The causal SNPs that contribute to autoimmune disease risk are often inherited along with neighboring neutral SNPs as a result of linkage disequilibrium. The index SNPs that are genotyped and associated with disease risk in GWAS implicate genomic loci — linkage disequilibrium blocks — composed of multiple linked SNPs (gray boxes). GWAS loci associated with autoimmune disease are enriched in genes (rectangles) that are preferentially expressed in particular immune cell subsets (autoimmune disease cell signatures; bottom left) (38) and encode proteins (circles) that participate in a disproportionate number of direct and indirect physical interactions to form biological pathways (autoimmune disease pathways; bottom right) (41). Expression patterns and protein interaction network analysis have been used to triage candidate genes within linkage disequilibrium blocks. These analyses also suggest pathogenic cell types, protein complexes, and pathways that are affected by disease variants, which begins to elucidate the biology underlying complex autoimmune diseases and could direct drug discovery efforts. Adapted with permission from American Journal of Human Genetics (38) and PLoS Genetics (41).