Variant report

Variant	esv990034
Chromosome Location	chr20:24562298-24563174
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	MYC	chr20:24562389-24562564	MCF-7	breast:	n/a	n/a
2	MYC	chr20:24562563-24562678	MCF-7	breast:	n/a	n/a
3	POLR2A	chr20:24562407-24562468	MCF-7	breast:	n/a	n/a
4	POLR2A	chr20:24562415-24562512	MCF-7	breast:	n/a	n/a
5	POLR2A	chr20:24562651-24562653	MCF-7	breast:	n/a	n/a
6	POLR2A	chr20:24562663-24562807	MCF-7	breast:	n/a	n/a
7	POLR2A	chr20:24562826-24562857	MCF-7	breast:	n/a	n/a
8	POLR2A	chr20:24562473-24562474	MCF-7	breast:	n/a	n/a
9	POLR2A	chr20:24562622-24562636	MCF-7	breast:	n/a	n/a
10	STAT1	chr20:24562381-24562423	GM12878	blood:	n/a	n/a
11	ZNF263	chr20:24562115-24563164	HEK293-T-REx	kidney:	n/a	chr20:24562466-24562487

Variant related genes	Relation type
SYNDIG1	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:37 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs531560576	chr20:24562388-24562389	ZNF genes & repeats Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs562244322	chr20:24562425-24562426	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs59861353	chr20:24562426-24562427	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs116989841	chr20:24562441-24562442	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs570966412	chr20:24562457-24562458	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs370449840	chr20:24562506-24562507	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs550519329	chr20:24562517-24562518	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs532396552	chr20:24562560-24562561	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs570333984	chr20:24562561-24562562	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs535479012	chr20:24562576-24562577	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs116721162	chr20:24562577-24562578	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs149399571	chr20:24562582-24562583	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs183738011	chr20:24562593-24562594	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs76582986	chr20:24562601-24562602	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs577762634	chr20:24562620-24562621	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs73905117	chr20:24562656-24562657	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs556852179	chr20:24562668-24562669	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs573581762	chr20:24562713-24562714	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs541848911	chr20:24562734-24562735	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs35954189	chr20:24562737-24562738	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs116503989	chr20:24562749-24562750	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs6049794	chr20:24562824-24562825	Weak transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs117708157	chr20:24562865-24562866	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs114440856	chr20:24562884-24562885	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs533585413	chr20:24562911-24562912	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
26	rs530451510	chr20:24562943-24562944	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs189412996	chr20:24562944-24562945	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs139755778	chr20:24562970-24562971	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs562823412	chr20:24563003-24563004	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs115367935	chr20:24563005-24563006	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs549001838	chr20:24563008-24563009	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs369420760	chr20:24563017-24563018	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs565546838	chr20:24563031-24563032	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs146994799	chr20:24563087-24563088	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs534560586	chr20:24563130-24563131	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs548492253	chr20:24563148-24563149	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs182322878	chr20:24563171-24563172	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

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
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
Cancer	20164919	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24538800-24570200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr20:24549800-24565800	Weak transcription	Thymus	Thymus
3	chr20:24553800-24564800	Weak transcription	Brain Anterior Caudate	brain
4	chr20:24554000-24564800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr20:24555800-24564000	Weak transcription	Brain Hippocampus Middle	brain
6	chr20:24558800-24562400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr20:24559800-24563200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:24559800-24564000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr20:24560800-24564800	Weak transcription	Brain Angular Gyrus	brain
10	chr20:24560800-24565000	Weak transcription	Fetal Muscle Leg	muscle
11	chr20:24561000-24565000	Weak transcription	Brain Substantia Nigra	brain
12	chr20:24561800-24562400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr20:24561800-24562800	Weak transcription	Fetal Brain Male	brain
14	chr20:24561800-24565000	Weak transcription	Brain Germinal Matrix	brain
15	chr20:24562000-24562400	Enhancers	Fetal Brain Female	brain
16	chr20:24562000-24562400	Weak transcription	Spleen	Spleen
17	chr20:24562000-24562600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr20:24562200-24562600	Enhancers	Esophagus	oesophagus
19	chr20:24562200-24562800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr20:24562200-24563000	Enhancers	Right Ventricle	heart
21	chr20:24562400-24562600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr20:24562400-24562600	Enhancers	Spleen	Spleen
23	chr20:24562400-24562800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr20:24562400-24563000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr20:24562400-24567400	Weak transcription	Fetal Brain Female	brain
26	chr20:24562600-24562800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr20:24562600-24565000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr20:24562600-24570000	Weak transcription	Spleen	Spleen
29	chr20:24562800-24563200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr20:24562800-24563400	Enhancers	Fetal Brain Male	brain
31	chr20:24562800-24564800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr20:24563000-24563600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr20:24563000-24564200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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