A score of 1f means "eQTL + TF binding / DNase peak", whereas a score of 1d means "eQTL + TF binding + any motif + DNase peak", and 1b means "eQTL + TF binding + any motif + DNase Footprint + DNase peak".\cite{help} 1a is the highest possible score, corresponding to the highest chance of functionality, followed in alphabetical order by the other "1" values (letters a through f). Of the 2,385 SNPs tested, only 2 (0.08%) had the highest score of 1a: namely,
Of these, the first is an intergenic variant that has only been reported in one study--namely, the one by Davies et al. (2018) included here.\cite{catalog}\cite{Davies_2018} The second is an intron that also has only ever been reported by Davies et al. (2018).\cite{catalog}\cite{Davies_2018}
Genome-wide significance
It is widely accepted that the appropriate p-value in GWASs, which is said to represent a "genome-wide significance" (GWS) level corresponding to p < 0.05, is 5*10-8.\cite{Fadista2016} Using this threshold, we can ask what percent of reported associations fell above, below, or exactly on this threshold. In these data, of the 2,719 reported associations, 913 (34%) had p-values above this threshold, 1,728 (64%) had p-values below the threshold (indicating that they displayed GWS), and 78 (3%) fell exactly on this threshold (i.e. p = 5*10-8). There is a clear increasing trend in the average -log(p) value over time, as illustrated in Figure 2 below; this indicates that associations reported are becoming more statistically significant, perhaps as a result of more rigorous methodology.