Variant report

Variant	nsv527711
Chromosome Location	chr20:52645166-52645541
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:52645224-52645292	ProgFib	skin:	n/a	n/a
2	POLR2A	chr20:52644898-52645206	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52643673..52645639-chr20:52687051..52688962,2	MCF-7	breast:
2	chr20:52645173..52647456-chr8:56684089..56685719,2	MCF-7	breast:

Variant related genes	Relation type
BCAS1	TF binding region
ENSG00000064787	chromatin interactions
ENSG00000167904	chromatin interactions
ENSG00000137574	chromatin interactions

Extended variants
information (count: 36 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs158551	chr20:52645166-52645167	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs61754122	chr20:52645167-52645168	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs374609444	chr20:52645216-52645217	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs549457924	chr20:52645219-52645220	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs534796037	chr20:52645240-52645241	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs561920968	chr20:52645252-52645253	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs201121458	chr20:52645265-52645266	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs377347859	chr20:52645283-52645284	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs200609261	chr20:52645290-52645291	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs199643719	chr20:52645309-52645310	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs201371925	chr20:52645320-52645321	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs369178055	chr20:52645333-52645334	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs570638388	chr20:52645335-52645336	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs373986689	chr20:52645337-52645338	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs537738564	chr20:52645338-52645339	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs150504348	chr20:52645341-52645342	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs376388302	chr20:52645357-52645358	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs139488468	chr20:52645362-52645363	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs150059555	chr20:52645363-52645364	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs145412907	chr20:52645364-52645365	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs180883984	chr20:52645392-52645393	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs377354616	chr20:52645396-52645397	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs186353345	chr20:52645404-52645405	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs555168043	chr20:52645425-52645426	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs371287680	chr20:52645428-52645429	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs367579124	chr20:52645432-52645433	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs370776672	chr20:52645435-52645436	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs75689739	chr20:52645454-52645455	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs373877569	chr20:52645461-52645462	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs201469401	chr20:52645475-52645476	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs76481467	chr20:52645487-52645488	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs371937753	chr20:52645496-52645497	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs146806249	chr20:52645509-52645510	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs373114175	chr20:52645528-52645529	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs466264	chr20:52645534-52645535	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs2072127	chr20:52645541-52645542	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:84)

Disease	PMID	Source
Gastric cancer	17908304	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Medulloblastoma	21979893	CNVD
Urothelial carcinoma	21177765	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Colorectal cancer	21645411	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	21693616	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Endometrial cancer	22040021	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
colon cancer	17210682	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	22028636	CNVD
Breast cancer	21264507	CNVD
Thyroid cancer	19087340	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Colorectal cancer	19359472	CNVD
Gastric cancer	17167181	CNVD
Myeloproliferative neoplasm	19047681	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Breast cancer	17603634	CNVD
Melanoma	18172304	CNVD
Breast cancer	16608533	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17133270	CNVD
Oral cancer	21386901	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Myelodysplastic syndrome	21251322	CNVD
Ductal carcinoma	22052326	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Gastric cancer	20585902	CNVD
Ductal carcinoma	18381933	CNVD
Cancer	21129771	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	20864512	CNVD
Ovarian cancer	22174824	CNVD
Lung cancer	16740712	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16620391	CNVD
Okamoto syndrome	17623483	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21785460	CNVD
Bladder cancer	21909424	CNVD
Biliary cancer	19435499	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Cervical cancer	16585170	CNVD
Ovarian cancer	20844748	CNVD
Hirschsprung''s Disease	21712996	CNVD
Breast cancer	21364760	CNVD
Breast cancer	20459607	CNVD
Gastric cancer	18160780	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52634800-52645400	Weak transcription	Fetal Lung	lung
2	chr20:52641400-52646000	Active TSS	Brain Anterior Caudate	brain
3	chr20:52641600-52646000	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
5	chr20:52641800-52646000	Active TSS	Brain Substantia Nigra	brain
6	chr20:52642200-52645400	Weak transcription	Brain Germinal Matrix	brain
7	chr20:52642200-52645600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr20:52642200-52645800	Active TSS	Brain Angular Gyrus	brain
9	chr20:52642400-52646000	Active TSS	Brain Hippocampus Middle	brain
10	chr20:52642600-52645400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr20:52642600-52645800	Active TSS	Brain Cingulate Gyrus	brain
12	chr20:52643200-52645400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr20:52643200-52645600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr20:52643400-52645200	Weak transcription	NHDF-Ad	bronchial
15	chr20:52643800-52646000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr20:52644600-52645600	Genic enhancers	Rectal Mucosa Donor 31	rectum
17	chr20:52644800-52645200	Genic enhancers	Fetal Stomach	stomach
18	chr20:52644800-52645200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
19	chr20:52644800-52645600	Enhancers	Fetal Brain Female	brain
20	chr20:52644800-52645600	Enhancers	Fetal Muscle Leg	muscle
21	chr20:52644800-52646000	Strong transcription	Gastric	stomach
22	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr20:52645000-52645200	Enhancers	Fetal Brain Male	brain
24	chr20:52645000-52645200	Flanking Active TSS	HSMMtube	muscle
25	chr20:52645000-52646400	Enhancers	Placenta	Placenta
26	chr20:52645200-52645600	Enhancers	HSMMtube	muscle
27	chr20:52645200-52645600	Enhancers	K562	blood
28	chr20:52645200-52646000	Enhancers	Fetal Stomach	stomach
29	chr20:52645200-52646400	Enhancers	NHDF-Ad	bronchial
30	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr20:52645400-52645800	Enhancers	Brain Germinal Matrix	brain
32	chr20:52645400-52646000	Enhancers	Fetal Lung	lung
33	chr20:52645400-52646400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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