Variant report

Variant	nsv586230
Chromosome Location	chr20:52645534-52654711
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr20:52652599-52652817	A549	lung:	n/a	chr20:52652797-52652809
2	CTCF	chr20:52649892-52649926	Lung_OC	lung:	n/a	n/a
3	GATA3	chr20:52646629-52646974	SH-SY5Y	brain:	n/a	n/a
4	POLR2A	chr20:52646455-52646601	ProgFib	skin:	n/a	n/a
5	RCOR1	chr20:52654150-52654334	K562	blood:	n/a	n/a
6	RCOR1	chr20:52654183-52654358	K562	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:11025812..11027987-chr20:52653374..52655752,2	MCF-7	breast:
2	chr17:57917278..57919596-chr20:52653625..52656516,2	MCF-7	breast:
3	chr20:52642833..52647245-chr20:52651317..52656592,5	MCF-7	breast:
4	chr20:52640367..52641889-chr20:52645625..52647973,2	K562	blood:
5	chr20:52646106..52649105-chr20:52656818..52659729,2	MCF-7	breast:
6	chr20:52648757..52649473-chr5:157170244..157171208,2	MCF-7	breast:
7	chr20:45987538..45989784-chr20:52646421..52648098,2	MCF-7	breast:
8	chr20:52647368..52649299-chr20:52654193..52656329,2	MCF-7	breast:
9	chr20:52647368..52649299-chr20:52654193..52656329,2	MCF-7	breast:
10	chr17:57915947..57917652-chr20:52646723..52649567,2	MCF-7	breast:
11	chr20:52645173..52647456-chr8:56684089..56685719,2	MCF-7	breast:
12	chr20:52643673..52645639-chr20:52687051..52688962,2	MCF-7	breast:
13	chr20:52646516..52648390-chr3:62045905..62047422,2	MCF-7	breast:
14	chr20:52626505..52628533-chr20:52652801..52654568,2	MCF-7	breast:
15	chr2:99769202..99772000-chr20:52646224..52647934,2	MCF-7	breast:

No data

Variant related genes	Relation type
BCAS1	TF binding region
ENSG00000064787	chromatin interactions
ENSG00000199004	chromatin interactions
ENSG00000155858	chromatin interactions
ENSG00000167904	chromatin interactions
ENSG00000144182	chromatin interactions
ENSG00000273155	chromatin interactions
ENSG00000135951	chromatin interactions
ENSG00000137574	chromatin interactions

Extended variants
information (count: 353 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:353 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	rs2072127	chr20:52645541-52645542	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs376756929	chr20:52645551-52645552	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs543189939	chr20:52645601-52645602	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs2072128	chr20:52645646-52645647	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
6	rs377340385	chr20:52645666-52645667	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs540891115	chr20:52645667-52645668	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs6068756	chr20:52645671-52645672	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs564273299	chr20:52645710-52645711	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs190183606	chr20:52645840-52645841	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs138832606	chr20:52645884-52645885	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs6064035	chr20:52645900-52645901	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs140524540	chr20:52645942-52645943	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs62215571	chr20:52645949-52645950	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs67082409	chr20:52645954-52645955	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs367933763	chr20:52646001-52646002	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs77699208	chr20:52646005-52646006	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs290453	chr20:52646029-52646030	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs558081495	chr20:52646061-52646062	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs532066155	chr20:52646082-52646083	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs150420907	chr20:52646109-52646110	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs290454	chr20:52646125-52646126	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs557683494	chr20:52646156-52646157	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs545356430	chr20:52646163-52646164	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs574121938	chr20:52646169-52646170	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs374742773	chr20:52646179-52646180	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs149498993	chr20:52646180-52646181	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs562595687	chr20:52646203-52646204	Enhancers Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs290455	chr20:52646235-52646236	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs372183098	chr20:52646248-52646249	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
31	rs181276635	chr20:52646251-52646252	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
32	rs144079320	chr20:52646310-52646311	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
33	rs138925019	chr20:52646328-52646329	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
34	rs543356309	chr20:52646403-52646404	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
35	rs376781089	chr20:52646407-52646408	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
36	rs563229136	chr20:52646436-52646437	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
37	rs532972284	chr20:52646439-52646440	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
38	rs2870303	chr20:52646486-52646487	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
39	rs546578858	chr20:52646602-52646603	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
40	rs55671222	chr20:52646627-52646628	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs6091809	chr20:52646671-52646672	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
42	rs552217050	chr20:52646679-52646680	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
43	rs147348164	chr20:52646682-52646683	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
44	rs112534941	chr20:52646683-52646684	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
45	rs6091810	chr20:52646708-52646709	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
46	rs185839026	chr20:52646719-52646720	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
47	rs190690666	chr20:52646748-52646749	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
48	rs35556195	chr20:52646750-52646751	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
49	rs571916298	chr20:52646799-52646800	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
50	rs537631416	chr20:52646865-52646866	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 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:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52641400-52646000	Active TSS	Brain Anterior Caudate	brain
2	chr20:52641600-52646000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
4	chr20:52641800-52646000	Active TSS	Brain Substantia Nigra	brain
5	chr20:52642200-52645600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr20:52642200-52645800	Active TSS	Brain Angular Gyrus	brain
7	chr20:52642400-52646000	Active TSS	Brain Hippocampus Middle	brain
8	chr20:52642600-52645800	Active TSS	Brain Cingulate Gyrus	brain
9	chr20:52643200-52645600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr20:52643800-52646000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr20:52644600-52645600	Genic enhancers	Rectal Mucosa Donor 31	rectum
12	chr20:52644800-52645600	Enhancers	Fetal Brain Female	brain
13	chr20:52644800-52645600	Enhancers	Fetal Muscle Leg	muscle
14	chr20:52644800-52646000	Strong transcription	Gastric	stomach
15	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr20:52645000-52646400	Enhancers	Placenta	Placenta
17	chr20:52645200-52645600	Enhancers	HSMMtube	muscle
18	chr20:52645200-52645600	Enhancers	K562	blood
19	chr20:52645200-52646000	Enhancers	Fetal Stomach	stomach
20	chr20:52645200-52646400	Enhancers	NHDF-Ad	bronchial
21	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr20:52645400-52645800	Enhancers	Brain Germinal Matrix	brain
23	chr20:52645400-52646000	Enhancers	Fetal Lung	lung
24	chr20:52645400-52646400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr20:52645600-52645800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr20:52645600-52645800	Flanking Active TSS	HSMMtube	muscle
27	chr20:52645600-52646000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr20:52645600-52646000	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr20:52645600-52646400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr20:52645800-52646000	Flanking Active TSS	Brain Angular Gyrus	brain
31	chr20:52645800-52646000	Enhancers	HSMMtube	muscle
32	chr20:52645800-52647200	Enhancers	Brain Cingulate Gyrus	brain
33	chr20:52646000-52646200	Active TSS	Brain Angular Gyrus	brain
34	chr20:52646000-52646200	Weak transcription	Brain Anterior Caudate	brain
35	chr20:52646000-52646200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr20:52646000-52646800	Enhancers	Brain Substantia Nigra	brain
37	chr20:52646000-52647200	Enhancers	Brain Hippocampus Middle	brain
38	chr20:52646000-52657000	Weak transcription	Gastric	stomach
39	chr20:52646000-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr20:52646200-52646600	Enhancers	Brain Angular Gyrus	brain
41	chr20:52646200-52646600	Enhancers	Brain Inferior Temporal Lobe	brain
42	chr20:52646200-52646800	Enhancers	Brain Anterior Caudate	brain
43	chr20:52646400-52647200	Enhancers	Fetal Brain Male	brain

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