Variant report

Variant	esv3449693
Chromosome Location	chr20:52784550-52785027
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	chr20:52784248-52785237	A549	lung:	n/a	n/a
2	ATF3	chr20:52784334-52785014	A549	lung:	n/a	n/a
3	BCL3	chr20:52772170-52791941	A549	lung:	n/a	chr20:52790491-52790504 chr20:52782584-52782593 chr20:52784755-52784763 chr20:52790858-52790871 chr20:52790857-52790870 chr20:52782583-52782592
4	BCL3	chr20:52784264-52785294	A549	lung:	n/a	chr20:52784755-52784763
5	CBX3	chr20:52784224-52785298	HCT-116	colon:	n/a	n/a
6	CEBPB	chr20:52784282-52785144	A549	lung:	n/a	n/a
7	CREB1	chr20:52784634-52785065	A549	lung:	n/a	n/a
8	CTCF	chr20:52784720-52784870	HRE	kidney:	n/a	n/a
9	CTCF	chr20:52784540-52784690	HepG2	liver:	n/a	n/a
10	CTCF	chr20:52784580-52784730	HCT-116	colon:	n/a	n/a
11	CTCF	chr20:52784600-52784750	HEK293	kidney:	n/a	n/a
12	E2F4	chr20:52784164-52785029	MCF10A-Er-Src	breast:	n/a	n/a
13	ELF1	chr20:52783507-52785252	A549	lung:	n/a	n/a
14	ELF1	chr20:52784327-52784986	A549	lung:	n/a	n/a
15	EP300	chr20:52782936-52785310	A549	lung:	n/a	chr20:52783664-52783674
16	EP300	chr20:52782097-52785248	A549	lung:	n/a	chr20:52783664-52783674 chr20:52782863-52782877 chr20:52782584-52782593 chr20:52782583-52782592
17	ETS1	chr20:52783389-52785294	A549	lung:	n/a	n/a
18	ETS1	chr20:52784518-52784929	A549	lung:	n/a	n/a
19	FOS	chr20:52784367-52785120	MCF10A-Er-Src	breast:	n/a	n/a
20	FOS	chr20:52784404-52785098	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr20:52784769-52785036	MCF10A-Er-Src	breast:	n/a	n/a
22	FOS	chr20:52784389-52785120	MCF10A-Er-Src	breast:	n/a	n/a
23	FOSL2	chr20:52784224-52785336	A549	lung:	n/a	n/a
24	FOSL2	chr20:52784340-52785068	A549	lung:	n/a	n/a
25	FOXA2	chr20:52784225-52784888	A549	lung:	n/a	n/a
26	GATA3	chr20:52776064-52785298	A549	lung:	n/a	chr20:52778354-52778363 chr20:52778722-52778732 chr20:52778722-52778731 chr20:52776796-52776806 chr20:52779429-52779436
27	JUND	chr20:52784395-52785208	A549	lung:	n/a	n/a
28	JUND	chr20:52783667-52785166	A549	lung:	n/a	n/a
29	MAX	chr20:52784269-52785276	A549	lung:	n/a	n/a
30	MAX	chr20:52784255-52785350	A549	lung:	n/a	n/a
31	MAX	chr20:52784323-52785267	HCT-116	colon:	n/a	n/a
32	MAX	chr20:52784300-52785307	HCT-116	colon:	n/a	n/a
33	MYC	chr20:52784402-52785058	MCF10A-Er-Src	breast:	n/a	n/a
34	MYC	chr20:52784451-52785059	MCF10A-Er-Src	breast:	n/a	n/a
35	NFIC	chr20:52784290-52784777	ECC-1	luminal epithelium:	n/a	n/a
36	NFIC	chr20:52784343-52785103	SK-N-SH	brain:	n/a	n/a
37	NFIC	chr20:52784335-52785158	SK-N-SH	brain:	n/a	n/a
38	PBX3	chr20:52784194-52785328	A549	lung:	n/a	n/a
39	PBX3	chr20:52784256-52785274	A549	lung:	n/a	n/a
40	POLR2A	chr20:52784624-52785114	A549	lung:	n/a	n/a
41	POLR2A	chr20:52784370-52785157	A549	lung:	n/a	n/a
42	POLR2A	chr20:52784355-52785218	HCT-116	colon:	n/a	n/a
43	POLR2A	chr20:52784343-52785163	A549	lung:	n/a	n/a
44	POLR2A	chr20:52770188-52790693	A549	lung:	n/a	n/a
45	POLR2A	chr20:52784377-52784709	ProgFib	skin:	n/a	n/a
46	POLR2A	chr20:52784501-52785059	A549	lung:	n/a	n/a
47	POLR2A	chr20:52784423-52785103	HCT-116	colon:	n/a	n/a
48	POLR2A	chr20:52784526-52784814	A549	lung:	n/a	n/a
49	POLR2A	chr20:52784883-52785122	A549	lung:	n/a	n/a
50	REST	chr20:52783230-52785235	A549	lung:	n/a	chr20:52784756-52784765

No.	Distal block	Cell Line	Cell type
1	chr17:56707293..56709240-chr20:52784800..52786462,3	MCF-7	breast:
2	chr10:124167947..124168775-chr20:52784636..52785297,2	MCF-7	breast:
3	chr20:52765302..52766219-chr20:52784081..52784986,2	MCF-7	breast:
4	chr17:57920588..57922273-chr20:52783196..52786191,2	MCF-7	breast:
5	chr17:56735532..56737839-chr20:52784476..52786335,2	MCF-7	breast:
6	chr20:45985630..45987626-chr20:52781307..52785210,3	MCF-7	breast:
7	chr17:56708786..56710592-chr20:52784898..52786437,2	MCF-7	breast:
8	chr20:52784538..52787745-chr20:55839134..55841996,3	MCF-7	breast:
9	chr20:52784393..52784975-chr20:52811607..52812127,2	MCF-7	breast:
10	chr17:56728473..56731849-chr20:52782841..52785983,3	MCF-7	breast:

Variant related genes	Relation type
CYP24A1	TF binding region
ENSG00000101144	chromatin interactions
ENSG00000226308	chromatin interactions
ENSG00000212195	chromatin interactions
ENSG00000202077	chromatin interactions

Extended variants
information (count: 24 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs184327650	chr20:52784551-52784552	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs375638411	chr20:52784572-52784573	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs61338465	chr20:52784588-52784589	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs188951690	chr20:52784590-52784591	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs2585431	chr20:52784612-52784613	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs557800351	chr20:52784624-52784625	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs149784922	chr20:52784652-52784653	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs368366622	chr20:52784660-52784661	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs545586433	chr20:52784675-52784676	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs145751686	chr20:52784704-52784705	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs576291981	chr20:52784758-52784759	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs541719982	chr20:52784759-52784760	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs561740631	chr20:52784793-52784794	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs148543718	chr20:52784807-52784808	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
15	rs539596969	chr20:52784817-52784818	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
16	rs564156074	chr20:52784826-52784827	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
17	rs533606182	chr20:52784861-52784862	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs182229286	chr20:52784867-52784868	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
19	rs570216998	chr20:52784872-52784873	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
20	rs557730585	chr20:52784879-52784880	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
21	rs552881940	chr20:52784922-52784923	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
22	rs142881299	chr20:52784981-52784982	Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
23	rs572814202	chr20:52785011-52785012	Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
24	rs566084582	chr20:52785026-52785027	Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	5 gene(s)	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
Colorectal cancer	21645411	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
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
Breast cancer	17603634	CNVD
Melanoma	18172304	CNVD
Breast cancer	16608533	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	17133270	CNVD
Oral cancer	21386901	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Myelodysplastic syndrome	21251322	CNVD
Ductal carcinoma	22052326	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Gastric cancer	20585902	CNVD
Ductal carcinoma	18381933	CNVD
Cancer	21129771	CNVD
Cancer	21183584	CNVD
Non-small cell lung cancer	20864512	CNVD
Ovarian cancer	22174824	CNVD
Lung cancer	16740712	CNVD
Wilms tumour	21544195	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	16620391	CNVD
Okamoto syndrome	17623483	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21785460	CNVD
Bladder cancer	21909424	CNVD
Biliary cancer	19435499	CNVD
Myelofibrosis	22110671	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Cervical cancer	16585170	CNVD
Ovarian cancer	20844748	CNVD
Hirschsprung''s Disease	21712996	CNVD
Breast cancer	21364760	CNVD
Breast cancer	20459607	CNVD
Gastric cancer	18160780	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21509527	CNVD
Medulloblastoma	16783165	CNVD

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52768800-52790200	Transcr. at gene 5' and 3'	A549	lung
2	chr20:52769200-52789400	Weak transcription	Esophagus	oesophagus
3	chr20:52769600-52785800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr20:52771200-52786000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr20:52777800-52784800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr20:52778800-52784600	Weak transcription	HepG2	liver
7	chr20:52784200-52786200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr20:52784200-52786200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:52784400-52784600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr20:52784400-52784600	Bivalent Enhancer	Osteobl	bone
11	chr20:52784400-52785200	Enhancers	HMEC	breast
12	chr20:52784400-52786400	Enhancers	NHEK	skin
13	chr20:52784600-52784800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr20:52784600-52784800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr20:52784600-52784800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:52784600-52785000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
17	chr20:52784600-52785200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr20:52784600-52785200	Enhancers	Hela-S3	cervix
19	chr20:52784600-52787200	Enhancers	HepG2	liver
20	chr20:52784800-52785000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr20:52784800-52785000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr20:52784800-52785000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr20:52784800-52785200	Enhancers	NH-A	brain

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