KDGV(Korean Database of Genomic Variants)

http://ksnp.cdc.go.kr

2009. 4

KDGV(Korean Database of Genomic Variants)

KSNP Database KARE Database KAREdb GWASaid

• 2004~2006년까지24명(질환별로각각다른24명)의SNP을발굴하고이를데이터베이스화

• KSNP데이터베이스는2,978개의gene의총12,995개의KSNP가등록

• gene(genesymbol,locusid),chromosome상의위치,SNPID(dbSNP,JSNP,KSNP),variationtype(snp,in/del,microsatellite)등의8개의검색항목을통한검색가능

KSNP Database

GWASaid

• Web-basedtoolforannotationandvisualizationofgenomewideassociationdata

• Automaticannotation/interpretationofgenomewideassociationresults

• TraceSNPinformationbasedonthelatestdbSNPbuild

• chromosomalplotgeneration(SNPassociation,pathway,geneontology,diseaseinformation)

• signalplotgeneration(SNPassociation,candidategene,hotspot,conservationinformation

KAREdb

• KARE데이터에대한association결과를제공

• SNPid(dbSNPid,Illuminaid)및안성/안산의population의p-value값을통한검색기능제공

• 총14개group(lipids,obesity,diabetesindex등)의57개의trait을분류하고,이에대한signalplot정보,clusterplot,snp정보를제공

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 hongiiv@nih.go.kr

KARE Database

• 한국인유전체분석사업의일환으로안성,안산지역사회역학코호트주민을대상으로대규모유전체분석사업(KARE프로젝트)을수행

• SNPid,염색체상의위치,genesymbol,geneannotation을통한SNP검색제공

• SNP의Genotypefrequency,Alleleinformation정보와LDplot정보제공

• 각SNP에대한signalplot정보제공

Database summary statistics

Total KARE SNP entries:

2,096,558(77% imputed)

Cluster Plot : 500,568

dbSNP: Build 129

HapMap: 2008. 06

KARE Database Browser Home Page

Search methods

• Keywordsearch• Clusterplotsearch• Chromosomebandsearch

Keyword search• UsewithadbSNPnumber:rs4801847• Usewithagenesymbol:BRCA2• Usewitharegion:chr1:1..100(chr#:start..end)• Searchmetawords• probe:usetofindIlluminaSNPprobeid• terms:usetofindaspecificgeneinNCBIEntrez• terms:bloodcellcount• terms:diabetesindex

Meta word search: terms

Cluster plot searchDownload compressed image file

dbSNP rs#

Chromosome band search

Search ResultSearch and Navigation track

Search result track - Overview track - Region track - Detail track

Track configure

Display setting

Add your own data

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

Browser NavigationMouse drag

Zoom inRecenterLeft move Right move

Region size

Region zoom in/out

HapMap & KHapMap Information

NCBI dbSNP Information

Genes, Contig, GC Content information

KARE SNP Information

Genotype frequency

Allele information

Table View

KARE SNP Information

Cluster Plot

High resolution image

LD plot InformationBased on data from HapMap populations

Populations selectable from “Configure... LD Plot” menu

http://cgs.cdc.go.krhttp://ksnp.cdc.go.krhttp://www.ngri.go.kr/SNP