We outline a strategy to use tissue-specific expression along with promoter module analysis to determine the putative functional context of candidate genes implicated in genome-wide association studies. First, genes are selected from candidate SNPs, followed by construction of a gene co-regulation network to expand the regulatory context of the candidate genes, functional analysis to determine putative functional roles, and subsequent analysis of regulatory elements. We describe these sub-strategies and variations, along with guidelines for alternatives in the overall analysis.