Variant report

Variant	nsv586232
Chromosome Location	chr20:52646926-52654412
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 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	RCOR1	chr20:52654183-52654358	K562	blood:	n/a	n/a
5	RCOR1	chr20:52654150-52654334	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

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

No data

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

Extended variants
information (count: 285 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:285 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs460076	chr20:52646926-52646927	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs150525649	chr20:52646970-52646971	Enhancers Weak transcription	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
3	rs553103220	chr20:52646979-52646980	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs139538589	chr20:52647030-52647031	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs183882056	chr20:52647053-52647054	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs558620382	chr20:52647099-52647100	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs577451646	chr20:52647114-52647115	Enhancers Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs543193540	chr20:52647211-52647212	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs563117658	chr20:52647212-52647213	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs573866442	chr20:52647231-52647232	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs542864855	chr20:52647233-52647234	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs188823739	chr20:52647242-52647243	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs559087496	chr20:52647254-52647255	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs528084069	chr20:52647281-52647282	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
15	rs150035446	chr20:52647285-52647286	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
16	rs564957762	chr20:52647315-52647316	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
17	rs565372315	chr20:52647322-52647323	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs145655759	chr20:52647329-52647330	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
19	rs367617031	chr20:52647370-52647371	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
20	rs2299711	chr20:52647379-52647380	Weak transcription	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs190900464	chr20:52647403-52647404	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
22	rs2299710	chr20:52647419-52647420	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
23	rs2299709	chr20:52647422-52647423	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
24	rs2299708	chr20:52647424-52647425	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
25	rs534298404	chr20:52647446-52647447	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
26	rs146615517	chr20:52647466-52647467	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs536548533	chr20:52647488-52647489	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs141413000	chr20:52647520-52647521	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs566796457	chr20:52647583-52647584	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs539010009	chr20:52647626-52647627	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs80016689	chr20:52647631-52647632	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs182658930	chr20:52647745-52647746	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs530434629	chr20:52647762-52647763	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs186907247	chr20:52647763-52647764	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs78823726	chr20:52647787-52647788	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs290456	chr20:52647808-52647809	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs1557853	chr20:52647823-52647824	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs290457	chr20:52647830-52647831	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs572783925	chr20:52647858-52647859	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs377541735	chr20:52647895-52647896	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs191729112	chr20:52647945-52647946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs184315166	chr20:52647952-52647953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs148916106	chr20:52647963-52647964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs561370241	chr20:52648018-52648019	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs530306917	chr20:52648052-52648053	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs547014952	chr20:52648084-52648085	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs567135153	chr20:52648130-52648131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs143659700	chr20:52648132-52648133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs552171520	chr20:52648155-52648156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs62215572	chr20:52648285-52648286	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	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:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52641600-52676400	Weak transcription	Stomach Mucosa	stomach
2	chr20:52644800-52666400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr20:52645200-52682200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr20:52645800-52647200	Enhancers	Brain Cingulate Gyrus	brain
5	chr20:52646000-52647200	Enhancers	Brain Hippocampus Middle	brain
6	chr20:52646000-52657000	Weak transcription	Gastric	stomach
7	chr20:52646000-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr20:52646400-52647200	Enhancers	Fetal Brain Male	brain

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