Variant report

Variant	nsv1060158
Chromosome Location	chr20:24887819-24918081
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:16)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:24892772..24894924-chr20:24896880..24898878,2	MCF-7	breast:
2	chr20:24764501..24765530-chr20:24898693..24899347,4	MCF-7	breast:
3	chr20:24892772..24894924-chr20:24896880..24898878,2	MCF-7	breast:
4	chr20:24887755..24889606-chr20:24897276..24899425,2	K562	blood:
5	chr20:24814781..24815580-chr20:24898686..24899395,4	MCF-7	breast:
6	chr20:24910467..24912747-chr20:24972358..24974415,2	MCF-7	breast:
7	chr20:24909343..24912693-chr20:24913170..24916017,4	MCF-7	breast:
8	chr20:24912941..24914562-chr20:24924394..24926104,2	MCF-7	breast:
9	chr20:24771465..24772208-chr20:24898686..24899202,2	MCF-7	breast:
10	chr20:24914439..24915971-chr20:24971852..24973942,2	MCF-7	breast:
11	chr20:24764506..24765162-chr20:24897617..24898498,2	MCF-7	breast:
12	chr20:24283582..24284398-chr20:24898678..24899422,2	MCF-7	breast:
13	chr20:24909343..24912693-chr20:24913170..24916017,4	MCF-7	breast:
14	chr20:24887755..24889606-chr20:24897276..24899425,2	K562	blood:
15	chr20:24914670..24916704-chr20:24919775..24921335,2	MCF-7	breast:
16	chr20:24763298..24765600-chr20:24898179..24900035,23	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C20orf3-1	chr20:24911284-24912866	ENSG00000250527
2	lnc-C20orf3-1	chr20:24913047-24913619	ENSG00000250527

No data

Variant related genes	Relation type
ENSG00000101474	chromatin interactions
YOD1	miRNA target sites
ZNF148	miRNA target sites

Extended variants
information (count: 1360 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:1360 , 50 per page) page: 1 2 3 4 5 6 7 ... 28

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs557018702	chr20:24887901-24887902	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs6106968	chr20:24887904-24887905	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs537846706	chr20:24887994-24887995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs536228678	chr20:24887999-24888000	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs548644930	chr20:24888031-24888032	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs567067915	chr20:24888039-24888040	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs552970815	chr20:24888048-24888049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs144149147	chr20:24888049-24888050	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs531199213	chr20:24888060-24888061	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs6114921	chr20:24888078-24888079	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs565217935	chr20:24888086-24888087	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs367890673	chr20:24888089-24888090	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs146069119	chr20:24888162-24888163	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs571225792	chr20:24888189-24888190	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs544103621	chr20:24888196-24888197	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs140017154	chr20:24888251-24888252	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs529332498	chr20:24888253-24888254	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs542733473	chr20:24888309-24888310	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs373804231	chr20:24888333-24888334	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs554053581	chr20:24888455-24888456	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs559273668	chr20:24888466-24888467	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs370453073	chr20:24888485-24888486	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs142255380	chr20:24888520-24888521	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs151280186	chr20:24888521-24888522	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs565723172	chr20:24888522-24888523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs371352267	chr20:24888531-24888532	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs375285472	chr20:24888632-24888633	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs531113623	chr20:24888723-24888724	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs112965471	chr20:24888742-24888743	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs62216695	chr20:24888760-24888761	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs386813535	chr20:24888775-24888776	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs115708735	chr20:24888776-24888777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs112301327	chr20:24888782-24888783	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs188525142	chr20:24888829-24888830	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs181030320	chr20:24888834-24888835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs558869485	chr20:24888836-24888837	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs575483520	chr20:24888852-24888853	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs544509037	chr20:24888872-24888873	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs554436978	chr20:24888917-24888918	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs113072526	chr20:24888970-24888971	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs56106395	chr20:24889007-24889008	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs56179484	chr20:24889015-24889016	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs558962196	chr20:24889025-24889026	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs577184470	chr20:24889077-24889078	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs142667269	chr20:24889149-24889150	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs201552846	chr20:24889175-24889176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs114736223	chr20:24889264-24889265	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs541345853	chr20:24889327-24889328	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs565559541	chr20:24889367-24889368	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs186016566	chr20:24889392-24889393	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

Disease	PMID	Source
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
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Breast cancer	16608533	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Breast cancer	17133270	CNVD
Thrombophilia	17576883	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Hepatocellular carcinoma	22174799	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
Oral cancer	21386901	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Gastric cancer	22014070	CNVD

Chromatin state (count:302 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24881200-24890200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr20:24890200-24891400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:24891000-24891200	Weak transcription	Spleen	Spleen
4	chr20:24891200-24891400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr20:24891400-24893600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:24891800-24892200	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr20:24891800-24892600	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr20:24891800-24896000	Weak transcription	Spleen	Spleen
9	chr20:24892000-24892800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
10	chr20:24892200-24892400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr20:24892200-24892600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr20:24892600-24898600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr20:24893600-24893800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr20:24893600-24894000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr20:24894000-24898400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr20:24894600-24894800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr20:24895200-24895600	Bivalent Enhancer	Fetal Stomach	stomach
18	chr20:24895400-24895800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr20:24895800-24898400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr20:24896000-24896800	Active TSS	Spleen	Spleen
21	chr20:24898000-24899600	Enhancers	Brain Hippocampus Middle	brain
22	chr20:24898400-24899800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr20:24898400-24900600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr20:24898600-24898800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr20:24898600-24898800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr20:24898600-24898800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr20:24898600-24898800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
28	chr20:24898600-24899000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr20:24898600-24899000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr20:24898600-24899200	Bivalent Enhancer	Fetal Muscle Leg	muscle
31	chr20:24898600-24899600	Enhancers	H1 Cell Line	embryonic stem cell
32	chr20:24898600-24899600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr20:24898600-24899800	Enhancers	Fetal Lung	lung
34	chr20:24898600-24899800	Bivalent Enhancer	Fetal Stomach	stomach
35	chr20:24898600-24899800	Enhancers	GM12878-XiMat	blood
36	chr20:24898600-24900000	Enhancers	Adipose Nuclei	Adipose
37	chr20:24898600-24901400	Enhancers	Placenta	Placenta
38	chr20:24898800-24899000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr20:24898800-24899000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr20:24898800-24899000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr20:24898800-24899000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr20:24898800-24899000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
43	chr20:24898800-24899200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr20:24898800-24899200	Enhancers	Primary B cells from peripheral blood	blood
45	chr20:24898800-24899200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr20:24898800-24899200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr20:24898800-24899200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr20:24898800-24899200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr20:24898800-24899200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr20:24898800-24899200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland

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