Variant report

Variant	nsv586020
Chromosome Location	chr20:41207365-41243236
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	BACH1	chr20:41216153-41216346	H1-hESC	embryonic stem cell:	n/a	chr20:41216218-41216232
2	CEBPB	chr20:41234470-41234614	K562	blood:	n/a	n/a
3	CEBPB	chr20:41218900-41219249	HepG2	liver:	n/a	chr20:41219078-41219089
4	CEBPB	chr20:41234364-41234717	HepG2	liver:	n/a	n/a
5	CEBPB	chr20:41240638-41240690	HepG2	liver:	n/a	chr20:41240677-41240688
6	CEBPB	chr20:41218872-41219099	H1-hESC	embryonic stem cell:	n/a	chr20:41219078-41219089
7	CEBPB	chr20:41218705-41219269	MCF-7	breast:	n/a	chr20:41219078-41219089
8	CEBPB	chr20:41218909-41219150	K562	blood:	n/a	chr20:41219078-41219089
9	CEBPB	chr20:41218940-41219204	IMR90	lung:	n/a	chr20:41219078-41219089
10	CEBPB	chr20:41218912-41219204	A549	lung:	n/a	chr20:41219078-41219089
11	CTCF	chr20:41223860-41224010	GM12873	blood:	n/a	n/a
12	CTCF	chr20:41238652-41239034	MCF-7	breast:	n/a	n/a
13	CTCF	chr20:41218700-41218850	Caco-2	colon:	n/a	n/a
14	CTCF	chr20:41238800-41238950	WERI-Rb-1	eye:	n/a	n/a
15	CTCF	chr20:41229986-41230013	GM10248	blood:	n/a	n/a
16	CTCF	chr20:41238813-41238946	HepG2	liver:	n/a	n/a
17	CTCF	chr20:41238833-41238962	K562	blood:	n/a	n/a
18	CTCF	chr20:41238760-41238910	MCF-7	breast:	n/a	n/a
19	CTCF	chr20:41238877-41238939	K562	blood:	n/a	n/a
20	CTCF	chr20:41218560-41218710	MCF-7	breast:	n/a	n/a
21	CTCF	chr20:41238859-41238976	MCF-7	breast:	n/a	n/a
22	CTCF	chr20:41238740-41238890	HEK293	kidney:	n/a	n/a
23	CTCF	chr20:41238767-41239033	MCF-7	breast:	n/a	n/a
24	CTCF	chr20:41218660-41218810	HEK293	kidney:	n/a	n/a
25	CTCF	chr20:41221060-41221210	GM12868	blood:	n/a	n/a
26	CTCF	chr20:41238800-41238950	NB4	blood:	n/a	n/a
27	CTCF	chr20:41238680-41238830	NHEK	skin:	n/a	n/a
28	CTCF	chr20:41218660-41218810	HRE	kidney:	n/a	n/a
29	CTCF	chr20:41218760-41218910	MCF-7	breast:	n/a	n/a
30	CTCF	chr20:41238800-41238950	GM06990	blood:	n/a	n/a
31	CTCF	chr20:41238860-41239010	MCF-7	breast:	n/a	n/a
32	CTCF	chr20:41238836-41239000	MCF-7	breast:	n/a	n/a
33	CTCF	chr20:41238881-41238962	HepG2	liver:	n/a	n/a
34	CTCF	chr20:41238840-41238990	Caco-2	colon:	n/a	n/a
35	CTCF	chr20:41218781-41218842	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr20:41218580-41218730	GM12871	blood:	n/a	n/a
37	EP300	chr20:41210765-41211300	MCF-7	breast:	n/a	n/a
38	JUND	chr20:41232317-41232668	HepG2	liver:	n/a	chr20:41232481-41232488 chr20:41232476-41232487 chr20:41232480-41232489 chr20:41232478-41232489 chr20:41232478-41232490 chr20:41232479-41232489 chr20:41232479-41232488 chr20:41232479-41232489
39	JUND	chr20:41240653-41240695	HepG2	liver:	n/a	n/a
40	JUND	chr20:41217558-41217859	HepG2	liver:	n/a	chr20:41217708-41217718 chr20:41217707-41217718 chr20:41217708-41217718 chr20:41217708-41217718 chr20:41217709-41217718 chr20:41217708-41217718
41	MAFK	chr20:41240811-41240964	HepG2	liver:	n/a	n/a
42	MAX	chr20:41213643-41213807	NB4	blood:	n/a	chr20:41213786-41213796
43	MYC	chr20:41215750-41215766	H1-hESC	embryonic stem cell:	n/a	n/a
44	NFYA	chr20:41232312-41232506	GM12878	blood:	n/a	n/a
45	NR2F2	chr20:41215817-41216492	MCF-7	breast:	n/a	n/a
46	POLR2A	chr20:41216153-41216384	MCF-7	breast:	n/a	n/a
47	POLR2A	chr20:41227443-41227484	A549	lung:	n/a	n/a
48	POLR2A	chr20:41216147-41216151	MCF-7	breast:	n/a	n/a
49	POLR2A	chr20:41221999-41222040	GM12878	blood:	n/a	n/a
50	POLR2A	chr20:41235106-41235130	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr20:41238748..41239268-chr20:41307296..41307807,2	MCF-7	breast:
2	chr20:41210269..41211939-chr20:41214857..41217644,2	MCF-7	breast:
3	chr20:41223845..41225575-chr20:41225576..41227086,2	MCF-7	breast:
4	chr20:41235856..41237826-chr20:41240786..41243321,2	K562	blood:
5	chr20:41221842..41223467-chr20:41282056..41284683,2	MCF-7	breast:
6	chr20:41223845..41225575-chr20:41225576..41227086,2	MCF-7	breast:
7	chr1:115299122..115302084-chr20:41239351..41241193,2	MCF-7	breast:
8	chr20:41232529..41235268-chr20:41239023..41240669,2	MCF-7	breast:
9	chr20:41219224..41221515-chr20:41224161..41226568,2	MCF-7	breast:
10	chr20:41219224..41221515-chr20:41224161..41226568,2	MCF-7	breast:
11	chr20:41210269..41211939-chr20:41214857..41217644,2	MCF-7	breast:
12	chr20:41232529..41235268-chr20:41239023..41240669,2	MCF-7	breast:
13	chr20:41183351..41185462-chr20:41211169..41213368,2	MCF-7	breast:
14	chr20:41235856..41237826-chr20:41240786..41243321,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRSF6-11	chr20:41235334-41235515	NONHSAT079803
2	lnc-SRSF6-11	chr20:41236034-41236199	NONHSAT079803

Variant related genes	Relation type
ENSG00000229892	TF binding region
ENSG00000009307	chromatin interactions

Extended variants
information (count: 1544 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:1544 , 50 per page) page: 1 2 3 4 5 6 7 ... 31

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6030341	chr20:41207365-41207366	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs576517759	chr20:41207481-41207482	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs545135142	chr20:41207502-41207503	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs565500460	chr20:41207524-41207525	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs200719616	chr20:41207531-41207532	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs531147846	chr20:41207541-41207542	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs6065514	chr20:41207542-41207543	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs370497196	chr20:41207543-41207544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs527835817	chr20:41207549-41207550	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs59370151	chr20:41207551-41207552	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs541337517	chr20:41207577-41207578	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs377569350	chr20:41207602-41207603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs561288968	chr20:41207614-41207615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs530326751	chr20:41207645-41207646	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs369239682	chr20:41207655-41207656	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs185079279	chr20:41207667-41207668	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs6102914	chr20:41207669-41207670	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs180981908	chr20:41207681-41207682	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs185603373	chr20:41207723-41207724	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs377574130	chr20:41207773-41207774	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs531532415	chr20:41207789-41207790	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs551938383	chr20:41207794-41207795	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs565875849	chr20:41207795-41207796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs200723488	chr20:41207803-41207804	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs59941593	chr20:41207809-41207810	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs534853973	chr20:41207818-41207819	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs369425647	chr20:41207821-41207822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs554799031	chr20:41207855-41207856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs188747954	chr20:41207911-41207912	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs537324372	chr20:41207913-41207914	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs556533790	chr20:41207948-41207949	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs576327551	chr20:41207959-41207960	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs545489508	chr20:41208011-41208012	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs558743780	chr20:41208012-41208013	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs149101442	chr20:41208062-41208063	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs374174381	chr20:41208096-41208097	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs541275756	chr20:41208119-41208120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs143140372	chr20:41208154-41208155	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs181643797	chr20:41208159-41208160	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs543723507	chr20:41208169-41208170	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs563318480	chr20:41208171-41208172	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs531971760	chr20:41208193-41208194	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs377503912	chr20:41208234-41208235	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs552139764	chr20:41208268-41208269	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs549916241	chr20:41208269-41208270	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs186729879	chr20:41208330-41208331	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs548436517	chr20:41208356-41208357	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs571121293	chr20:41208370-41208371	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs537362752	chr20:41208408-41208409	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs116156631	chr20:41208427-41208428	Weak transcription	n/a	n/a	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
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
Autism	22495311	CNVD
Anaplastic large cell lymphoma	18179710	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
Soft tissue tumor	16732325	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
Bladder cancer	21909424	CNVD
Breast cancer	17603634	CNVD
Melanoma	18172304	CNVD
Breast cancer	16608533	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Breast cancer	21364760	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17133270	CNVD
Oral cancer	21386901	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Ovarian cancer	19193619	CNVD
Breast cancer	21785460	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Myelodysplastic syndrome	17634407	CNVD
Myelodysplastic syndrome	21251322	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Ductal carcinoma	22052326	CNVD
Prostate cancer	18632612	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Gastric cancer	16891809	CNVD
Multiple myeloma	16616336	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Malignant melanoma	17260012	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Colorectal cancer	16774939	CNVD
Myelofibrosis	22110671	CNVD
Cervical cancer	21062161	CNVD
Ovarian neoplasms	16753589	CNVD
Non-small cell lung cancer	21829676	CNVD
Gastric cancer	20585902	CNVD
Ductal carcinoma	18381933	CNVD
Cancer	21129771	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41205000-41210000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr20:41205200-41207400	Enhancers	Pancreas	Pancrea
3	chr20:41206000-41207400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr20:41206800-41216200	Weak transcription	Gastric	stomach
5	chr20:41207400-41215400	Weak transcription	Pancreas	Pancrea
6	chr20:41207400-41218600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr20:41209800-41210800	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr20:41210000-41210800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr20:41210400-41210800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr20:41210800-41212800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr20:41212800-41213600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr20:41213000-41213600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr20:41215400-41217800	Enhancers	Pancreas	Pancrea
14	chr20:41216200-41216400	Enhancers	Gastric	stomach
15	chr20:41216400-41216800	Weak transcription	Gastric	stomach
16	chr20:41217400-41218000	Enhancers	NHEK	skin
17	chr20:41217800-41221600	Weak transcription	Pancreas	Pancrea
18	chr20:41218600-41219200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr20:41219200-41240200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr20:41221600-41226200	Enhancers	Pancreas	Pancrea
21	chr20:41222600-41223600	Enhancers	Fetal Muscle Leg	muscle
22	chr20:41226200-41232400	Weak transcription	Pancreas	Pancrea
23	chr20:41227000-41227800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr20:41227400-41228000	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr20:41227400-41228000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr20:41227400-41228200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr20:41228000-41231200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr20:41231200-41233400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr20:41232400-41232600	Enhancers	Pancreas	Pancrea
30	chr20:41232600-41233000	Weak transcription	Pancreas	Pancrea
31	chr20:41232800-41234400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr20:41233000-41234800	Enhancers	Pancreas	Pancrea
33	chr20:41233800-41234200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr20:41234200-41234600	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr20:41234400-41234800	Enhancers	NHEK	skin
36	chr20:41234800-41236000	Weak transcription	NHEK	skin
37	chr20:41236000-41236600	Enhancers	NHEK	skin
38	chr20:41240000-41241600	Enhancers	Fetal Brain Male	brain
39	chr20:41240000-41242800	Enhancers	Fetal Muscle Leg	muscle
40	chr20:41240200-41240400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr20:41240200-41240800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
42	chr20:41240400-41240600	Bivalent Enhancer	Fetal Brain Female	brain
43	chr20:41240400-41240800	Enhancers	Fetal Muscle Trunk	muscle
44	chr20:41240400-41241400	Enhancers	Fetal Stomach	stomach
45	chr20:41240600-41242200	Enhancers	Fetal Brain Female	brain
46	chr20:41241000-41242200	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr20:41241800-41242400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr20:41242800-41243000	Enhancers	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links