Variant report

Variant	nsv1058339
Chromosome Location	chr20:864512-890349
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:873612..875715-chr20:890183..892090,2	MCF-7	breast:
2	chr20:890014..892494-chr20:895153..897440,2	MCF-7	breast:
3	chr20:809347..810136-chr20:883815..884702,3	MCF-7	breast:
4	chr20:858282..861279-chr20:864400..866707,2	K562	blood:
5	chr20:822258..824551-chr20:869597..872027,2	MCF-7	breast:
6	chr20:857198..860086-chr20:873899..876217,2	MCF-7	breast:
7	chr20:873612..875715-chr20:890183..892090,2	MCF-7	breast:
8	chr20:859998..862638-chr20:865942..867662,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101280	chromatin interactions

Extended variants
information (count: 1025 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:1025 , 50 per page) page: 1 2 3 4 5 6 7 ... 21

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3787565	chr20:864512-864513	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs6118076	chr20:864562-864563	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs527730822	chr20:864588-864589	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs143269008	chr20:864606-864607	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs564312333	chr20:864614-864615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs113168500	chr20:864621-864622	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs373383521	chr20:864639-864640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs3787566	chr20:864640-864641	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs545214406	chr20:864652-864653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs3787567	chr20:864660-864661	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs570003106	chr20:864666-864667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs530639934	chr20:864708-864709	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs79252129	chr20:864729-864730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs182702457	chr20:864798-864799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs565885611	chr20:864801-864802	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs534381304	chr20:864821-864822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs557876338	chr20:864826-864827	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs571152930	chr20:864833-864834	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs537084400	chr20:864889-864890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs556698164	chr20:864890-864891	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs576298827	chr20:864928-864929	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs139314191	chr20:864956-864957	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs535748571	chr20:864970-864971	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs555497936	chr20:864985-864986	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs572343498	chr20:864987-864988	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs6118079	chr20:864997-864998	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs6055559	chr20:865054-865055	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs6118080	chr20:865059-865060	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs543768285	chr20:865091-865092	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs6108109	chr20:865107-865108	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs529156721	chr20:865144-865145	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs549309392	chr20:865154-865155	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs151258833	chr20:865179-865180	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs528335270	chr20:865183-865184	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs186697083	chr20:865250-865251	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
36	rs34253995	chr20:865299-865300	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs571287059	chr20:865304-865305	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs6077320	chr20:865366-865367	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs371673089	chr20:865371-865372	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs191408233	chr20:865419-865420	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs535735613	chr20:865454-865455	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs6055560	chr20:865537-865538	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs572281910	chr20:865550-865551	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs545087973	chr20:865601-865602	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs184615060	chr20:865605-865606	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs578026493	chr20:865622-865623	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs55955946	chr20:865665-865666	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs398081184	chr20:865667-865668	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs398088198	chr20:865668-865669	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs200211515	chr20:865669-865670	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Intellectual disability	22045946	CNVD
Glioblastoma multiforme	22286061	CNVD
Hepatocellular carcinoma	22174799	CNVD
Colorectal cancer	19455253	CNVD
Ovarian cancer	20844748	CNVD
Breast cancer	17603634	CNVD
Colorectal cancer	19359472	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Intracranial aneurysm	16715129	CNVD
Colorectal cancer	16774939	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Medulloblastoma	21979893	CNVD
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Gastric cancer	17908304	CNVD
small cell lung cancer	20016488	CNVD
Urothelial carcinoma	21177765	CNVD
lymphocytic leukemia	21291569	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Ewing''s sarcoma	17952124	CNVD
Oral cancer	21386901	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	18438408	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	17426248	CNVD
Colorectal cancer	21645411	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:276 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:854600-869000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr20:862200-865400	Weak transcription	Spleen	Spleen
3	chr20:862600-866000	Weak transcription	Osteobl	bone
4	chr20:862800-865600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr20:863200-865600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:863200-865600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr20:863800-865400	Weak transcription	NHEK	skin
8	chr20:865200-866200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:865200-866400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
10	chr20:865400-865600	Enhancers	Ovary	ovary
11	chr20:865400-865600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
12	chr20:865400-865600	Bivalent Enhancer	Stomach Mucosa	stomach
13	chr20:865400-865800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr20:865400-866000	Enhancers	H1 Cell Line	embryonic stem cell
15	chr20:865400-866000	ZNF genes & repeats	Spleen	Spleen
16	chr20:865400-866200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr20:865400-866200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr20:865400-866200	Enhancers	Fetal Brain Male	brain
19	chr20:865400-866200	Bivalent Enhancer	Placenta	Placenta
20	chr20:865400-866200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
21	chr20:865400-866200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
22	chr20:865400-866400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr20:865400-866600	Enhancers	Adipose Nuclei	Adipose
24	chr20:865600-865800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr20:865600-865800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr20:865600-865800	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr20:865600-865800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
28	chr20:865600-865800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
29	chr20:865600-865800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
30	chr20:865600-865800	Bivalent Enhancer	Thymus	Thymus
31	chr20:865600-866000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr20:865600-866000	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
33	chr20:865600-866000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr20:865600-866000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr20:865600-866000	Enhancers	Brain Cingulate Gyrus	brain
36	chr20:865600-866000	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr20:865600-866000	Enhancers	Gastric	stomach
38	chr20:865600-866000	Enhancers	Lung	lung
39	chr20:865600-866000	Flanking Active TSS	Ovary	ovary
40	chr20:865600-866000	Bivalent Enhancer	Psoas Muscle	Psoas
41	chr20:865600-866000	Enhancers	Right Atrium	heart
42	chr20:865600-866000	Bivalent Enhancer	HMEC	breast
43	chr20:865600-866200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr20:865600-866200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr20:865600-866200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr20:865600-866200	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr20:865600-866200	Bivalent Enhancer	Fetal Stomach	stomach
48	chr20:865600-866200	Enhancers	Left Ventricle	heart
49	chr20:865600-866200	Enhancers	Right Ventricle	heart
50	chr20:865600-866400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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