In very recent work, Kichaev et al. [8] introduce a new method (PAINTOR) that leverages functional data for improved fine-mapping. The method also outputs annotations associated with disease. While the method is clearly effective in increasing fine-mapping resolution, it is unclear whether the method is effective at ranking cell types; for example, cell types identified as contributing the most to HDL, LDL, and Triglycerides (using data from Teslovich et al. [27]) are muscle, kidney, and fetal small intestine, respectively, whereas the top cell types for those three phenotypes identified using our method (also using data from Teslovich et al. [27]) are liver, liver, and liver. The uncertain effectiveness of this method in ranking cell types may be because it is primarily aimed at fine-mapping and thus considers only genome-wide significant loci.
