We applied similar modeling approaches to local IBD-based h2 (Figures 3c, 3d), estimating the proportion of total h2 attributable to local genetic variation. Our mean local IBD h2 was 0.03, with mean(h2local IBD)/mean(h2) = 0.23. This ratio is somewhat lower than those reported for MuTHER (>0.30), perhaps partly attributable to their focus on genes with higher total heritability.8 A definitive statement of average per-gene ratios (h2local IBD/h2) will require more complex modeling to handle correlation structures in the measurements and underlying true structure. However, the results from our large sample support the view that local genetic variation explains only a minority of transcriptomic heritability, and much of the unexplained variation is among genes with modest h2. A regression approach (Supplementary Figure 5) shows that ~35% of the variation in estimated h2 can be explained by the predictors.
