korean database of genomic variants
DESCRIPTION
Korean Database of Genomic Variants, KDGVTRANSCRIPT
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KDGV(Korean Database of Genomic Variants)
http://ksnp.cdc.go.kr
2009. 4
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KDGV(Korean Database of Genomic Variants)
KSNP Database KARE Database KAREdb GWASaid
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• 2004~2006년까지24명(질환별로각각다른24명)의SNP을발굴하고이를데이터베이스화
• KSNP데이터베이스는2,978개의gene의총12,995개의KSNP가등록
• gene(genesymbol,locusid),chromosome상의위치,SNPID(dbSNP,JSNP,KSNP),variationtype(snp,in/del,microsatellite)등의8개의검색항목을통한검색가능
KSNP Database
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GWASaid
• Web-basedtoolforannotationandvisualizationofgenomewideassociationdata
• Automaticannotation/interpretationofgenomewideassociationresults
• TraceSNPinformationbasedonthelatestdbSNPbuild
• chromosomalplotgeneration(SNPassociation,pathway,geneontology,diseaseinformation)
• signalplotgeneration(SNPassociation,candidategene,hotspot,conservationinformation
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KAREdb
• KARE데이터에대한association결과를제공
• SNPid(dbSNPid,Illuminaid)및안성/안산의population의p-value값을통한검색기능제공
• 총14개group(lipids,obesity,diabetesindex등)의57개의trait을분류하고,이에대한signalplot정보,clusterplot,snp정보를제공
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KARE Database Overview• Based on version 1.69 of GMOD GBrowse
• Contains all of the gene information normally present in International HapMap project
• Ensembl genes, Entrez genes, dbSNP SNPs, Copy Number Variation
• Please send questions, problems or apparent errors to [email protected]
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KARE Database
• 한국인유전체분석사업의일환으로안성,안산지역사회역학코호트주민을대상으로대규모유전체분석사업(KARE프로젝트)을수행
• SNPid,염색체상의위치,genesymbol,geneannotation을통한SNP검색제공
• SNP의Genotypefrequency,Alleleinformation정보와LDplot정보제공
• 각SNP에대한signalplot정보제공
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Database summary statistics
Total KARE SNP entries:
2,096,558(77% imputed)
Cluster Plot : 500,568
dbSNP: Build 129
HapMap: 2008. 06
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KARE Database Browser Home Page
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Search methods
• Keywordsearch• Clusterplotsearch• Chromosomebandsearch
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Keyword search• UsewithadbSNPnumber:rs4801847• Usewithagenesymbol:BRCA2• Usewitharegion:chr1:1..100(chr#:start..end)• Searchmetawords• probe:usetofindIlluminaSNPprobeid• terms:usetofindaspecificgeneinNCBIEntrez• terms:bloodcellcount• terms:diabetesindex
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Meta word search: terms
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Cluster plot searchDownload compressed image file
dbSNP rs#
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Chromosome band search
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Search ResultSearch and Navigation track
Search result track - Overview track - Region track - Detail track
Track configure
Display setting
Add your own data
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KARE Data track config• Genotyped Allele Frequency view with pie chart• These are selected from the “Tracks” menu and appear as tracks near
the bottom of the display• Tracks for all SNPs and the SNPs on selected HapMap are also available
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Browser NavigationMouse drag
Zoom inRecenterLeft move Right move
Region size
Region zoom in/out
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HapMap & KHapMap Information
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NCBI dbSNP Information
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Genes, Contig, GC Content information
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KARE SNP Information
Genotype frequency
Allele information
Table View
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KARE SNP Information
Cluster Plot
High resolution image
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LD plot InformationBased on data from HapMap populations
Populations selectable from “Configure... LD Plot” menu
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http://cgs.cdc.go.krhttp://ksnp.cdc.go.krhttp://www.ngri.go.kr/SNP