Phenotype-associated loci from genome-wide association studies (GWAS) are usually non-coding, and functionally interpreting them is a challenge due to linkage disequilibrium (LD) and our almost complete inability to predict regulatory function directly from non-coding sequence. Therefore, regulatory genomic data such as maps of enhancers and transcription factor binding sites are essential to interpreting GWAS, developing mechanistic hypotheses, and ultimately understanding the genetic architecture of complex traits and disease (1–3). For human geneticists, these regulatory data can be unwieldy to translate from a genome browser to insights about a set of genomically-dispersed disease variants. HaploReg (4) integrates regulatory genomic maps together in the context of haplotype blocks, allowing researchers to intersect regulatory elements with genetic variants to quickly formulate functional hypotheses, both through dissection of multiple variants within a haplotype block and through global enrichment analysis of a set of associated loci. HaploReg annotation of GWAS has successfully been applied for haplotype fine-mapping (5–9) and enrichment analysis (7,10,11).
