Variant report

Variant	nsv909516
Chromosome Location	chr18:28910615-28946104
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	BATF	chr18:28935984-28936266	GM12878	blood:	n/a	n/a
2	BHLHE40	chr18:28923503-28923515	K562	blood:	n/a	n/a
3	CTCF	chr18:28919280-28919430	GM12873	blood:	n/a	n/a
4	CTCF	chr18:28919280-28919430	HepG2	liver:	n/a	n/a
5	CTCF	chr18:28934460-28934610	NHEK	skin:	n/a	n/a
6	CTCF	chr18:28923480-28923630	HPAF	blood vessel:	n/a	n/a
7	CTCF	chr18:28920900-28921050	HepG2	liver:	n/a	n/a
8	EBF1	chr18:28937658-28937669	GM12878	blood:	n/a	n/a
9	EP300	chr18:28939143-28939161	K562	blood:	n/a	n/a
10	FOS	chr18:28943024-28943233	MCF10A-Er-Src	breast:	n/a	n/a
11	FOS	chr18:28937684-28937821	MCF10A-Er-Src	breast:	n/a	chr18:28937774-28937784 chr18:28937684-28937692 chr18:28937685-28937692
12	FOXA1	chr18:28933350-28933627	HepG2	liver:	n/a	n/a
13	FOXA2	chr18:28933118-28933671	A549	lung:	n/a	n/a
14	FOXA2	chr18:28933200-28933723	A549	lung:	n/a	n/a
15	GATA3	chr18:28938615-28939314	MCF-7	breast:	n/a	chr18:28939213-28939222 chr18:28939212-28939222 chr18:28939211-28939224 chr18:28939213-28939220 chr18:28939206-28939227
16	GATA3	chr18:28938507-28939055	MCF-7	breast:	n/a	n/a
17	GATA3	chr18:28938620-28939146	MCF-7	breast:	n/a	n/a
18	JUN	chr18:28926233-28926287	K562	blood:	n/a	n/a
19	MAFF	chr18:28944182-28944532	HepG2	liver:	n/a	chr18:28944348-28944366
20	MAFF	chr18:28939446-28939661	HepG2	liver:	n/a	n/a
21	MAFF	chr18:28944240-28944473	K562	blood:	n/a	chr18:28944348-28944366
22	MAFK	chr18:28939449-28939628	HepG2	liver:	n/a	chr18:28939539-28939550 chr18:28939555-28939572
23	MAFK	chr18:28944235-28944516	K562	blood:	n/a	chr18:28944349-28944363 chr18:28944350-28944365 chr18:28944350-28944361 chr18:28944350-28944366 chr18:28944350-28944361 chr18:28944351-28944362
24	MAFK	chr18:28944186-28944521	HepG2	liver:	n/a	chr18:28944349-28944363 chr18:28944350-28944365 chr18:28944350-28944361 chr18:28944350-28944366 chr18:28944350-28944361 chr18:28944351-28944362
25	MAFK	chr18:28944200-28944522	IMR90	lung:	n/a	chr18:28944349-28944363 chr18:28944350-28944365 chr18:28944350-28944361 chr18:28944350-28944366 chr18:28944350-28944361 chr18:28944351-28944362
26	MAFK	chr18:28939422-28939712	IMR90	lung:	n/a	chr18:28939539-28939550 chr18:28939555-28939572
27	MAFK	chr18:28944201-28944525	HepG2	liver:	n/a	chr18:28944349-28944363 chr18:28944350-28944365 chr18:28944350-28944361 chr18:28944350-28944366 chr18:28944350-28944361 chr18:28944351-28944362
28	MAFK	chr18:28939398-28939717	HepG2	liver:	n/a	chr18:28939539-28939550 chr18:28939555-28939572
29	MXI1	chr18:28940434-28940626	Hela-S3	cervix:	n/a	n/a
30	NFIC	chr18:28935905-28936469	GM12878	blood:	n/a	n/a
31	POLR2A	chr18:28935079-28935176	MCF-7	breast:	n/a	n/a
32	POLR2A	chr18:28933402-28933545	MCF-7	breast:	n/a	n/a
33	POLR2A	chr18:28921190-28921340	MCF10A-Er-Src	breast:	n/a	n/a
34	POLR2A	chr18:28911050-28911340	MCF10A-Er-Src	breast:	n/a	n/a
35	POLR2A	chr18:28914988-28915127	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr18:28911617-28911690	MCF10A-Er-Src	breast:	n/a	n/a
37	RAD21	chr18:28919173-28919476	HepG2	liver:	n/a	n/a
38	RFX5	chr18:28936521-28936589	GM12878	blood:	n/a	n/a
39	RFX5	chr18:28942378-28942475	HepG2	liver:	n/a	n/a
40	RFX5	chr18:28910590-28910738	K562	blood:	n/a	n/a
41	RUNX3	chr18:28935919-28936287	GM12878	blood:	n/a	n/a
42	RUNX3	chr18:28935846-28936393	GM12878	blood:	n/a	n/a
43	SETDB1	chr18:28941188-28941915	U2OS	brain:	n/a	n/a
44	SETDB1	chr18:28934480-28934839	U2OS	brain:	n/a	n/a
45	STAT3	chr18:28937523-28937939	MCF10A-Er-Src	breast:	n/a	chr18:28937790-28937813 chr18:28937790-28937798 chr18:28937697-28937708
46	STAT3	chr18:28937656-28937881	MCF10A-Er-Src	breast:	n/a	chr18:28937790-28937813 chr18:28937790-28937798 chr18:28937697-28937708
47	STAT3	chr18:28925355-28925474	MCF10A-Er-Src	breast:	n/a	n/a
48	STAT3	chr18:28940362-28940365	MCF10A-Er-Src	breast:	n/a	n/a
49	STAT3	chr18:28918443-28918622	MCF10A-Er-Src	breast:	n/a	n/a
50	STAT3	chr18:28942074-28942216	MCF10A-Er-Src	breast:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr18:28935651-28935701	HCPEpiC	choroid plexus:	n/a
2	chr18:28935651-28935701	NT2-D1	testis:	n/a
3	chr18:28935651-28935701	HL-60	blood:	n/a
4	chr18:28935651-28935701	A549	lung:	n/a
5	chr18:28935651-28935701	IMR90	lung:	fetal
6	chr18:28935651-28935701	HCF	heart:	n/a
7	chr18:28935651-28935701	SKMC	muscle:	n/a
8	chr18:28935651-28935701	NH-A	brain:	n/a
9	chr18:28935651-28935701	SK-N-MC	brain:	n/a
10	chr18:28935651-28935701	Hepatocyte	liver:	n/a
11	chr18:28935651-28935701	NHBE	bronchial:	n/a
12	chr18:28935651-28935701	AG04449	skin:	fetal
13	chr18:28935651-28935701	ECC-1	luminal epithelium:	n/a
14	chr18:28935651-28935701	Jurkat	blood:	n/a
15	chr18:28935651-28935701	AG09319	gingival:	n/a
16	chr18:28935651-28935701	HMEC	breast:	n/a
17	chr18:28935651-28935701	RPTEC	kidney:	n/a
18	chr18:28935651-28935701	LNCaP	prostate:	n/a
19	chr18:28935651-28935701	HIPEpiC	eye:	n/a
20	chr18:28935651-28935701	PANC-1	pancreas:	n/a
21	chr18:28935651-28935701	Hela-S3	cervix:	n/a
22	chr18:28935651-28935701	HRCEpiC	kidney:	n/a
23	chr18:28935651-28935701	MCF-7	breast:	n/a
24	chr18:28935651-28935701	PFSK-1	brain:	n/a
25	chr18:28935651-28935701	HNPCEpiC	eye:	n/a
26	chr18:28935651-28935701	HAEpiC	amniotic membrane:	n/a
27	chr18:28935651-28935701	ProgFib	skin:	n/a
28	chr18:28935651-28935701	ovcar-3	ovarian:	n/a
29	chr18:28935651-28935701	AG10803	skin:	n/a
30	chr18:28935651-28935701	SAEC	small airway:	n/a
31	chr18:28935651-28935701	BJ	skin:	n/a
32	chr18:28935651-28935701	HEEpiC	esophagus:	n/a
33	chr18:28935651-28935701	H1-hESC	embryonic stem cell:	embryo
34	chr18:28935651-28935701	K562	blood:	n/a
35	chr18:28935651-28935701	AoSMC	blood vessel:	n/a
36	chr18:28935651-28935701	GM12892	blood:	n/a
37	chr18:28935651-28935701	NB4	blood:	n/a
38	chr18:28935651-28935701	HPAEpiC	pulmonary alveolar:	n/a
39	chr18:28935651-28935701	AG09309	skin:	n/a
40	chr18:28935651-28935701	CMK	blood:	n/a
41	chr18:28935651-28935701	BE2_C	brain:	n/a
42	chr18:28935651-28935701	PrEC	prostate:	n/a
43	chr18:28935651-28935701	NHDF-neo	bronchial:	n/a
44	chr18:28935651-28935701	GM12878	blood:	n/a
45	chr18:28935651-28935701	HRPEpiC	eye:	n/a
46	chr18:28935651-28935701	HRE	kidney:	n/a
47	chr18:28935651-28935701	HEK293	kidney:	embryo
48	chr18:28935651-28935701	HCM	heart:	n/a
49	chr18:28935651-28935701	GM12891	blood:	n/a
50	chr18:28935651-28935701	SK-N-SH	brain:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:28932546..28935472-chr18:29078101..29080400,2	K562	blood:
2	chr18:28921968..28924892-chr18:28925686..28928058,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DSC1-1	chr18:28923347-28923661	ENSG00000266729.1
2	lnc-DSC1-1	chr18:28927631-28927783	ENSG00000266729.1
3	lnc-DSC1-1	chr18:28934275-28934416	ENSG00000266729.1
4	lnc-DSC1-1	chr18:28927683-28927783	ENSG00000266729.1
5	lnc-DSC1-1	chr18:28934275-28934416	ENSG00000266729.1
6	lnc-DSC1-1	chr18:28944112-28944248	ENSG00000266729.1
7	lnc-DSC1-1	chr18:28933863-28933899	ENSG00000266729.1
8	lnc-DSC1-1	chr18:28927683-28927783	ENSG00000266729.1
9	lnc-DSC1-1	chr18:28923331-28923661	ENSG00000266729.1

Variant related genes	Relation type
ENSG00000266729	TF binding region
DSG1	TF binding region
RNU6-167P	TF binding region
ENSG00000266729	CpG island
DSG1	CpG island
RNU6-167P	CpG island
ENSG00000134760	chromatin interactions
ENSG00000046604	chromatin interactions

Extended variants
information (count: 1347 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:1347 , 50 per page) page: 1 2 3 4 5 6 7 ... 27

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs2199301	chr18:28910615-28910616	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs537968760	chr18:28910629-28910630	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs185980979	chr18:28910644-28910645	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs7242392	chr18:28910675-28910676	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs34284297	chr18:28910681-28910682	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs535416355	chr18:28910692-28910693	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs2219582	chr18:28910719-28910720	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs572645356	chr18:28910761-28910762	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs148498633	chr18:28910775-28910776	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs540049928	chr18:28910800-28910801	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs558087331	chr18:28910823-28910824	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs146324547	chr18:28910843-28910844	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs543548124	chr18:28910852-28910853	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs16961648	chr18:28910868-28910869	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs573721471	chr18:28910876-28910877	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs541025035	chr18:28910904-28910905	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs7229263	chr18:28910908-28910909	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs77112556	chr18:28910914-28910915	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs551617877	chr18:28910931-28910932	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs79856922	chr18:28910941-28910942	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs563359095	chr18:28910995-28910996	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs530572254	chr18:28911009-28911010	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs115862180	chr18:28911099-28911100	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs373915465	chr18:28911110-28911111	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs182819897	chr18:28911123-28911124	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs535502178	chr18:28911153-28911154	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs16961649	chr18:28911170-28911171	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs142902369	chr18:28911181-28911182	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs560022258	chr18:28911198-28911199	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs151089008	chr18:28911263-28911264	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs576574298	chr18:28911301-28911302	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs537633135	chr18:28911304-28911305	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs568240620	chr18:28911308-28911309	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs555548834	chr18:28911309-28911310	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs16961650	chr18:28911318-28911319	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs34293567	chr18:28911323-28911324	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs140015681	chr18:28911359-28911360	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs144910484	chr18:28911360-28911361	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs187143776	chr18:28911387-28911388	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs2901125	chr18:28911448-28911449	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs190754170	chr18:28911498-28911499	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs530654776	chr18:28911516-28911517	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs548760993	chr18:28911518-28911519	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs563262586	chr18:28911573-28911574	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs182982295	chr18:28911576-28911577	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs16961651	chr18:28911606-28911607	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs188546846	chr18:28911637-28911638	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs200607879	chr18:28911643-28911644	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs147414301	chr18:28911666-28911667	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs539781726	chr18:28911685-28911686	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Esophageal squamous carcinoma	18350619	CNVD
Follicular lymphoma	20505157	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	18923191	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Trisomy 18 syndrome	17576883	CNVD
lymphocytic leukemia	21291569	CNVD
Barrett''s syndrome	19417022	CNVD
Ewing''s sarcoma	17952124	CNVD
Multiple myeloma	17550852	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Glioblastoma multiforme	21922591	CNVD
Melanoma	18172304	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Lung cancer	18438408	CNVD
18q deletion syndrome	19533772	CNVD
Acute myeloid leukemia	16864856	CNVD
Colorectal cancer	21102417	CNVD
Colorectal cancer	20709793	CNVD
Pancreatic cancer	21811562	CNVD
Basal cell lymphoma	21115979	CNVD
Mucosa-associated lymphoid tissue lymphomas	21459788	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
colon cancer	17210682	CNVD
Breast cancer	21785460	CNVD
Hepatocellular carcinoma	16750200	CNVD
Prostate cancer	16573809	CNVD
Autism	16446308	CNVD
Colorectal cancer	19359472	CNVD
Colorectal cancer	16272173	CNVD
Human rectal carcinomas	16397240	CNVD
Medulloblastoma	18056178	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Cancer	16751803	CNVD
Metanephric adenoma	20802469	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	17133270	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Colorectal cancer	16774939	CNVD
Colorectal cancer	21297112	CNVD
Myelofibrosis	22110671	CNVD
Colorectal cancer	21645411	CNVD
Glioblastoma multiforme	17002787	CNVD
Cancer	21183584	CNVD
Breast cancer	17603634	CNVD
Thyroid cancer	19087340	CNVD
Urothelial carcinoma	21177765	CNVD
Oral cancer	21386901	CNVD
Colorectal cancer	16912164	CNVD
Renal cell carcinoma	19150565	CNVD
Multiple myeloma	16616336	CNVD
Colorectal cancer	19150955	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21364760	CNVD
Pancreatic cancer	21811587	CNVD
Breast cancer	22522925	CNVD
Prostate cancer	22341455	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28899600-28927200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr18:28904800-28933800	Weak transcription	Esophagus	oesophagus
3	chr18:28910600-28913600	Strong transcription	Liver	Liver
4	chr18:28913400-28914000	Enhancers	Fetal Heart	heart
5	chr18:28913600-28925000	Weak transcription	Liver	Liver
6	chr18:28917600-28918000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr18:28917600-28918000	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr18:28917600-28918000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr18:28917600-28918000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr18:28925000-28926800	Strong transcription	Liver	Liver
11	chr18:28926800-28934200	Weak transcription	Liver	Liver
12	chr18:28933800-28934200	Active TSS	K562	blood
13	chr18:28933800-28935400	ZNF genes & repeats	Esophagus	oesophagus
14	chr18:28934200-28934400	Enhancers	Placenta Amnion	Placenta Amnion
15	chr18:28934200-28934600	ZNF genes & repeats	K562	blood
16	chr18:28934200-28935200	Strong transcription	Liver	Liver
17	chr18:28934400-28934800	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
18	chr18:28934400-28942800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr18:28934600-28934800	ZNF genes & repeats	Pancreas	Pancrea
20	chr18:28935200-28936800	Weak transcription	Liver	Liver
21	chr18:28935400-28942600	Weak transcription	Esophagus	oesophagus
22	chr18:28942400-28943200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr18:28942600-28943000	ZNF genes & repeats	Esophagus	oesophagus
24	chr18:28942600-28943200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr18:28942800-28943200	Enhancers	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links