What have we learned from six years of GWAS in autoimmune diseases, and what is next?

► Genome-wide association studies in autoimmune diseases have yielded hundreds of risk loci. ► Two broad approaches have been taken to interpret GWAS data. ► 'Bottom-up' approaches study the function of individual alleles, genes, and proteins. ► 'Top-down' approaches examine collections of risk alleles to construct relevant pathways. ► Combining GWAS data with functional data types can elucidate disease mechanism.