Summary of a pipeline for functional annotation of common variants at cancer susceptibility loci. After the identification of common variants associated with disease, fine mapping of the susceptibility loci is a required step in resolving likely causal allele(s). Integrating fine-mapping data with genome-wide analysis of noncoding regulatory elements may be used to identify the putative functional targets of trait-associated alleles. Performing expression quantitative trait locus (eQTL) analysis in normal and/or cancer tissues can be used to link susceptibility SNPs overlapping regulatory elements with candidate susceptibility genes. Finally, a combination of in vitro and in vivo functional assays can be used to characterize the mechanisms and roles in disease etiology of both candidate regulatory elements and candidate genes.