Variant report

Variant	esv3358653
Chromosome Location	chr20:23454952-23459450
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	chr20:23457266-23457336	GM19239	blood:	n/a	n/a
4	CTCF	chr20:23456100-23456250	HEK293	kidney:	n/a	chr20:23456220-23456229
5	CTCF	chr20:23455380-23455410	Spleen_OC	spleen:	n/a	n/a
6	CTCF	chr20:23456160-23456310	HepG2	liver:	n/a	chr20:23456220-23456229
7	MAFK	chr20:23454633-23454952	HepG2	liver:	n/a	chr20:23454799-23454814
8	NFATC1	chr20:23456847-23457205	GM12878	blood:	n/a	n/a
9	NFATC1	chr20:23456811-23457420	GM12878	blood:	n/a	n/a
10	PBX3	chr20:23456864-23457242	GM12878	blood:	n/a	n/a
11	POLR2A	chr20:23457131-23457455	HepG2	liver:	n/a	n/a
12	STAT5A	chr20:23456847-23457264	GM12878	blood:	n/a	n/a
13	SUZ12	chr20:23456943-23457524	H1-hESC	embryonic stem cell:	n/a	n/a
14	TCF12	chr20:23456979-23457562	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23454015..23456705-chr20:23459387..23462774,3	MCF-7	breast:

Variant related genes	Relation type
CST12P	TF binding region
ENSG00000226344	chromatin interactions

Extended variants
information (count: 249 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:249 , 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	rs113172696	chr20:23454979-23454980	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs367991621	chr20:23455001-23455002	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs541430061	chr20:23455009-23455010	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs6137970	chr20:23455011-23455012	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs111849077	chr20:23455028-23455029	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs112556834	chr20:23455056-23455057	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs76761205	chr20:23455079-23455080	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs192467485	chr20:23455107-23455108	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs564489396	chr20:23455109-23455110	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs139745922	chr20:23455115-23455116	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs6106667	chr20:23455120-23455121	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs563598536	chr20:23455136-23455137	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs112583988	chr20:23455149-23455150	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs529411673	chr20:23455160-23455161	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs113336885	chr20:23455175-23455176	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs140049971	chr20:23455181-23455182	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs185105616	chr20:23455224-23455225	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs532918529	chr20:23455274-23455275	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs528541350	chr20:23455294-23455295	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs551522037	chr20:23455304-23455305	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs76520583	chr20:23455308-23455309	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs112028963	chr20:23455310-23455311	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs113816913	chr20:23455339-23455340	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs63261161	chr20:23455347-23455348	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs370036424	chr20:23455349-23455350	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs539608088	chr20:23455358-23455359	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs374112748	chr20:23455365-23455366	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs370443768	chr20:23455369-23455370	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs189484374	chr20:23455426-23455427	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs7260910	chr20:23455443-23455444	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs535522215	chr20:23455446-23455447	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs35183078	chr20:23455476-23455477	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs200167184	chr20:23455512-23455513	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs112920106	chr20:23455517-23455518	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs142083025	chr20:23455592-23455593	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs7260983	chr20:23455615-23455616	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs114213930	chr20:23455649-23455650	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs564233799	chr20:23455666-23455667	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs557990927	chr20:23455754-23455755	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs577932771	chr20:23455763-23455764	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs543583130	chr20:23455766-23455767	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs563890136	chr20:23455770-23455771	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs574193567	chr20:23455772-23455773	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs191994025	chr20:23455793-23455794	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs7351246	chr20:23455800-23455801	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs556880268	chr20:23455818-23455819	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs13037914	chr20:23455820-23455821	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs185242723	chr20:23455824-23455825	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs111452296	chr20:23455854-23455855	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs551812698	chr20:23455856-23455857	Enhancers Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	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:36 , 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	chr20:23451000-23455200	Enhancers	iPS-15b Cell Line	embryonic stem cell
3	chr20:23451400-23456200	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr20:23452400-23455200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr20:23452600-23455200	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr20:23452600-23455200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr20:23453000-23455000	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr20:23453400-23455400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr20:23454400-23455600	Weak transcription	Fetal Thymus	thymus
10	chr20:23454400-23455800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:23455200-23455800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr20:23455200-23464800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr20:23455600-23456400	Enhancers	Fetal Thymus	thymus
14	chr20:23455800-23456000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr20:23455800-23456000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
16	chr20:23455800-23456200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr20:23455800-23456200	Bivalent Enhancer	HepG2	liver
18	chr20:23455800-23456800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr20:23456200-23456400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
20	chr20:23456400-23457800	Weak transcription	Fetal Thymus	thymus
21	chr20:23456800-23459400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr20:23457000-23457400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr20:23457000-23457400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:23457000-23457400	ZNF genes & repeats	Fetal Kidney	kidney
25	chr20:23457000-23457400	ZNF genes & repeats	Gastric	stomach
26	chr20:23457000-23458000	Enhancers	Esophagus	oesophagus
27	chr20:23457400-23457600	Enhancers	Fetal Kidney	kidney
28	chr20:23457400-23458000	Weak transcription	Gastric	stomach
29	chr20:23457600-23458200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr20:23457800-23458200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr20:23457800-23458200	Enhancers	Fetal Thymus	thymus
32	chr20:23458000-23459400	Weak transcription	Esophagus	oesophagus
33	chr20:23458200-23459400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr20:23459400-23459800	Enhancers	Esophagus	oesophagus
35	chr20:23459400-23460200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr20:23459400-23460200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell

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