Variant report

Variant	esv3345812
Chromosome Location	chr20:25059286-25059573
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:62)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr20:25059364-25059414	GM12892	blood:	n/a
2	chr20:25059364-25059414	GM12892	blood:	n/a
3	chr20:25059364-25059414	HMEC	breast:	n/a
4	chr20:25059364-25059414	CMK	blood:	n/a
5	chr20:25059364-25059414	HRCEpiC	kidney:	n/a
6	chr20:25059364-25059414	HepG2	liver:	n/a
7	chr20:25059364-25059414	ovcar-3	ovarian:	n/a
8	chr20:25059364-25059414	PFSK-1	brain:	n/a
9	chr20:25059364-25059414	NH-A	brain:	n/a
10	chr20:25059364-25059414	Hepatocyte	liver:	n/a
11	chr20:25059364-25059414	RPTEC	kidney:	n/a
12	chr20:25059364-25059414	Jurkat	blood:	n/a
13	chr20:25059364-25059414	T-47D	breast:	n/a
14	chr20:25059364-25059414	GM12891	blood:	n/a
15	chr20:25059364-25059414	GM19239	blood:	n/a
16	chr20:25059364-25059414	HNPCEpiC	eye:	n/a
17	chr20:25059364-25059414	SKMC	muscle:	n/a
18	chr20:25059364-25059414	HAEpiC	amniotic membrane:	n/a
19	chr20:25059364-25059414	HCM	heart:	n/a
20	chr20:25059364-25059414	AG09319	gingival:	n/a
21	chr20:25059364-25059414	HEK293	kidney:	embryo
22	chr20:25059364-25059414	AG04449	skin:	fetal
23	chr20:25059364-25059414	ProgFib	skin:	n/a
24	chr20:25059364-25059414	AG09309	skin:	n/a
25	chr20:25059364-25059414	HCT-116	colon:	n/a
26	chr20:25059364-25059414	PANC-1	pancreas:	n/a
27	chr20:25059364-25059414	AG10803	skin:	n/a
28	chr20:25059364-25059414	AG04450	lung:	fetal
29	chr20:25059364-25059414	BJ	skin:	n/a
30	chr20:25059364-25059414	SAEC	small airway:	n/a
31	chr20:25059364-25059414	HPAEpiC	pulmonary alveolar:	n/a
32	chr20:25059364-25059414	SK-N-SH_RA	brain:	n/a
33	chr20:25059364-25059414	HRPEpiC	eye:	n/a
34	chr20:25059364-25059414	HUVEC	blood vessel:	n/a
35	chr20:25059364-25059414	GM06990	blood:	n/a
36	chr20:25059364-25059414	NT2-D1	testis:	n/a
37	chr20:25059364-25059414	AoSMC	blood vessel:	n/a
38	chr20:25059364-25059414	K562	blood:	n/a
39	chr20:25059364-25059414	HCF	heart:	n/a
40	chr20:25059364-25059414	PrEC	prostate:	n/a
41	chr20:25059364-25059414	IMR90	lung:	fetal
42	chr20:25059364-25059414	NB4	blood:	n/a
43	chr20:25059364-25059414	NHDF-neo	bronchial:	n/a
44	chr20:25059364-25059414	ECC-1	luminal epithelium:	n/a
45	chr20:25059364-25059414	HEEpiC	esophagus:	n/a
46	chr20:25059364-25059414	HRE	kidney:	n/a
47	chr20:25059364-25059414	HL-60	blood:	n/a
48	chr20:25059364-25059414	A549	lung:	n/a
49	chr20:25059364-25059414	LNCaP	prostate:	n/a
50	chr20:25059364-25059414	HIPEpiC	eye:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25058836..25060785-chr20:25065657..25068597,2	K562	blood:
2	chr20:24972184..24974531-chr20:25057258..25059368,3	MCF-7	breast:
3	chr20:25054332..25057280-chr20:25059401..25062693,3	K562	blood:

No data

Variant related genes	Relation type
VSX1	CpG island
ENSG00000101474	chromatin interactions

Extended variants
information (count: 26 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs564352827	chr20:25059292-25059293	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs540862655	chr20:25059338-25059339	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs371478673	chr20:25059345-25059346	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs376724584	chr20:25059361-25059362	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs563903530	chr20:25059364-25059365	Weak transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs199755218	chr20:25059365-25059366	Weak transcription Enhancers	CpG island Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs528277026	chr20:25059375-25059376	Weak transcription Enhancers	CpG island	1 gene(s)	Overlapped CNVs	n/a
8	rs56157240	chr20:25059381-25059382	Weak transcription Enhancers	CpG island	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs552343074	chr20:25059383-25059384	Weak transcription Enhancers	CpG island	1 gene(s)	Overlapped CNVs	n/a
10	rs373947722	chr20:25059403-25059404	Enhancers Weak transcription Bivalent Enhancer	CpG island	1 gene(s)	Overlapped CNVs	n/a
11	rs562912096	chr20:25059406-25059407	Enhancers Weak transcription Bivalent Enhancer	CpG island	1 gene(s)	Overlapped CNVs	n/a
12	rs201758357	chr20:25059411-25059412	Enhancers Weak transcription Bivalent Enhancer	CpG island	1 gene(s)	Overlapped CNVs	n/a
13	rs548563431	chr20:25059414-25059415	Enhancers Weak transcription Bivalent Enhancer	CpG island	1 gene(s)	Overlapped CNVs	n/a
14	rs199870772	chr20:25059419-25059420	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs534477257	chr20:25059420-25059421	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
16	rs368840437	chr20:25059424-25059425	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs6138482	chr20:25059442-25059443	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
18	rs200369946	chr20:25059480-25059481	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs75365206	chr20:25059496-25059497	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs201313323	chr20:25059497-25059498	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs144917154	chr20:25059512-25059513	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs555943681	chr20:25059516-25059517	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
23	rs138766673	chr20:25059536-25059537	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
24	rs200103903	chr20:25059540-25059541	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs12480307	chr20:25059546-25059547	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
26	rs143099682	chr20:25059564-25059565	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:55)

Disease	PMID	Source
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	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
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Breast cancer	16608533	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Breast cancer	17133270	CNVD
Thrombophilia	17576883	CNVD
Myelofibrosis	22110671	CNVD
Mental retardation	21062444	CNVD
Hepatocellular carcinoma	22174799	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
Oral cancer	21386901	CNVD

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25057200-25060600	Enhancers	Dnd41	blood
2	chr20:25058800-25059400	Weak transcription	Colonic Mucosa	Colon
3	chr20:25058800-25061800	Weak transcription	Pancreas	Pancrea
4	chr20:25059400-25059600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
5	chr20:25059400-25059800	Enhancers	Colonic Mucosa	Colon
6	chr20:25059400-25060200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum

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