MOTIVATION: Genome-wide association studies (GWAS) generate relationships 
between hundreds of thousands of single nucleotide polymorphisms (SNPs) and 
complex phenotypes. The contribution of the traditionally overlooked copy number 
variations (CNVs) to complex traits is also being actively studied. To 
facilitate the interpretation of the data and the designing of follow-up 
experimental validations, we have developed a database that enables the sensible 
prioritization of these variants by combining several approaches, involving not 
only publicly available physical and functional annotations but also multilocus 
linkage disequilibrium (LD) annotations as well as annotations of expression 
quantitative trait loci (eQTLs).
RESULTS: For each SNP, the SCAN database provides: (i) summary information from 
eQTL mapping of HapMap SNPs to gene expression (evaluated by the Affymetrix exon 
array) in the full set of HapMap CEU (Caucasians from UT, USA) and YRI (Yoruba 
people from Ibadan, Nigeria) samples; (ii) LD information, in the case of a 
HapMap SNP, including what genes have variation in strong LD (pairwise or 
multilocus LD) with the variant and how well the SNP is covered by different 
high-throughput platforms; (iii) summary information available from public 
databases (e.g. physical and functional annotations); and (iv) summary 
information from other GWAS. For each gene, SCAN provides annotations on: (i) 
eQTLs for the gene (both local and distant SNPs) and (ii) the coverage of all 
variants in the HapMap at that gene on each high-throughput platform. For each 
genomic region, SCAN provides annotations on: (i) physical and functional 
annotations of all SNPs, genes and known CNVs within the region and (ii) all 
genes regulated by the eQTLs within the region.
AVAILABILITY: http://www.scandb.org.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics 
online.