Variant report

Variant	esv3341096
Chromosome Location	chr20:23638652-23642850
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	ARID3A	chr20:23641160-23641439	K562	blood:	n/a	n/a
2	ARID3A	chr20:23640739-23642649	HepG2	liver:	n/a	n/a
3	ARID3A	chr20:23639396-23640169	HepG2	liver:	n/a	n/a
4	ATF1	chr20:23641191-23641461	K562	blood:	n/a	n/a
5	ATF3	chr20:23641112-23641413	K562	blood:	n/a	n/a
6	BCL3	chr20:23640593-23640987	GM12878	blood:	n/a	n/a
7	BCL3	chr20:23640580-23641005	GM12878	blood:	n/a	n/a
8	BHLHE40	chr20:23641125-23641440	HepG2	liver:	n/a	n/a
9	BHLHE40	chr20:23640945-23641483	K562	blood:	n/a	n/a
10	CEBPB	chr20:23641181-23641467	IMR90	lung:	n/a	n/a
11	CEBPB	chr20:23641058-23641516	HepG2	liver:	n/a	n/a
12	CEBPB	chr20:23642180-23642406	IMR90	lung:	n/a	chr20:23642317-23642328
13	CEBPB	chr20:23642081-23642475	HepG2	liver:	n/a	chr20:23642317-23642328
14	CEBPB	chr20:23641224-23641479	K562	blood:	n/a	n/a
15	CEBPB	chr20:23641150-23641517	HepG2	liver:	n/a	n/a
16	CEBPB	chr20:23642287-23642378	H1-hESC	embryonic stem cell:	n/a	chr20:23642317-23642328
17	CEBPB	chr20:23642163-23642399	K562	blood:	n/a	chr20:23642317-23642328
18	CEBPB	chr20:23642025-23642637	HepG2	liver:	n/a	chr20:23642317-23642328
19	CEBPB	chr20:23641985-23642627	HepG2	liver:	n/a	chr20:23642317-23642328
20	CEBPB	chr20:23641146-23641512	K562	blood:	n/a	n/a
21	CEBPB	chr20:23641219-23641393	HepG2	liver:	n/a	n/a
22	CEBPB	chr20:23641209-23641444	Hela-S3	cervix:	n/a	n/a
23	CEBPB	chr20:23642178-23642466	A549	lung:	n/a	chr20:23642317-23642328
24	CEBPB	chr20:23642261-23642432	Hela-S3	cervix:	n/a	chr20:23642317-23642328
25	CEBPB	chr20:23641818-23642580	HepG2	liver:	n/a	chr20:23642317-23642328
26	CEBPD	chr20:23642124-23642620	HepG2	liver:	n/a	chr20:23642316-23642327
27	CEBPD	chr20:23639736-23640087	HepG2	liver:	n/a	n/a
28	CEBPD	chr20:23640863-23641460	HepG2	liver:	n/a	n/a
29	CEBPD	chr20:23642088-23642679	HepG2	liver:	n/a	chr20:23642316-23642327
30	CHD2	chr20:23642088-23642521	HepG2	liver:	n/a	n/a
31	CTCF	chr20:23642360-23642510	Caco-2	colon:	n/a	n/a
32	CUX1	chr20:23641209-23641451	K562	blood:	n/a	n/a
33	EBF1	chr20:23642077-23642259	GM12878	blood:	n/a	chr20:23642163-23642176 chr20:23642164-23642175
34	ELF1	chr20:23642057-23642564	HepG2	liver:	n/a	n/a
35	ELF1	chr20:23642062-23642528	HepG2	liver:	n/a	n/a
36	EP300	chr20:23640962-23641472	K562	blood:	n/a	chr20:23641336-23641350 chr20:23641337-23641345
37	EP300	chr20:23641038-23642522	HepG2	liver:	n/a	chr20:23641336-23641350 chr20:23641878-23641887 chr20:23641337-23641345
38	EP300	chr20:23639221-23640166	HepG2	liver:	n/a	n/a
39	EP300	chr20:23640735-23642969	HepG2	liver:	n/a	chr20:23641336-23641350 chr20:23641878-23641887 chr20:23641337-23641345
40	EP300	chr20:23641936-23642671	HepG2	liver:	n/a	n/a
41	EP300	chr20:23639567-23640120	HepG2	liver:	n/a	n/a
42	FOXA1	chr20:23641924-23642699	HepG2	liver:	n/a	n/a
43	FOXA1	chr20:23639318-23640180	HepG2	liver:	n/a	n/a
44	FOXA1	chr20:23641936-23642639	HepG2	liver:	n/a	n/a
45	FOXA1	chr20:23639544-23640140	HepG2	liver:	n/a	n/a
46	FOXA1	chr20:23641884-23642621	HepG2	liver:	n/a	n/a
47	FOXA1	chr20:23641920-23642723	HepG2	liver:	n/a	n/a
48	FOXA1	chr20:23639522-23640186	HepG2	liver:	n/a	n/a
49	FOXA1	chr20:23639522-23640215	HepG2	liver:	n/a	n/a
50	FOXA2	chr20:23641988-23642669	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23400166..23402418-chr20:23639659..23642260,2	K562	blood:

Variant related genes	Relation type
ENSG00000225056	TF binding region
ENSG00000125814	chromatin interactions

Extended variants
information (count: 222 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:222 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs577043406	chr20:23638759-23638760	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs6114216	chr20:23638765-23638766	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs562534417	chr20:23638782-23638783	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs576352610	chr20:23638785-23638786	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs542054683	chr20:23638798-23638799	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs561731546	chr20:23638807-23638808	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs113191373	chr20:23638812-23638813	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs547392596	chr20:23638824-23638825	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs564142267	chr20:23638870-23638871	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs77624908	chr20:23638880-23638881	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs550495094	chr20:23638904-23638905	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs570253147	chr20:23638915-23638916	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs372074402	chr20:23638940-23638941	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs535615820	chr20:23638943-23638944	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs375476712	chr20:23638966-23638967	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs6083209	chr20:23638969-23638970	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs138643070	chr20:23638971-23638972	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs74768511	chr20:23638989-23638990	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs143608645	chr20:23639093-23639094	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs549930297	chr20:23639110-23639111	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs6083210	chr20:23639119-23639120	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs6083211	chr20:23639164-23639165	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs79762610	chr20:23639178-23639179	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs557852560	chr20:23639180-23639181	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs6083212	chr20:23639191-23639192	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs369839048	chr20:23639193-23639194	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs144263162	chr20:23639194-23639195	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs539349730	chr20:23639195-23639196	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs532881317	chr20:23639206-23639207	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs544763570	chr20:23639218-23639219	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs186475827	chr20:23639238-23639239	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs113605540	chr20:23639261-23639262	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs147154143	chr20:23639262-23639263	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs367911638	chr20:23639268-23639269	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs11467102	chr20:23639287-23639288	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs58973420	chr20:23639290-23639291	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs542017583	chr20:23639308-23639309	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs560340719	chr20:23639309-23639310	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs373383455	chr20:23639330-23639331	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs572155200	chr20:23639333-23639334	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs191326574	chr20:23639342-23639343	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs563921499	chr20:23639352-23639353	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs146382747	chr20:23639366-23639367	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs113325572	chr20:23639367-23639368	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs8115833	chr20:23639384-23639385	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
46	rs368935630	chr20:23639392-23639393	Enhancers Weak transcription Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs188874831	chr20:23639419-23639420	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs567233228	chr20:23639432-23639433	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs148078033	chr20:23639442-23639443	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs372640743	chr20:23639462-23639463	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Wilms tumour	21544195	CNVD
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
Prostate cancer	18632612	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
small cell lung cancer	17426248	CNVD
Breast cancer	21364760	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23622800-23640000	Weak transcription	Stomach Mucosa	stomach
2	chr20:23633000-23639400	Enhancers	HepG2	liver
3	chr20:23635600-23641600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:23636800-23640600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr20:23636800-23640800	Weak transcription	Aorta	Aorta
6	chr20:23637000-23639200	Weak transcription	Psoas Muscle	Psoas
7	chr20:23637000-23640600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr20:23637200-23639000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr20:23637200-23640000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr20:23637200-23640600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr20:23637200-23640800	Weak transcription	Fetal Muscle Leg	muscle
12	chr20:23637200-23641000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr20:23637200-23641600	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr20:23637200-23643600	Weak transcription	Right Atrium	heart
15	chr20:23637200-23660000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr20:23637400-23639000	Weak transcription	Fetal Lung	lung
17	chr20:23637400-23639400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr20:23637400-23640800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr20:23637400-23641000	Weak transcription	Esophagus	oesophagus
20	chr20:23637800-23644200	Enhancers	Fetal Intestine Large	intestine
21	chr20:23638000-23638800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr20:23638000-23640200	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr20:23638200-23639200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr20:23638200-23640000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr20:23638200-23640600	Weak transcription	Adipose Nuclei	Adipose
26	chr20:23638200-23642200	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr20:23638400-23639400	Enhancers	HUVEC	blood vessel
28	chr20:23638400-23644200	Enhancers	Fetal Intestine Small	intestine
29	chr20:23638600-23639000	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr20:23638600-23640200	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr20:23638600-23641800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr20:23638600-23642000	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr20:23638800-23639200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr20:23639000-23639200	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr20:23639000-23639400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr20:23639000-23639400	Active TSS	Breast Myoepithelial Primary Cells	Breast
37	chr20:23639000-23639400	Enhancers	Fetal Lung	lung
38	chr20:23639200-23639400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr20:23639200-23639400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr20:23639200-23639400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr20:23639200-23640000	Enhancers	Psoas Muscle	Psoas
42	chr20:23639200-23640200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr20:23639200-23640800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr20:23639400-23639800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr20:23639400-23639800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr20:23639400-23640400	Weak transcription	Fetal Lung	lung
47	chr20:23639400-23640800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr20:23639400-23643200	Flanking Active TSS	HepG2	liver
49	chr20:23639800-23640000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr20:23639800-23643400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links