Variant report

Variant	esv3399488
Chromosome Location	chr20:23455752-23458650
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	BCL3	chr20:23456780-23457368	GM12878	blood:	n/a	n/a
2	BCL3	chr20:23456839-23457441	GM12878	blood:	n/a	n/a
3	CTCF	chr20:23456100-23456250	HEK293	kidney:	n/a	chr20:23456220-23456229
4	CTCF	chr20:23457266-23457336	GM19239	blood:	n/a	n/a
5	CTCF	chr20:23456160-23456310	HepG2	liver:	n/a	chr20:23456220-23456229
6	NFATC1	chr20:23456847-23457205	GM12878	blood:	n/a	n/a
7	NFATC1	chr20:23456811-23457420	GM12878	blood:	n/a	n/a
8	PBX3	chr20:23456864-23457242	GM12878	blood:	n/a	n/a
9	POLR2A	chr20:23457131-23457455	HepG2	liver:	n/a	n/a
10	STAT5A	chr20:23456847-23457264	GM12878	blood:	n/a	n/a
11	SUZ12	chr20:23456943-23457524	H1-hESC	embryonic stem cell:	n/a	n/a
12	TCF12	chr20:23456979-23457562	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
CST12P	TF binding region

Extended variants
information (count: 181 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:181 , 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	rs557990927	chr20:23455754-23455755	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs577932771	chr20:23455763-23455764	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs543583130	chr20:23455766-23455767	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs563890136	chr20:23455770-23455771	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs574193567	chr20:23455772-23455773	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs191994025	chr20:23455793-23455794	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs7351246	chr20:23455800-23455801	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs556880268	chr20:23455818-23455819	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs13037914	chr20:23455820-23455821	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs185242723	chr20:23455824-23455825	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs111452296	chr20:23455854-23455855	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs551812698	chr20:23455856-23455857	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs75517181	chr20:23455861-23455862	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs7261178	chr20:23455883-23455884	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs189746645	chr20:23455884-23455885	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs181394580	chr20:23455889-23455890	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs535337993	chr20:23455890-23455891	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs531740852	chr20:23455943-23455944	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs549018316	chr20:23455970-23455971	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs186031224	chr20:23455972-23455973	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs2983283	chr20:23455973-23455974	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs2983284	chr20:23455981-23455982	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs117038786	chr20:23455983-23455984	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs537739589	chr20:23456016-23456017	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
25	rs557415264	chr20:23456017-23456018	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
26	rs188306174	chr20:23456033-23456034	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
27	rs373852198	chr20:23456037-23456038	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
28	rs71766724	chr20:23456038-23456039	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
29	rs71183342	chr20:23456042-23456043	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
30	rs542861244	chr20:23456045-23456046	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
31	rs559761296	chr20:23456055-23456056	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
32	rs200914904	chr20:23456080-23456081	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
33	rs113002203	chr20:23456143-23456144	Weak transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs577630841	chr20:23456156-23456157	Weak transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs538621944	chr20:23456180-23456181	Weak transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs373201162	chr20:23456191-23456192	Weak transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs545543996	chr20:23456214-23456215	Weak transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs375099802	chr20:23456219-23456220	Weak transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs145926309	chr20:23456223-23456224	Weak transcription Enhancers Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs553853313	chr20:23456331-23456332	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs1028525	chr20:23456344-23456345	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
42	rs186062999	chr20:23456349-23456350	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs6036421	chr20:23456350-23456351	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs148902502	chr20:23456352-23456353	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs143625045	chr20:23456361-23456362	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs565409616	chr20:23456368-23456369	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs576707378	chr20:23456385-23456386	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs534391744	chr20:23456386-23456387	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs1028524	chr20:23456406-23456407	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
50	rs6137971	chr20:23456429-23456430	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:59)

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
Bipolar disorder	19114987	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23446600-23465600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr20:23451400-23456200	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr20:23454400-23455800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr20:23455200-23455800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr20:23455200-23464800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr20:23455600-23456400	Enhancers	Fetal Thymus	thymus
7	chr20:23455800-23456000	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr20:23455800-23456000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
9	chr20:23455800-23456200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr20:23455800-23456200	Bivalent Enhancer	HepG2	liver
11	chr20:23455800-23456800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr20:23456200-23456400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
13	chr20:23456400-23457800	Weak transcription	Fetal Thymus	thymus
14	chr20:23456800-23459400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr20:23457000-23457400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr20:23457000-23457400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr20:23457000-23457400	ZNF genes & repeats	Fetal Kidney	kidney
18	chr20:23457000-23457400	ZNF genes & repeats	Gastric	stomach
19	chr20:23457000-23458000	Enhancers	Esophagus	oesophagus
20	chr20:23457400-23457600	Enhancers	Fetal Kidney	kidney
21	chr20:23457400-23458000	Weak transcription	Gastric	stomach
22	chr20:23457600-23458200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr20:23457800-23458200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr20:23457800-23458200	Enhancers	Fetal Thymus	thymus
25	chr20:23458000-23459400	Weak transcription	Esophagus	oesophagus
26	chr20:23458200-23459400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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