Variant report

Variant	esv3323428
Chromosome Location	chr20:25518256-25518846
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25518724..25523016-chr20:25601749..25604904,3	MCF-7	breast:
2	chr20:25512408..25515336-chr20:25515482..25519858,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000213742	chromatin interactions
ENSG00000170191	chromatin interactions

Extended variants
information (count: 27 )
Associated
traits (count: 55 )

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs529799433	chr20:25518294-25518295	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs115913879	chr20:25518302-25518303	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs543973210	chr20:25518303-25518304	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs6050669	chr20:25518346-25518347	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs563468883	chr20:25518417-25518418	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs74582000	chr20:25518437-25518438	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs542900751	chr20:25518493-25518494	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs562953978	chr20:25518498-25518499	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs528045159	chr20:25518522-25518523	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs368058848	chr20:25518552-25518553	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs530377828	chr20:25518554-25518555	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs28565216	chr20:25518573-25518574	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs571198715	chr20:25518577-25518578	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs913790	chr20:25518584-25518585	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs550266280	chr20:25518591-25518592	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs187443655	chr20:25518606-25518607	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs569875346	chr20:25518612-25518613	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs535670281	chr20:25518631-25518632	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs375266493	chr20:25518632-25518633	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs555612871	chr20:25518638-25518639	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs146946892	chr20:25518708-25518709	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs535041125	chr20:25518709-25518710	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs558122659	chr20:25518726-25518727	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs577994466	chr20:25518775-25518776	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs138130401	chr20:25518779-25518780	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs192588154	chr20:25518805-25518806	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs140815237	chr20:25518811-25518812	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	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
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
small cell lung cancer	20016488	CNVD

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr20:25498200-25519400	Weak transcription	Gastric	stomach
4	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
7	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:25507400-25518400	Weak transcription	A549	lung
9	chr20:25507600-25519600	Weak transcription	Fetal Intestine Large	intestine
10	chr20:25511200-25520200	Weak transcription	Fetal Brain Male	brain
11	chr20:25513400-25519200	Enhancers	Liver	Liver
12	chr20:25513600-25518600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr20:25513600-25519400	Weak transcription	Esophagus	oesophagus
14	chr20:25513800-25520400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr20:25513800-25521200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr20:25514200-25521000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr20:25514400-25520000	Weak transcription	NHLF	lung
18	chr20:25514400-25520800	Weak transcription	Fetal Kidney	kidney
19	chr20:25514400-25522400	Weak transcription	NH-A	brain
20	chr20:25514800-25519200	Weak transcription	Right Atrium	heart
21	chr20:25514800-25520000	Weak transcription	Osteobl	bone
22	chr20:25514800-25520400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr20:25515000-25519000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr20:25515000-25519600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr20:25515000-25520200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr20:25515000-25520200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr20:25515200-25518600	Weak transcription	Right Ventricle	heart
28	chr20:25515200-25519200	Weak transcription	Pancreas	Pancrea
29	chr20:25515400-25519200	Weak transcription	Colon Smooth Muscle	Colon
30	chr20:25515400-25519600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr20:25515400-25520600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr20:25515600-25519600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr20:25515600-25519800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr20:25515600-25520200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr20:25515800-25518400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr20:25515800-25519200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr20:25515800-25519400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr20:25515800-25519400	Weak transcription	Fetal Heart	heart
39	chr20:25515800-25519800	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr20:25516000-25519800	Weak transcription	Fetal Thymus	thymus
41	chr20:25516000-25520200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr20:25516200-25519800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr20:25516600-25519000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr20:25516800-25520000	Weak transcription	NHDF-Ad	bronchial
45	chr20:25517000-25518600	Weak transcription	Left Ventricle	heart
46	chr20:25517000-25519200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr20:25517000-25519200	Weak transcription	Ovary	ovary
48	chr20:25517000-25519400	Weak transcription	Adipose Nuclei	Adipose
49	chr20:25517000-25519400	Weak transcription	Brain Anterior Caudate	brain
50	chr20:25517000-25519600	Weak transcription	Brain Angular Gyrus	brain

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