Variant report

Variant	esv3403644
Chromosome Location	chr20:52484570-52487118
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:95)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:95 , 50 per page) page: 1 2

No.	Distal block	Cell Line	Cell type
1	chr17:59471125..59471637-chr20:52485944..52486582,2	MCF-7	breast:
2	chr20:52224263..52224919-chr20:52486339..52487302,2	MCF-7	breast:
3	chr12:66506885..66508576-chr20:52484476..52487409,2	MCF-7	breast:
4	chr20:52370915..52371906-chr20:52486506..52487009,2	MCF-7	breast:
5	chr17:59713012..59713653-chr20:52486037..52486698,3	MCF-7	breast:
6	chr17:57919387..57922338-chr20:52486678..52488392,3	MCF-7	breast:
7	chr20:52444785..52445389-chr20:52486199..52486870,2	MCF-7	breast:
8	chr1:114471924..114472700-chr20:52486067..52486923,2	MCF-7	breast:
9	chr17:59491669..59494227-chr20:52486642..52489549,2	MCF-7	breast:
10	chr20:52366518..52369128-chr20:52482212..52484704,2	K562	blood:
11	chr20:52484766..52486838-chr4:146637094..146638832,2	MCF-7	breast:
12	chr17:57920817..57923301-chr20:52482910..52485730,2	MCF-7	breast:
13	chr20:52481182..52483675-chr20:52485548..52487289,2	K562	blood:
14	chr20:52483421..52485868-chr20:55831559..55834264,2	MCF-7	breast:
15	chr17:57914372..57916442-chr20:52486421..52488125,2	MCF-7	breast:
16	chr20:52390064..52391133-chr20:52486352..52487037,3	MCF-7	breast:
17	chr20:52293720..52294594-chr20:52486327..52486831,2	MCF-7	breast:
18	chr20:52372399..52373184-chr20:52486045..52487009,4	MCF-7	breast:
19	chr20:52486459..52486987-chr3:64016036..64016946,2	MCF-7	breast:
20	chr20:52484288..52486178-chr4:88957310..88959480,2	MCF-7	breast:
21	chr20:52193542..52196598-chr20:52485372..52487556,88	MCF-7	breast:
22	chr17:59494089..59494792-chr20:52486104..52486943,2	MCF-7	breast:
23	chr20:52209805..52211171-chr20:52486045..52486721,5	MCF-7	breast:
24	chr20:52198566..52199340-chr20:52486130..52486973,2	MCF-7	breast:
25	chr20:52484501..52486317-chr6:34526583..34529198,2	MCF-7	breast:
26	chr20:52401623..52403995-chr20:52486040..52487259,28	MCF-7	breast:
27	chr20:52480121..52486257-chr20:55824427..55830996,6	MCF-7	breast:
28	chr20:52195366..52195877-chr20:52484212..52484846,2	MCF-7	breast:
29	chr17:59530190..59532912-chr20:52483591..52486439,2	MCF-7	breast:
30	chr20:52478179..52488683-chr20:55835744..55846940,26	MCF-7	breast:
31	chr20:52484717..52486672-chr20:52490016..52492250,2	K562	blood:
32	chr20:52194164..52194825-chr20:52486237..52486842,2	MCF-7	breast:
33	chr20:52486423..52487978-chr20:52491566..52493506,2	K562	blood:
34	chr20:52229027..52230007-chr20:52485802..52487058,7	MCF-7	breast:
35	chr19:10763818..10766592-chr20:52482564..52485159,2	MCF-7	breast:
36	chr20:52229047..52230576-chr20:52485932..52487448,15	MCF-7	breast:
37	chr20:50416767..50419794-chr20:52481301..52484620,4	MCF-7	breast:
38	chr20:52479383..52482682-chr20:52485789..52487570,3	K562	blood:
39	chr20:52485654..52487265-chr20:52530091..52533503,52	MCF-7	breast:
40	chr20:52251331..52252269-chr20:52486087..52486825,3	MCF-7	breast:
41	chr20:52422157..52422923-chr20:52486273..52486879,2	MCF-7	breast:
42	chr20:52483037..52485677-chr9:12813088..12815674,2	MCF-7	breast:
43	chr20:52486123..52487483-chr20:52531651..52533119,11	MCF-7	breast:
44	chr20:52486045..52486985-chr20:55818756..55819874,4	MCF-7	breast:
45	chr20:52194976..52196071-chr20:52485853..52487276,31	MCF-7	breast:
46	chr20:52233059..52233901-chr20:52486110..52486787,2	MCF-7	breast:
47	chr20:52485183..52487690-chrX:47516398..47518387,2	MCF-7	breast:
48	chr20:52483057..52485404-chr20:52528984..52531501,2	K562	blood:
49	chr12:58298965..58299695-chr20:52486173..52486891,2	MCF-7	breast:
50	chr17:57923074..57925214-chr20:52484890..52487156,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000129351	chromatin interactions
ENSG00000236352	chromatin interactions
ENSG00000158373	chromatin interactions
ENSG00000226124	chromatin interactions
ENSG00000101115	chromatin interactions
ENSG00000202077	chromatin interactions
ENSG00000126756	chromatin interactions
ENSG00000101144	chromatin interactions
ENSG00000168298	chromatin interactions
ENSG00000226308	chromatin interactions
ENSG00000163349	chromatin interactions
ENSG00000197555	chromatin interactions
ENSG00000171940	chromatin interactions
ENSG00000062716	chromatin interactions
ENSG00000235448	chromatin interactions
ENSG00000235527	chromatin interactions
ENSG00000259146	chromatin interactions
ENSG00000267280	chromatin interactions
ENSG00000235415	chromatin interactions
ENSG00000267100	chromatin interactions
ENSG00000267064	chromatin interactions
ENSG00000241721	chromatin interactions
ENSG00000201524	chromatin interactions
ENSG00000106069	chromatin interactions
ENSG00000225563	chromatin interactions
ENSG00000187013	chromatin interactions

Extended variants
information (count: 107 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:107 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543131418	chr20:52484598-52484599	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
2	rs77591862	chr20:52484623-52484624	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
3	rs577533681	chr20:52484650-52484651	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
4	rs78282915	chr20:52484652-52484653	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
5	rs532196928	chr20:52484695-52484696	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	12 gene(s)	Overlapped CNVs	n/a
6	rs545737836	chr20:52484729-52484730	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
7	rs144910575	chr20:52484800-52484801	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
8	rs6022819	chr20:52484834-52484835	Weak transcription Enhancers	Chromatin interactive region	13 gene(s)	Overlapped CNVs	n/a
9	rs8114312	chr20:52484852-52484853	Weak transcription Enhancers	Chromatin interactive region	13 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs13038143	chr20:52484888-52484889	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs543765979	chr20:52484897-52484898	Weak transcription Enhancers	Chromatin interactive region	11 gene(s)	Overlapped CNVs	n/a
12	rs13037872	chr20:52484966-52484967	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs551641435	chr20:52484968-52484969	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
14	rs571630241	chr20:52484972-52484973	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
15	rs112630898	chr20:52484973-52484974	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
16	rs537021840	chr20:52484991-52484992	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
17	rs189489947	chr20:52485012-52485013	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
18	rs180678063	chr20:52485019-52485020	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
19	rs67612742	chr20:52485084-52485085	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
20	rs13043214	chr20:52485093-52485094	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
21	rs13043222	chr20:52485107-52485108	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
22	rs71337342	chr20:52485120-52485121	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
23	rs13042127	chr20:52485123-52485124	Weak transcription Enhancers	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
24	rs186170056	chr20:52485160-52485161	Weak transcription Enhancers	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
25	rs28640176	chr20:52485163-52485164	Weak transcription Enhancers	Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
26	rs189432485	chr20:52485230-52485231	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
27	rs181226919	chr20:52485236-52485237	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
28	rs186471694	chr20:52485275-52485276	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
29	rs547868204	chr20:52485288-52485289	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
30	rs559596973	chr20:52485292-52485293	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
31	rs61430147	chr20:52485293-52485294	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
32	rs370709508	chr20:52485298-52485299	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
33	rs374371779	chr20:52485299-52485300	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
34	rs375675929	chr20:52485302-52485303	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
35	rs58300177	chr20:52485319-52485320	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
36	rs58756865	chr20:52485321-52485322	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
37	rs59312322	chr20:52485326-52485327	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
38	rs59656354	chr20:52485331-52485332	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
39	rs60607183	chr20:52485332-52485333	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
40	rs567612013	chr20:52485365-52485366	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
41	rs6022820	chr20:52485379-52485380	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
42	rs533529884	chr20:52485404-52485405	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
43	rs7344120	chr20:52485408-52485409	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
44	rs7347151	chr20:52485409-52485410	Weak transcription	Chromatin interactive region	10 gene(s)	Overlapped CNVs	n/a
45	rs183171124	chr20:52485467-52485468	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
46	rs7508879	chr20:52485495-52485496	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
47	rs186309703	chr20:52485505-52485506	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
48	rs3971348	chr20:52485506-52485507	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
49	rs60397572	chr20:52485514-52485515	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
50	rs373359919	chr20:52485520-52485521	Weak transcription	Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:82)

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
Colorectal cancer	16774939	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

Chromatin state (count:364 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52479400-52484800	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr20:52480000-52484600	Enhancers	Fetal Muscle Leg	muscle
3	chr20:52480000-52484800	Enhancers	Fetal Intestine Large	intestine
4	chr20:52480000-52484800	Enhancers	Fetal Intestine Small	intestine
5	chr20:52480000-52485000	Enhancers	H9 Cell Line	embryonic stem cell
6	chr20:52480000-52485000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr20:52480200-52484800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr20:52480200-52484800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr20:52480200-52484800	Enhancers	Colonic Mucosa	Colon
10	chr20:52480200-52484800	Enhancers	Stomach Mucosa	stomach
11	chr20:52480200-52485200	Enhancers	Primary B cells from peripheral blood	blood
12	chr20:52480200-52485200	Enhancers	Placenta	Placenta
13	chr20:52480600-52484600	Enhancers	Brain Germinal Matrix	brain
14	chr20:52480800-52485000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr20:52481600-52484600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr20:52481600-52484800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr20:52481600-52485000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr20:52481800-52484600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr20:52481800-52489200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr20:52482000-52484600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr20:52482200-52484800	Flanking Active TSS	NHEK	skin
22	chr20:52482400-52484600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr20:52482400-52484600	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr20:52482400-52484800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr20:52482400-52484800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
26	chr20:52482400-52484800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
27	chr20:52482400-52484800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr20:52482600-52484600	Enhancers	Small Intestine	intestine
29	chr20:52482600-52484800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr20:52482800-52484600	Enhancers	K562	blood
31	chr20:52482800-52484600	Enhancers	NH-A	brain
32	chr20:52482800-52484800	Enhancers	Primary B cells from cord blood	blood
33	chr20:52482800-52484800	Enhancers	Fetal Brain Female	brain
34	chr20:52482800-52484800	Enhancers	Thymus	Thymus
35	chr20:52482800-52485000	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr20:52482800-52485800	Weak transcription	Left Ventricle	heart
37	chr20:52482800-52485800	Weak transcription	Ovary	ovary
38	chr20:52482800-52486000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr20:52482800-52486000	Weak transcription	Lung	lung
40	chr20:52482800-52486200	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr20:52482800-52489200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr20:52482800-52489400	Weak transcription	Aorta	Aorta
43	chr20:52482800-52489800	Weak transcription	Esophagus	oesophagus
44	chr20:52482800-52492000	Weak transcription	Gastric	stomach
45	chr20:52483000-52484600	Enhancers	Brain Anterior Caudate	brain
46	chr20:52483000-52484600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr20:52483000-52484800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr20:52483000-52485200	Enhancers	Fetal Thymus	thymus
49	chr20:52483200-52484600	Enhancers	Fetal Kidney	kidney
50	chr20:52483200-52484600	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links