Variant report

Variant	esv3439121
Chromosome Location	chr18:28563754-28568052
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	ATF3	chr18:28567365-28567764	K562	blood:	n/a	n/a
2	BCL3	chr18:28565565-28566218	GM12878	blood:	n/a	n/a
3	BCL3	chr18:28565645-28566202	GM12878	blood:	n/a	n/a
4	BHLHE40	chr18:28567429-28567823	K562	blood:	n/a	n/a
5	CBX3	chr18:28567269-28567924	HCT-116	colon:	n/a	n/a
6	CEBPB	chr18:28567533-28567769	ECC-1	luminal epithelium:	n/a	n/a
7	CEBPB	chr18:28567480-28567900	MCF-7	breast:	n/a	n/a
8	CEBPB	chr18:28567174-28568016	HCT-116	colon:	n/a	chr18:28567195-28567204 chr18:28567195-28567206 chr18:28567195-28567204 chr18:28567195-28567204 chr18:28567193-28567204 chr18:28567193-28567206 chr18:28567195-28567204
9	CEBPB	chr18:28567063-28567818	K562	blood:	n/a	chr18:28567195-28567204 chr18:28567195-28567206 chr18:28567195-28567204 chr18:28567195-28567204 chr18:28567193-28567204 chr18:28567193-28567206 chr18:28567195-28567204
10	CEBPB	chr18:28567071-28567285	HepG2	liver:	n/a	chr18:28567195-28567204 chr18:28567195-28567206 chr18:28567195-28567204 chr18:28567195-28567204 chr18:28567193-28567204 chr18:28567193-28567206 chr18:28567195-28567204
11	CEBPB	chr18:28567414-28567894	MCF-7	breast:	n/a	n/a
12	CEBPB	chr18:28567093-28567877	Hela-S3	cervix:	n/a	chr18:28567195-28567204 chr18:28567195-28567206 chr18:28567195-28567204 chr18:28567195-28567204 chr18:28567193-28567204 chr18:28567193-28567206 chr18:28567195-28567204
13	CHD2	chr18:28567431-28567763	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr18:28565983-28566055	MCF-7	breast:	n/a	n/a
15	CTCF	chr18:28567260-28567410	HCT-116	colon:	n/a	n/a
16	CTCF	chr18:28565803-28565947	MCF-7	breast:	n/a	n/a
17	CTCF	chr18:28565793-28565938	GM19239	blood:	n/a	n/a
18	CTCF	chr18:28565772-28565993	MCF-7	breast:	n/a	n/a
19	E2F4	chr18:28567409-28567725	MCF10A-Er-Src	breast:	n/a	n/a
20	EGR1	chr18:28567274-28567918	HCT-116	colon:	n/a	chr18:28567683-28567698
21	EGR1	chr18:28567320-28567960	MCF-7	breast:	n/a	chr18:28567683-28567698
22	EGR1	chr18:28567350-28567813	MCF-7	breast:	n/a	chr18:28567683-28567698
23	EGR1	chr18:28567289-28568025	HCT-116	colon:	n/a	chr18:28567683-28567698
24	EGR1	chr18:28567361-28567729	K562	blood:	n/a	chr18:28567683-28567698
25	EGR1	chr18:28567389-28567778	K562	blood:	n/a	chr18:28567683-28567698
26	EP300	chr18:28567368-28567739	K562	blood:	n/a	n/a
27	EP300	chr18:28567396-28567878	Hela-S3	cervix:	n/a	chr18:28567733-28567742
28	FOS	chr18:28566922-28567130	MCF10A-Er-Src	breast:	n/a	n/a
29	FOS	chr18:28567289-28567813	MCF10A-Er-Src	breast:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
30	FOS	chr18:28567347-28567813	MCF10A-Er-Src	breast:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
31	FOS	chr18:28567383-28567813	MCF10A-Er-Src	breast:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
32	FOS	chr18:28566739-28567812	MCF10A-Er-Src	breast:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
33	FOSL1	chr18:28567223-28567897	HCT-116	colon:	n/a	chr18:28567564-28567575 chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
34	FOSL1	chr18:28567382-28567707	K562	blood:	n/a	chr18:28567564-28567575 chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
35	FOSL1	chr18:28567261-28567897	HCT-116	colon:	n/a	chr18:28567564-28567575 chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
36	FOSL1	chr18:28567311-28567707	K562	blood:	n/a	chr18:28567564-28567575 chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
37	FOSL2	chr18:28567430-28567627	A549	lung:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
38	FOSL2	chr18:28567307-28567842	MCF-7	breast:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
39	FOSL2	chr18:28567338-28567759	MCF-7	breast:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
40	FOXA2	chr18:28567400-28567752	A549	lung:	n/a	n/a
41	FOXA2	chr18:28567404-28567789	A549	lung:	n/a	n/a
42	GATA3	chr18:28567467-28567854	MCF-7	breast:	n/a	chr18:28567564-28567573
43	GATA3	chr18:28565944-28566214	MCF-7	breast:	n/a	chr18:28566074-28566084 chr18:28566072-28566082 chr18:28566075-28566082 chr18:28566075-28566084
44	HDAC2	chr18:28567441-28567808	MCF-7	breast:	n/a	chr18:28567699-28567713 chr18:28567744-28567758 chr18:28567697-28567711
45	HMGN3	chr18:28567489-28567655	K562	blood:	n/a	n/a
46	JUN	chr18:28567390-28567753	K562	blood:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
47	JUN	chr18:28567378-28567749	K562	blood:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
48	JUND	chr18:28567357-28567798	Hela-S3	cervix:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
49	JUND	chr18:28567379-28567783	MCF-7	breast:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575
50	JUND	chr18:28567341-28567809	K562	blood:	n/a	chr18:28567566-28567574 chr18:28567565-28567575 chr18:28567565-28567575 chr18:28567565-28567575

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:28567247..28569402-chr18:28680129..28682819,2	K562	blood:

Variant related genes	Relation type
ENSG00000265670	TF binding region
RNU6-857P	TF binding region
ENSG00000134755	chromatin interactions
ENSG00000265888	chromatin interactions

Extended variants
information (count: 198 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:198 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs574359942	chr18:28563766-28563767	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs9965297	chr18:28563779-28563780	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs561380051	chr18:28563785-28563786	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs113785627	chr18:28563795-28563796	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs182109596	chr18:28563841-28563842	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs2572367	chr18:28563844-28563845	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs573274505	chr18:28563902-28563903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs541166986	chr18:28563907-28563908	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs549332760	chr18:28563986-28563987	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs79354647	chr18:28563987-28563988	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs572231443	chr18:28564022-28564023	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs111486005	chr18:28564057-28564058	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs532187346	chr18:28564119-28564120	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs112191510	chr18:28564129-28564130	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs532505221	chr18:28564134-28564135	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs75475878	chr18:28564150-28564151	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs188317284	chr18:28564168-28564169	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs112276288	chr18:28564174-28564175	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs548927537	chr18:28564200-28564201	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs111449461	chr18:28564237-28564238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs534444286	chr18:28564243-28564244	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs112007314	chr18:28564290-28564291	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs570479021	chr18:28564311-28564312	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs375975270	chr18:28564336-28564337	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs112550595	chr18:28564351-28564352	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs150416280	chr18:28564404-28564405	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs532855091	chr18:28564427-28564428	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs544923624	chr18:28564438-28564439	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs574127566	chr18:28564439-28564440	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs138212013	chr18:28564457-28564458	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs149624908	chr18:28564465-28564466	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs536046136	chr18:28564476-28564477	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs201633191	chr18:28564477-28564478	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs370285732	chr18:28564478-28564479	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs79152031	chr18:28564480-28564481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs77254066	chr18:28564482-28564483	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs577304331	chr18:28564496-28564497	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs111250367	chr18:28564517-28564518	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs572262788	chr18:28564522-28564523	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs183681823	chr18:28564528-28564529	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs76934025	chr18:28564559-28564560	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs543908375	chr18:28564561-28564562	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs188356559	chr18:28564563-28564564	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs112266087	chr18:28564614-28564615	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs147294820	chr18:28564678-28564679	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs530164174	chr18:28564885-28564886	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs542530403	chr18:28564887-28564888	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs111668357	chr18:28564891-28564892	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs139378840	chr18:28564927-28564928	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs552709633	chr18:28564944-28564945	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:70)

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
Melanoma	20877625	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:28560800-28565800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr18:28563000-28566800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr18:28563200-28565800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr18:28563600-28565800	Weak transcription	NHEK	skin
5	chr18:28565200-28567200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr18:28565800-28566000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:28565800-28566000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:28565800-28566000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr18:28565800-28566000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:28565800-28566000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr18:28565800-28566000	Enhancers	Pancreas	Pancrea
12	chr18:28565800-28566000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr18:28565800-28566000	Enhancers	HMEC	breast
14	chr18:28565800-28566200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr18:28565800-28566200	Enhancers	Esophagus	oesophagus
16	chr18:28565800-28566200	Enhancers	Fetal Brain Male	brain
17	chr18:28565800-28566200	Enhancers	Lung	lung
18	chr18:28565800-28567200	Enhancers	NHEK	skin
19	chr18:28566000-28566200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr18:28566000-28567400	Weak transcription	Pancreas	Pancrea
21	chr18:28566000-28567400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr18:28566000-28567800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr18:28566200-28567200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr18:28566200-28567200	Weak transcription	HMEC	breast
25	chr18:28566200-28567800	Weak transcription	Fetal Brain Male	brain
26	chr18:28566200-28572400	Weak transcription	Esophagus	oesophagus
27	chr18:28566200-28600600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr18:28566400-28568400	Enhancers	Placenta Amnion	Placenta Amnion
29	chr18:28566800-28569400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr18:28567200-28567400	Enhancers	Hela-S3	cervix
31	chr18:28567200-28567600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr18:28567200-28568200	Enhancers	Fetal Intestine Small	intestine
33	chr18:28567200-28568600	Flanking Active TSS	NHEK	skin
34	chr18:28567200-28568800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr18:28567200-28568800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr18:28567200-28568800	Enhancers	HMEC	breast
37	chr18:28567400-28567600	Enhancers	Fetal Intestine Large	intestine
38	chr18:28567400-28567600	Enhancers	Pancreas	Pancrea
39	chr18:28567400-28567800	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr18:28567400-28567800	Enhancers	A549	lung
41	chr18:28567400-28567800	Flanking Active TSS	Hela-S3	cervix
42	chr18:28567400-28567800	Enhancers	K562	blood
43	chr18:28567400-28568200	Enhancers	Placenta	Placenta
44	chr18:28567400-28568400	Enhancers	Stomach Mucosa	stomach
45	chr18:28567400-28568800	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr18:28567600-28569400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr18:28567800-28568000	Flanking Active TSS	A549	lung
48	chr18:28567800-28568000	Enhancers	Hela-S3	cervix
49	chr18:28567800-28568400	Enhancers	Fetal Brain Male	brain
50	chr18:28567800-28568600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links