Korea BioInformation Center Byoung-Chul Kim SNP@Promoter : A database of Human SNPs (Single Nucleotide Polymorphisms) within putative promoter region Korea BioInformation Center Byoung-Chul Kim

Korean Bioinformation Center (KOBIC) The national bioinformatics center of Korea Mission is to integrate of diverse biological information Genome information Biodiversity information Bioresource information Work towards the development of international training programs on bioinformatics Develop bioinformatics tools and resources which need your participation BioWiki (online knowledgebase of biology) BioPipe (Bioworkflow engine) 2

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Korea BioInformation Center Byoung-Chul Kim SNP@Promoter : A database of Human SNPs (Single Nucleotide Polymorphisms) within putative promoter region Korea BioInformation Center Byoung-Chul Kim

What are SNPs (Single Nucleotide Polymorphisms) Common DNA sequence variations among individuals in genome wherein the least frequent allele has an abundance of 1% or greater. Make up about 90% of all human genetic variation Occurs every 100 to 300 bases along the 3-billion-bases human genome Some SNPs are reported to be highly related to diseases or influence cells response to a drug

SNPs have various functions G/T promoter G/T G/C GU AG TFBS 5’UTR atggacgtactggtg tctgagtgctccgcg 3’UTR A/G G/T Type 1 transcript Type 2 transcript Type 3 transcript Type 1 protein M D V L V S E C S A Altering the encoded protein Alternative splicing Premature termination Transcription regulation M D V L V S E S S A Type 2 protein Type 3 protein

KOBIC Variome Project Http://variome.net

SNP@Promoter is constructed such as… Identification of putative promoter regions NCBI Entez Genes NCBI Human Genome Transfac Prediction of Transcription factor binding sites NCBI dbSNP SNPs within regulatory region UCSC human conservation score Calculation of Evolution conservation score in TFBS KEGG HGMD OMIM GAD GOA Integration of Functional annotation databases

We can improve the predictive sensitivity of TFBS Prediction of TFBS have high false-positive rate Evolutionarily conserved regions within or adjoining the gene often serve as critical cis-regulatory regions SNP@Promoter show the predicted TFBS with evolutionary conservation score UCSC GENOME BROWSER

What can you do with SNP@Promoter? Gene Predicted TFBS Ontology Conservation of TFBS Pathway Annotation SNP within Promoter SNP within TFBS GAD GOA OMIM UCSC Disease association KEGG NCBI dbSNP Transfac HGMD Human Genome NCBI Gene

Example : Atopy associated genes and SNPs

Atopy associated gene list

SNPs in atopy associated gene

Graphic viewer

Conclusions http://variome.kobic.re.kr SNP@promoter is a database Predict functional SNPs Provide a platform for biologists for finding functional SNPs http://variome.kobic.re.kr http://variome.kobic.re.kr/SNPatPromoter/