanking Active TSS	NHDF-Ad	bronchial
39	chr4:54600600-54601200	Flanking Active TSS	NHLF	lung
40	chr4:54600600-54601200	Flanking Active TSS	Osteobl	bone
41	chr4:54600600-54601400	Flanking Active TSS	NH-A	brain
42	chr4:54600600-54601800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr4:54600600-54601800	Enhancers	HMEC	breast
44	chr4:54600600-54601800	Enhancers	NHEK	skin
45	chr4:54600800-54601000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:54600800-54601000	Bivalent Enhancer	Fetal Lung	lung
47	chr4:54600800-54601200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr4:54600800-54601200	Flanking Active TSS	HUVEC	blood vessel
49	chr4:54600800-54601400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr4:54600800-54601800	Flanking Active TSS	Muscle Satellite Cultured Cells	--

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