In contrast to changes in protein-coding sequences, the significance of noncoding DNA variation in human disease has been minimally explored. A recent torrent of genome-wide association studies suggests that noncoding variation represents a significant risk factor for common disorders, but the mechanisms by which they contribute to disease remain largely obscure. Distant-acting transcriptional enhancers - a major category of functional noncoding DNA - are likely involved in many developmental and disease-relevant processes. Genome-wide approaches for their discovery and functional characterization are now available and provide a growing knowledgebase for the systematic exploration of their role in human biology and disease susceptibility.