SNPLogic (http://www.snplogic.org) brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system for design and analysis of genotyping projects. SNPLogic integrates information about the genetic context of SNPs (gene, chromosomal region, functional location, haplotypes tags and overlap with transcription factor binding sites, splicing sites, miRNAs and evolutionarily conserved regions), genotypic data (allele frequencies per population and validation method), coverage of commercial arrays (ParAllele, Affymetrix and Illumina), functional predictions (modeled on structure and sequence) and connections or established associations (biological pathways, gene ontology terms and OMIM disease terms). The SNPLogic web interface facilitates construction and annotation of user-defined SNP lists that can be saved, shared and exported. Thus, SNPLogic can be used to identify and prioritize candidate SNPs, assess custom and commercial arrays panels and annotate new SNP data with publicly available information. We have found integration of SNP annotation in the context of pathway information and functional prediction scores to be a powerful approach to the analysis and interpretation of SNP-disease association data.