Variant report

Variant	nsv458980
Chromosome Location	chr20:41228738-41284782
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	chr20:41269498-41269701	HepG2	liver:	n/a	chr20:41269631-41269642
3	CEBPB	chr20:41234364-41234717	HepG2	liver:	n/a	n/a
4	CEBPB	chr20:41279055-41279225	H1-hESC	embryonic stem cell:	n/a	chr20:41279114-41279125
5	CEBPB	chr20:41282814-41283026	HepG2	liver:	n/a	chr20:41282919-41282930
6	CEBPB	chr20:41265532-41265732	HepG2	liver:	n/a	chr20:41265590-41265603 chr20:41265591-41265602
7	CEBPB	chr20:41234470-41234614	K562	blood:	n/a	n/a
8	CEBPB	chr20:41274989-41275199	HepG2	liver:	n/a	n/a
9	CEBPB	chr20:41251310-41251377	HepG2	liver:	n/a	n/a
10	CEBPB	chr20:41240638-41240690	HepG2	liver:	n/a	chr20:41240677-41240688
11	CTCF	chr20:41238860-41239010	MCF-7	breast:	n/a	n/a
12	CTCF	chr20:41249720-41249870	WI-38	lung:	n/a	n/a
13	CTCF	chr20:41238877-41238939	K562	blood:	n/a	n/a
14	CTCF	chr20:41238740-41238890	HEK293	kidney:	n/a	n/a
15	CTCF	chr20:41280200-41280350	GM12868	blood:	n/a	n/a
16	CTCF	chr20:41238800-41238950	WERI-Rb-1	eye:	n/a	n/a
17	CTCF	chr20:41238840-41238990	Caco-2	colon:	n/a	n/a
18	CTCF	chr20:41238767-41239033	MCF-7	breast:	n/a	n/a
19	CTCF	chr20:41266833-41266917	Lung_OC	lung:	n/a	n/a
20	CTCF	chr20:41238800-41238950	NB4	blood:	n/a	n/a
21	CTCF	chr20:41251400-41251550	GM12866	blood:	n/a	n/a
22	CTCF	chr20:41238859-41238976	MCF-7	breast:	n/a	n/a
23	CTCF	chr20:41238760-41238910	MCF-7	breast:	n/a	n/a
24	CTCF	chr20:41238813-41238946	HepG2	liver:	n/a	n/a
25	CTCF	chr20:41238833-41238962	K562	blood:	n/a	n/a
26	CTCF	chr20:41238881-41238962	HepG2	liver:	n/a	n/a
27	CTCF	chr20:41238680-41238830	NHEK	skin:	n/a	n/a
28	CTCF	chr20:41238836-41239000	MCF-7	breast:	n/a	n/a
29	CTCF	chr20:41279180-41279330	GM12873	blood:	n/a	n/a
30	CTCF	chr20:41238652-41239034	MCF-7	breast:	n/a	n/a
31	CTCF	chr20:41238800-41238950	GM06990	blood:	n/a	n/a
32	CTCF	chr20:41261016-41261073	GM10266	blood:	n/a	n/a
33	CTCF	chr20:41282980-41283130	K562	blood:	n/a	n/a
34	CTCF	chr20:41229986-41230013	GM10248	blood:	n/a	n/a
35	E2F4	chr20:41274271-41274430	MCF10A-Er-Src	breast:	n/a	n/a
36	ELF1	chr20:41276014-41276213	K562	blood:	n/a	chr20:41276139-41276150 chr20:41276139-41276150 chr20:41276137-41276150 chr20:41276140-41276149
37	FAM48A	chr20:41261723-41261813	GM12878	blood:	n/a	n/a
38	FOXA1	chr20:41248958-41249342	HepG2	liver:	n/a	n/a
39	FOXA2	chr20:41248969-41249241	A549	lung:	n/a	n/a
40	FOXA2	chr20:41248867-41249464	A549	lung:	n/a	n/a
41	GATA3	chr20:41283634-41283781	SH-SY5Y	brain:	n/a	n/a
42	GATA3	chr20:41257405-41257971	MCF-7	breast:	n/a	n/a
43	GATA3	chr20:41266551-41267131	MCF-7	breast:	n/a	n/a
44	JUN	chr20:41276234-41276338	HepG2	liver:	n/a	chr20:41276265-41276278
45	JUND	chr20:41240653-41240695	HepG2	liver:	n/a	n/a
46	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
47	JUND	chr20:41266984-41267239	HepG2	liver:	n/a	chr20:41267115-41267122 chr20:41267115-41267124 chr20:41267114-41267123 chr20:41267115-41267123 chr20:41267113-41267124
48	MAFF	chr20:41267814-41268140	HepG2	liver:	n/a	n/a
49	MAFF	chr20:41267887-41268078	K562	blood:	n/a	n/a
50	MAFK	chr20:41240811-41240964	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:115299122..115302084-chr20:41239351..41241193,2	MCF-7	breast:
2	chr1:115299061..115301144-chr20:41248782..41252439,3	MCF-7	breast:
3	chr20:41221842..41223467-chr20:41282056..41284683,2	MCF-7	breast:
4	chr20:41238748..41239268-chr20:41307296..41307807,2	MCF-7	breast:
5	chr20:41235856..41237826-chr20:41240786..41243321,2	K562	blood:
6	chr20:41232529..41235268-chr20:41239023..41240669,2	MCF-7	breast:
7	chr20:41232529..41235268-chr20:41239023..41240669,2	MCF-7	breast:
8	chr20:41235856..41237826-chr20:41240786..41243321,2	K562	blood:
9	chr1:115296501..115298139-chr20:41277950..41280016,2	MCF-7	breast:

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

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

Extended variants
information (count: 2250 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:2250 , 50 per page) page: 1 2 3 4 5 6 7 ... 45

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6102926	chr20:41228738-41228739	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs8123681	chr20:41228763-41228764	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs556706058	chr20:41228776-41228777	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs201422471	chr20:41228782-41228783	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs544769550	chr20:41228855-41228856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs564661576	chr20:41228925-41228926	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs146155121	chr20:41228928-41228929	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs546301383	chr20:41228929-41228930	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs539491030	chr20:41228960-41228961	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs528966787	chr20:41228970-41228971	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs548712074	chr20:41228982-41228983	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs568611425	chr20:41228983-41228984	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs537675405	chr20:41228986-41228987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs201760204	chr20:41228994-41228995	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs140162462	chr20:41229018-41229019	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs571470716	chr20:41229021-41229022	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs534043739	chr20:41229048-41229049	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs6093692	chr20:41229079-41229080	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs185560219	chr20:41229087-41229088	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs369968297	chr20:41229157-41229158	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs566911928	chr20:41229163-41229164	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs187988892	chr20:41229190-41229191	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs143816774	chr20:41229198-41229199	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs112807604	chr20:41229201-41229202	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs544494588	chr20:41229212-41229213	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs6093693	chr20:41229217-41229218	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs565076900	chr20:41229221-41229222	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs540882306	chr20:41229226-41229227	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs6093694	chr20:41229279-41229280	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs528905357	chr20:41229302-41229303	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs529130369	chr20:41229307-41229308	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs370615039	chr20:41229310-41229311	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs148962689	chr20:41229318-41229319	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs562280033	chr20:41229319-41229320	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs531405184	chr20:41229339-41229340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs35766489	chr20:41229351-41229352	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs6093695	chr20:41229353-41229354	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs6102927	chr20:41229364-41229365	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs6093696	chr20:41229368-41229369	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs562611822	chr20:41229376-41229377	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs77705978	chr20:41229377-41229378	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs532939807	chr20:41229410-41229411	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs578056065	chr20:41229415-41229416	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs76501763	chr20:41229423-41229424	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs539171297	chr20:41229475-41229476	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs6102928	chr20:41229500-41229501	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs569755969	chr20:41229566-41229567	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs191246613	chr20:41229569-41229570	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs142863823	chr20:41229589-41229590	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs183833620	chr20:41229592-41229593	Weak transcription	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:48 , 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	chr20:41228000-41231200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr20:41231200-41233400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr20:41232400-41232600	Enhancers	Pancreas	Pancrea
6	chr20:41232600-41233000	Weak transcription	Pancreas	Pancrea
7	chr20:41232800-41234400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr20:41233000-41234800	Enhancers	Pancreas	Pancrea
9	chr20:41233800-41234200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:41234200-41234600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr20:41234400-41234800	Enhancers	NHEK	skin
12	chr20:41234800-41236000	Weak transcription	NHEK	skin
13	chr20:41236000-41236600	Enhancers	NHEK	skin
14	chr20:41240000-41241600	Enhancers	Fetal Brain Male	brain
15	chr20:41240000-41242800	Enhancers	Fetal Muscle Leg	muscle
16	chr20:41240200-41240400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr20:41240200-41240800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr20:41240400-41240600	Bivalent Enhancer	Fetal Brain Female	brain
19	chr20:41240400-41240800	Enhancers	Fetal Muscle Trunk	muscle
20	chr20:41240400-41241400	Enhancers	Fetal Stomach	stomach
21	chr20:41240600-41242200	Enhancers	Fetal Brain Female	brain
22	chr20:41241000-41242200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr20:41241800-41242400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr20:41242800-41243000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr20:41249200-41249600	Active TSS	ES-I3 Cell Line	embryonic stem cell
26	chr20:41249200-41249600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr20:41249200-41249800	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr20:41249200-41249800	Active TSS	Duodenum Mucosa	Duodenum
29	chr20:41251400-41252000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr20:41251400-41253800	Enhancers	NHEK	skin
31	chr20:41251600-41253600	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr20:41251800-41252400	Enhancers	H1 Cell Line	embryonic stem cell
33	chr20:41251800-41252600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr20:41253600-41270200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr20:41257000-41258200	Enhancers	Liver	Liver
36	chr20:41263000-41263400	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr20:41263000-41264200	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr20:41270200-41270800	Enhancers	Pancreas	Pancrea
39	chr20:41270200-41271600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr20:41271600-41300800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr20:41277000-41277400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr20:41278600-41279400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr20:41278800-41279400	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr20:41279000-41279400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr20:41281000-41281400	Enhancers	Gastric	stomach
46	chr20:41281200-41281600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr20:41281400-41285600	Weak transcription	Gastric	stomach
48	chr20:41284200-41285600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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