Variant report

Variant	esv3496004
Chromosome Location	chr20:25829408-25838116
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	chr20:25604447..25606097-chr20:25837225..25840203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170191	chromatin interactions
ENSG00000213742	chromatin interactions

Extended variants
information (count: 790 )
Associated
traits (count: 44 )

Variant overlapped rSNPs/rCNVs (count:790 , 50 per page) page: 1 2 3 4 5 6 7 ... 16

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs575924435	chr20:25829409-25829410	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs79037868	chr20:25829435-25829436	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs73348912	chr20:25829436-25829437	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs75119730	chr20:25829470-25829471	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs544860447	chr20:25829472-25829473	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs561450151	chr20:25829484-25829485	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
7	rs62214070	chr20:25829502-25829503	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs530090197	chr20:25829504-25829505	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs540308958	chr20:25829505-25829506	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs560117478	chr20:25829535-25829536	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs532429487	chr20:25829589-25829590	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs74892539	chr20:25829595-25829596	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
13	rs375103710	chr20:25829596-25829597	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
14	rs76523023	chr20:25829600-25829601	Weak transcription Strong transcription Enhancers ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
15	rs6132871	chr20:25829604-25829605	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs6132872	chr20:25829606-25829607	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs531432809	chr20:25829607-25829608	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs62214071	chr20:25829608-25829609	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs62214072	chr20:25829616-25829617	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs140667459	chr20:25829620-25829621	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs568307408	chr20:25829624-25829625	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs71332664	chr20:25829628-25829629	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs533777563	chr20:25829638-25829639	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs6138687	chr20:25829641-25829642	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs6132873	chr20:25829643-25829644	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs574489416	chr20:25829665-25829666	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs539504469	chr20:25829672-25829673	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs62214073	chr20:25829688-25829689	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs556314357	chr20:25829745-25829746	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs575884567	chr20:25829758-25829759	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs538088786	chr20:25829759-25829760	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs140240837	chr20:25829761-25829762	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs113967964	chr20:25829763-25829764	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs201008189	chr20:25829773-25829774	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs6132874	chr20:25829779-25829780	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs139905817	chr20:25829783-25829784	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs140605219	chr20:25829796-25829797	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs540931278	chr20:25829804-25829805	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
39	rs113984278	chr20:25829810-25829811	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
40	rs76138495	chr20:25829829-25829830	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
41	rs560082797	chr20:25829846-25829847	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
42	rs75652262	chr20:25829849-25829850	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
43	rs143703993	chr20:25829852-25829853	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
44	rs79006706	chr20:25829866-25829867	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
45	rs186880240	chr20:25829877-25829878	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
46	rs377729236	chr20:25829897-25829898	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
47	rs112624470	chr20:25829908-25829909	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
48	rs370100663	chr20:25829909-25829910	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
49	rs376302839	chr20:25829914-25829915	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
50	rs199633764	chr20:25829918-25829919	Weak transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:44)

Disease	PMID	Source
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
Anaplastic large cell lymphoma	18179710	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Bladder cancer	21909424	CNVD
Esophageal cancer	21851588	CNVD
Chordoma	18071362	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	21364760	CNVD
small cell lung cancer	20016488	CNVD
Colorectal cancer	16774939	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:335 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25826000-25832200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:25826000-25833200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr20:25826000-25833600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr20:25826000-25833800	Weak transcription	Aorta	Aorta
5	chr20:25826000-25833800	Weak transcription	HSMMtube	muscle
6	chr20:25826200-25832600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr20:25826200-25833600	Weak transcription	Brain Anterior Caudate	brain
8	chr20:25826200-25833600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr20:25826200-25833600	Weak transcription	Brain Substantia Nigra	brain
10	chr20:25826200-25833600	Weak transcription	Right Ventricle	heart
11	chr20:25828000-25829600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr20:25828400-25833600	Weak transcription	Left Ventricle	heart
13	chr20:25828800-25829800	Strong transcription	Brain Inferior Temporal Lobe	brain
14	chr20:25828800-25829800	Strong transcription	Stomach Smooth Muscle	stomach
15	chr20:25828800-25830600	ZNF genes & repeats	Fetal Stomach	stomach
16	chr20:25829000-25829600	Strong transcription	Brain Angular Gyrus	brain
17	chr20:25829000-25829600	ZNF genes & repeats	Spleen	Spleen
18	chr20:25829200-25829600	ZNF genes & repeats	Pancreas	Pancrea
19	chr20:25829400-25829800	Enhancers	Lung	lung
20	chr20:25829400-25830800	Weak transcription	Gastric	stomach
21	chr20:25829400-25831800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr20:25829400-25832000	Weak transcription	Dnd41	blood
23	chr20:25829400-25833600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr20:25829400-25833600	Weak transcription	Brain Hippocampus Middle	brain
25	chr20:25829400-25833600	Weak transcription	Colonic Mucosa	Colon
26	chr20:25829400-25833600	Weak transcription	Esophagus	oesophagus
27	chr20:25829400-25833600	Weak transcription	Fetal Lung	lung
28	chr20:25829400-25833600	Weak transcription	Ovary	ovary
29	chr20:25829400-25834200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr20:25829400-25836200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr20:25829600-25830400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr20:25829600-25833600	Weak transcription	Brain Angular Gyrus	brain
33	chr20:25829600-25833600	Weak transcription	Pancreas	Pancrea
34	chr20:25829600-25833600	Weak transcription	Spleen	Spleen
35	chr20:25829800-25833600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr20:25829800-25833600	Weak transcription	Fetal Muscle Leg	muscle
37	chr20:25829800-25833600	Weak transcription	Lung	lung
38	chr20:25829800-25833600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr20:25830400-25831200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr20:25830600-25833600	Weak transcription	Fetal Stomach	stomach
41	chr20:25830800-25831000	Enhancers	Gastric	stomach
42	chr20:25830800-25831000	Enhancers	HepG2	liver
43	chr20:25831000-25831200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr20:25831000-25831200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
45	chr20:25831000-25831200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
46	chr20:25831000-25831200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr20:25831000-25831400	Enhancers	ES-I3 Cell Line	embryonic stem cell
48	chr20:25831000-25831400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
49	chr20:25831000-25833400	Weak transcription	HepG2	liver
50	chr20:25831000-25833800	Weak transcription	Gastric	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links