Variant report

Variant	nsv1065004
Chromosome Location	chr20:52647808-52665631
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:181)
CpG islands
(count:0)
Chromatin interactive
region (count:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:181 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ARID3A	chr20:52660800-52661065	K562	blood:	n/a	n/a
2	ATF2	chr20:52660569-52661110	GM12878	blood:	n/a	n/a
3	ATF2	chr20:52660603-52661076	GM12878	blood:	n/a	n/a
4	ATF3	chr20:52660702-52661099	K562	blood:	n/a	n/a
5	BATF	chr20:52660667-52661056	GM12878	blood:	n/a	n/a
6	BATF	chr20:52660645-52661119	GM12878	blood:	n/a	n/a
7	BCL11A	chr20:52660768-52661068	GM12878	blood:	n/a	chr20:52660971-52660980 chr20:52660970-52660979
8	BHLHE40	chr20:52660756-52661015	K562	blood:	n/a	n/a
9	BRCA1	chr20:52660410-52660416	HepG2	liver:	n/a	n/a
10	CBX3	chr20:52660706-52661028	K562	blood:	n/a	n/a
11	CBX3	chr20:52660708-52661021	K562	blood:	n/a	n/a
12	CCNT2	chr20:52660716-52661053	K562	blood:	n/a	n/a
13	CCNT2	chr20:52663681-52664125	K562	blood:	n/a	n/a
14	CEBPB	chr20:52658997-52661146	MCF-7	breast:	n/a	chr20:52659372-52659385 chr20:52659372-52659383 chr20:52659617-52659629
15	CEBPB	chr20:52660694-52661096	A549	lung:	n/a	n/a
16	CEBPB	chr20:52660834-52661014	A549	lung:	n/a	n/a
17	CEBPB	chr20:52663588-52663955	K562	blood:	n/a	n/a
18	CEBPB	chr20:52660758-52660996	K562	blood:	n/a	n/a
19	CEBPB	chr20:52652599-52652817	A549	lung:	n/a	chr20:52652797-52652809
20	CEBPB	chr20:52658684-52661814	MCF-7	breast:	n/a	chr20:52659372-52659385 chr20:52659372-52659383 chr20:52659617-52659629
21	CEBPB	chr20:52660644-52661125	K562	blood:	n/a	n/a
22	CEBPB	chr20:52659371-52659387	HepG2	liver:	n/a	chr20:52659372-52659385 chr20:52659372-52659383
23	CEBPB	chr20:52660901-52660966	HepG2	liver:	n/a	n/a
24	CEBPB	chr20:52660557-52661108	K562	blood:	n/a	n/a
25	CEBPB	chr20:52660784-52661093	IMR90	lung:	n/a	n/a
26	CEBPB	chr20:52663571-52663913	K562	blood:	n/a	n/a
27	CEBPD	chr20:52660584-52661091	K562	blood:	n/a	n/a
28	CEBPD	chr20:52660650-52661087	K562	blood:	n/a	n/a
29	CTCF	chr20:52660300-52660450	GM12873	blood:	n/a	n/a
30	CTCF	chr20:52649892-52649926	Lung_OC	lung:	n/a	n/a
31	CTCF	chr20:52660340-52660490	HMEC	breast:	n/a	n/a
32	CTCF	chr20:52660300-52660450	RPTEC	kidney:	n/a	n/a
33	CTCF	chr20:52660340-52660490	HEEpiC	esophagus:	n/a	n/a
34	CTCF	chr20:52660260-52660529	A549	lung:	n/a	n/a
35	CTCF	chr20:52660307-52660434	GM12878	blood:	n/a	n/a
36	CTCF	chr20:52660358-52660382	NHEK	skin:	n/a	n/a
37	CTCF	chr20:52660300-52660450	GM12875	blood:	n/a	n/a
38	CTCF	chr20:52660263-52660556	K562	blood:	n/a	n/a
39	CTCF	chr20:52660320-52660470	GM06990	blood:	n/a	n/a
40	CTCF	chr20:52664120-52664270	K562	blood:	n/a	n/a
41	CTCF	chr20:52660360-52660430	Hela-S3	cervix:	n/a	n/a
42	CTCF	chr20:52660300-52660450	SAEC	small airway:	n/a	n/a
43	CTCF	chr20:52660280-52660430	Caco-2	colon:	n/a	n/a
44	CTCF	chr20:52660280-52660430	MCF-7	breast:	n/a	n/a
45	CTCF	chr20:52660292-52660481	K562	blood:	n/a	n/a
46	CTCF	chr20:52660320-52660470	AoAF	blood vessel:	n/a	n/a
47	CTCF	chr20:52660320-52660470	GM12864	blood:	n/a	n/a
48	CTCF	chr20:52660328-52660439	Gliobla	brain:	n/a	n/a
49	CTCF	chr20:52660200-52660350	A549	lung:	n/a	n/a
50	CTCF	chr20:52660240-52660390	K562	blood:	n/a	n/a

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52557746..52563146-chr20:52657006..52659772,4	MCF-7	breast:
2	chr20:52647368..52649299-chr20:52654193..52656329,2	MCF-7	breast:
3	chr17:56735097..56736691-chr20:52662317..52665029,2	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	chr20:52643210..52646138-chr20:52658422..52660423,2	K562	blood:
7	chr17:57915947..57917652-chr20:52646723..52649567,2	MCF-7	breast:
8	chr20:52637587..52640113-chr20:52663021..52665849,2	MCF-7	breast:
9	chr20:52646106..52649105-chr20:52656818..52659729,2	MCF-7	breast:
10	chr20:52659902..52660887-chr20:52678920..52680381,7	MCF-7	breast:
11	chr20:52648757..52649473-chr5:157170244..157171208,2	MCF-7	breast:
12	chr20:52642833..52647245-chr20:52651317..52656592,5	MCF-7	breast:
13	chr20:52647368..52649299-chr20:52654193..52656329,2	MCF-7	breast:
14	chr20:52659945..52660854-chr20:52815931..52816527,2	MCF-7	breast:
15	chr19:11025812..11027987-chr20:52653374..52655752,2	MCF-7	breast:
16	chr1:121484253..121484817-chr20:52659977..52660776,2	MCF-7	breast:
17	chr17:59805932..59807613-chr20:52665362..52667872,2	MCF-7	breast:
18	chr20:52655188..52657937-chr20:55839006..55840900,2	MCF-7	breast:
19	chr20:52621471..52622138-chr20:52658585..52659278,2	MCF-7	breast:
20	chr17:57920665..57924197-chr20:52662636..52665586,3	MCF-7	breast:
21	chr20:52646516..52648390-chr3:62045905..62047422,2	MCF-7	breast:
22	chr20:52637408..52640155-chr20:52655059..52656752,2	MCF-7	breast:
23	chr2:99769202..99772000-chr20:52646224..52647934,2	MCF-7	breast:
24	chr17:56707748..56711068-chr20:52660176..52663748,3	MCF-7	breast:
25	chr20:52640367..52641889-chr20:52645625..52647973,2	K562	blood:
26	chr20:52646106..52649105-chr20:52656818..52659729,2	MCF-7	breast:
27	chr20:45987538..45989784-chr20:52646421..52648098,2	MCF-7	breast:

No data

Variant related genes	Relation type
BCAS1	TF binding region
ENSG00000202077	chromatin interactions
ENSG00000135951	chromatin interactions
ENSG00000199004	chromatin interactions
ENSG00000212195	chromatin interactions
ENSG00000273155	chromatin interactions
ENSG00000064787	chromatin interactions
ENSG00000101144	chromatin interactions
ENSG00000155858	chromatin interactions
ENSG00000144182	chromatin interactions

Extended variants
information (count: 741 )
Associated
traits (count: 84 )

Variant overlapped rSNPs/rCNVs (count:741 , 50 per page) page: 1 2 3 4 5 6 7 ... 15

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs290456	chr20:52647808-52647809	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs1557853	chr20:52647823-52647824	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs290457	chr20:52647830-52647831	Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs572783925	chr20:52647858-52647859	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs377541735	chr20:52647895-52647896	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs191729112	chr20:52647945-52647946	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs184315166	chr20:52647952-52647953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs148916106	chr20:52647963-52647964	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs561370241	chr20:52648018-52648019	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs530306917	chr20:52648052-52648053	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs547014952	chr20:52648084-52648085	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs567135153	chr20:52648130-52648131	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs143659700	chr20:52648132-52648133	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs552171520	chr20:52648155-52648156	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs62215572	chr20:52648285-52648286	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs537950938	chr20:52648286-52648287	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs187503538	chr20:52648305-52648306	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs463288	chr20:52648368-52648369	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs567386779	chr20:52648378-52648379	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs536431391	chr20:52648399-52648400	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs572089906	chr20:52648403-52648404	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs374358217	chr20:52648411-52648412	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs141014909	chr20:52648429-52648430	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs545070351	chr20:52648467-52648468	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs150134626	chr20:52648593-52648594	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs545288123	chr20:52648629-52648630	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs576584688	chr20:52648631-52648632	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs558591297	chr20:52648699-52648700	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs575309361	chr20:52648720-52648721	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs138863298	chr20:52648772-52648773	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs192909287	chr20:52648809-52648810	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs2214529	chr20:52648812-52648813	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs546835015	chr20:52648813-52648814	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs540845478	chr20:52648824-52648825	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs35234385	chr20:52648861-52648862	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs572730445	chr20:52648872-52648873	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs540274779	chr20:52648890-52648891	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs562721019	chr20:52648898-52648899	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs560448532	chr20:52648918-52648919	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs114967428	chr20:52648938-52648939	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs142817014	chr20:52648960-52648961	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs531478876	chr20:52648963-52648964	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs290458	chr20:52648994-52648995	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs6091811	chr20:52649002-52649003	Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs115712006	chr20:52649014-52649015	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs568519310	chr20:52649094-52649095	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs146998000	chr20:52649105-52649106	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs534007741	chr20:52649123-52649124	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs553147259	chr20:52649135-52649136	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs74523554	chr20:52649222-52649223	Weak transcription	Chromatin interactive region	1 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:63 , 50 per page) page: 1 2

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	chr20:52646000-52657000	Weak transcription	Gastric	stomach
5	chr20:52646000-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr20:52654800-52656400	Enhancers	K562	blood
7	chr20:52655200-52656400	Enhancers	Fetal Kidney	kidney
8	chr20:52655200-52657200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr20:52655200-52658200	Enhancers	Fetal Stomach	stomach
10	chr20:52656400-52656800	Weak transcription	Fetal Kidney	kidney
11	chr20:52656400-52656800	Weak transcription	K562	blood
12	chr20:52656800-52657200	Enhancers	Colon Smooth Muscle	Colon
13	chr20:52656800-52657400	Enhancers	Fetal Kidney	kidney
14	chr20:52656800-52657400	Enhancers	K562	blood
15	chr20:52657000-52657400	Enhancers	Gastric	stomach
16	chr20:52657000-52657800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr20:52657000-52657800	Enhancers	HSMMtube	muscle
18	chr20:52657200-52657600	Enhancers	NHDF-Ad	bronchial
19	chr20:52657400-52658600	Weak transcription	K562	blood
20	chr20:52657600-52659400	Weak transcription	NHDF-Ad	bronchial
21	chr20:52657800-52659600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:52657800-52664800	Weak transcription	HSMMtube	muscle
23	chr20:52658200-52659400	Weak transcription	Fetal Stomach	stomach
24	chr20:52658600-52660000	Enhancers	K562	blood
25	chr20:52659400-52660400	Enhancers	Fetal Stomach	stomach
26	chr20:52659400-52661000	Enhancers	NHDF-Ad	bronchial
27	chr20:52659600-52659800	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr20:52659600-52660600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr20:52659600-52661000	Enhancers	GM12878-XiMat	blood
30	chr20:52659600-52661800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr20:52659800-52660600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr20:52660000-52660400	Enhancers	Fetal Brain Male	brain
33	chr20:52660000-52660600	Enhancers	Fetal Lung	lung
34	chr20:52660000-52660800	Flanking Active TSS	K562	blood
35	chr20:52660000-52661000	Enhancers	NHLF	lung
36	chr20:52660000-52661200	Enhancers	Osteobl	bone
37	chr20:52660200-52660400	Enhancers	Right Atrium	heart
38	chr20:52660200-52660600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:52660200-52661600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr20:52660200-52661600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr20:52660400-52661000	Enhancers	HMEC	breast
42	chr20:52660400-52664200	Weak transcription	Right Atrium	heart
43	chr20:52660600-52660800	Enhancers	Duodenum Smooth Muscle	Duodenum
44	chr20:52660800-52661600	Enhancers	K562	blood
45	chr20:52661000-52661400	Weak transcription	NHDF-Ad	bronchial
46	chr20:52661000-52661400	Weak transcription	NHLF	lung
47	chr20:52661200-52665000	Weak transcription	Osteobl	bone
48	chr20:52661400-52661600	Enhancers	NHDF-Ad	bronchial
49	chr20:52661400-52661600	Enhancers	NHLF	lung
50	chr20:52661600-52664800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links