Figure 6. Phenotypic effects associated with deletions.

(A) The significance levels (-log(p-value)) of phenotypic associations of deletions with genome-wide association studies (GWAS) traits as a function of their emergence time. Gray points indicate non-ancient deletions. Purple and orange points indicate non-exonic ancient deletions with GWAS hits and exonic ancient deletions with GWAS hits, respectively. The genes whose exons are covered by ancient deletions, and the traits associated with ancient deletions are mentioned in the plot. (B) The significance levels (-log(p-value)) and sizes of expression level changes of nearby HLA genes associated with the presence of the deletion esv3608584. Each color refers to a different HLA gene. Each point in a given color represents a different tissue. Only those tissues whose expression level changes are statistically significant are shown here.