Variant report

Variant	nsv1066761
Chromosome Location	chr20:41226302-41269430
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	chr20:41262897-41263215	H1-hESC	embryonic stem cell:	n/a	n/a
2	CEBPB	chr20:41265532-41265732	HepG2	liver:	n/a	chr20:41265590-41265603 chr20:41265591-41265602
3	CEBPB	chr20:41234364-41234717	HepG2	liver:	n/a	n/a
4	CEBPB	chr20:41251310-41251377	HepG2	liver:	n/a	n/a
5	CEBPB	chr20:41240638-41240690	HepG2	liver:	n/a	chr20:41240677-41240688
6	CEBPB	chr20:41234470-41234614	K562	blood:	n/a	n/a
7	CTCF	chr20:41261016-41261073	GM10266	blood:	n/a	n/a
8	CTCF	chr20:41238740-41238890	HEK293	kidney:	n/a	n/a
9	CTCF	chr20:41238859-41238976	MCF-7	breast:	n/a	n/a
10	CTCF	chr20:41238881-41238962	HepG2	liver:	n/a	n/a
11	CTCF	chr20:41238800-41238950	GM06990	blood:	n/a	n/a
12	CTCF	chr20:41238833-41238962	K562	blood:	n/a	n/a
13	CTCF	chr20:41238877-41238939	K562	blood:	n/a	n/a
14	CTCF	chr20:41249720-41249870	WI-38	lung:	n/a	n/a
15	CTCF	chr20:41238767-41239033	MCF-7	breast:	n/a	n/a
16	CTCF	chr20:41266833-41266917	Lung_OC	lung:	n/a	n/a
17	CTCF	chr20:41238800-41238950	NB4	blood:	n/a	n/a
18	CTCF	chr20:41238760-41238910	MCF-7	breast:	n/a	n/a
19	CTCF	chr20:41238813-41238946	HepG2	liver:	n/a	n/a
20	CTCF	chr20:41238680-41238830	NHEK	skin:	n/a	n/a
21	CTCF	chr20:41238860-41239010	MCF-7	breast:	n/a	n/a
22	CTCF	chr20:41238652-41239034	MCF-7	breast:	n/a	n/a
23	CTCF	chr20:41238836-41239000	MCF-7	breast:	n/a	n/a
24	CTCF	chr20:41229986-41230013	GM10248	blood:	n/a	n/a
25	CTCF	chr20:41238840-41238990	Caco-2	colon:	n/a	n/a
26	CTCF	chr20:41251400-41251550	GM12866	blood:	n/a	n/a
27	CTCF	chr20:41238800-41238950	WERI-Rb-1	eye:	n/a	n/a
28	FAM48A	chr20:41261723-41261813	GM12878	blood:	n/a	n/a
29	FOXA1	chr20:41248958-41249342	HepG2	liver:	n/a	n/a
30	FOXA2	chr20:41248867-41249464	A549	lung:	n/a	n/a
31	FOXA2	chr20:41248969-41249241	A549	lung:	n/a	n/a
32	GATA3	chr20:41257405-41257971	MCF-7	breast:	n/a	n/a
33	GATA3	chr20:41266551-41267131	MCF-7	breast:	n/a	n/a
34	JUND	chr20:41266984-41267239	HepG2	liver:	n/a	chr20:41267115-41267122 chr20:41267115-41267124 chr20:41267114-41267123 chr20:41267115-41267123 chr20:41267113-41267124
35	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
36	JUND	chr20:41240653-41240695	HepG2	liver:	n/a	n/a
37	MAFF	chr20:41267887-41268078	K562	blood:	n/a	n/a
38	MAFF	chr20:41267814-41268140	HepG2	liver:	n/a	n/a
39	MAFK	chr20:41267830-41268134	HepG2	liver:	n/a	chr20:41267964-41267981
40	MAFK	chr20:41267797-41268140	HepG2	liver:	n/a	chr20:41267964-41267981
41	MAFK	chr20:41262913-41263216	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAFK	chr20:41267821-41268080	K562	blood:	n/a	chr20:41267964-41267981
43	MAFK	chr20:41267901-41268137	IMR90	lung:	n/a	chr20:41267964-41267981
44	MAFK	chr20:41240811-41240964	HepG2	liver:	n/a	n/a
45	MAX	chr20:41252208-41252222	NB4	blood:	n/a	n/a
46	NFYA	chr20:41232312-41232506	GM12878	blood:	n/a	n/a
47	NR2F2	chr20:41257415-41257980	MCF-7	breast:	n/a	n/a
48	POLR2A	chr20:41227428-41227515	MCF-7	breast:	n/a	n/a
49	POLR2A	chr20:41263629-41263767	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr20:41234992-41235093	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	chr1:115299122..115302084-chr20:41239351..41241193,2	MCF-7	breast:
3	chr20:41219224..41221515-chr20:41224161..41226568,2	MCF-7	breast:
4	chr20:41232529..41235268-chr20:41239023..41240669,2	MCF-7	breast:
5	chr20:41223845..41225575-chr20:41225576..41227086,2	MCF-7	breast:
6	chr1:115299061..115301144-chr20:41248782..41252439,3	MCF-7	breast:
7	chr20:41235856..41237826-chr20:41240786..41243321,2	K562	blood:
8	chr20:41232529..41235268-chr20:41239023..41240669,2	MCF-7	breast:
9	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: 1740 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:1740 , 50 per page) page: 1 2 3 4 5 6 7 ... 35

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6030355	chr20:41226353-41226354	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs566654186	chr20:41226371-41226372	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs547407807	chr20:41226372-41226373	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs560900515	chr20:41226375-41226376	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs530143464	chr20:41226388-41226389	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs549902756	chr20:41226415-41226416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs569812061	chr20:41226452-41226453	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs539248756	chr20:41226506-41226507	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs552480631	chr20:41226542-41226543	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs181504989	chr20:41226543-41226544	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs548788809	chr20:41226558-41226559	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs148082330	chr20:41226590-41226591	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs554610157	chr20:41226640-41226641	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs376229587	chr20:41226647-41226648	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs186933286	chr20:41226701-41226702	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs6016844	chr20:41226726-41226727	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs557118347	chr20:41226735-41226736	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs371022200	chr20:41226755-41226756	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs373150231	chr20:41226763-41226764	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs568489369	chr20:41226775-41226776	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs138133133	chr20:41226787-41226788	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs545993496	chr20:41226883-41226884	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs374063648	chr20:41226916-41226917	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs79768513	chr20:41226918-41226919	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs191775312	chr20:41226953-41226954	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs541681231	chr20:41226994-41226995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs183971377	chr20:41227045-41227046	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs577353976	chr20:41227048-41227049	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs112545615	chr20:41227053-41227054	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs530083228	chr20:41227060-41227061	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs6093689	chr20:41227116-41227117	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs556952019	chr20:41227124-41227125	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs373424312	chr20:41227138-41227139	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs532466585	chr20:41227179-41227180	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs34818330	chr20:41227188-41227189	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs75011843	chr20:41227197-41227198	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs370267092	chr20:41227202-41227203	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs528806466	chr20:41227246-41227247	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs147007777	chr20:41227265-41227266	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs78118567	chr20:41227282-41227283	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs13040940	chr20:41227309-41227310	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs77437568	chr20:41227329-41227330	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs113294204	chr20:41227335-41227336	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs186406127	chr20:41227344-41227345	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs6093690	chr20:41227405-41227406	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs138156657	chr20:41227443-41227444	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs115390058	chr20:41227463-41227464	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs4358190	chr20:41227471-41227472	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs541621075	chr20:41227501-41227502	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs555271733	chr20:41227509-41227510	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

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

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:41219200-41240200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:41226200-41232400	Weak transcription	Pancreas	Pancrea
3	chr20:41227000-41227800	Enhancers	Monocytes-CD14+_RO01746	blood
4	chr20:41227400-41228000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr20:41227400-41228000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr20:41227400-41228200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr20:41228000-41231200	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr20:41231200-41233400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr20:41232400-41232600	Enhancers	Pancreas	Pancrea
10	chr20:41232600-41233000	Weak transcription	Pancreas	Pancrea
11	chr20:41232800-41234400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr20:41233000-41234800	Enhancers	Pancreas	Pancrea
13	chr20:41233800-41234200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr20:41234200-41234600	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr20:41234400-41234800	Enhancers	NHEK	skin
16	chr20:41234800-41236000	Weak transcription	NHEK	skin
17	chr20:41236000-41236600	Enhancers	NHEK	skin
18	chr20:41240000-41241600	Enhancers	Fetal Brain Male	brain
19	chr20:41240000-41242800	Enhancers	Fetal Muscle Leg	muscle
20	chr20:41240200-41240400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr20:41240200-41240800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr20:41240400-41240600	Bivalent Enhancer	Fetal Brain Female	brain
23	chr20:41240400-41240800	Enhancers	Fetal Muscle Trunk	muscle
24	chr20:41240400-41241400	Enhancers	Fetal Stomach	stomach
25	chr20:41240600-41242200	Enhancers	Fetal Brain Female	brain
26	chr20:41241000-41242200	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr20:41241800-41242400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr20:41242800-41243000	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr20:41249200-41249600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr20:41249200-41249600	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr20:41249200-41249800	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr20:41249200-41249800	Active TSS	Duodenum Mucosa	Duodenum
33	chr20:41251400-41252000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr20:41251400-41253800	Enhancers	NHEK	skin
35	chr20:41251600-41253600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr20:41251800-41252400	Enhancers	H1 Cell Line	embryonic stem cell
37	chr20:41251800-41252600	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr20:41253600-41270200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr20:41257000-41258200	Enhancers	Liver	Liver
40	chr20:41263000-41263400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr20:41263000-41264200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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