Disentangling effects of colocalizing genomic annotations to functionally prioritize non-coding variants within complex trait loci

Identifying genomic annotations that differentiate causal from associated variants is critical to fine-map disease loci. While many studies have identified non-coding annotations overlapping disease variants, these annotations colocalize, complicating fine-mapping efforts. We demonstrate that conventional enrichment tests are inflated and cannot distinguish causal effects from colocalizing annotations. We developed a sensitive and specific statistical approach that is able to identify independent effects from colocalizing annotations. We first confirm that gene regulatory variants map to DNase-I hypersensitive sites (DHS) near transcription start sites. We then show that (1) 15-35% of causal variants within disease loci map to DHS independent of other annotations; (2) breast cancer and rheumatoid arthritis loci harbor potentially causal variants near the summits of histone marks rather than full peak bodies; and (3) variants associated with height are highly enriched for embryonic stem cell DHS sites. We highlight specific loci where we can most effectively prioritize causal variation.