Using the three constructed parcels without any missing data, the distribution of p-values was compared across SNPs with high (p < 5e-8) and low (p > 5e-3) QSNP estimates from the item-level Genomic SEM analysis of neuroticism for SNPs that were genome-wide significant in at least one of the parcels. These results indicated that, for SNPs with a higher QSNP for the common factor, there was more discordance of effect sizes among three lower-order factors relative to SNPs that produced lower heterogeneity estimates (Supplementary Figure 19). The average difference between the highest and lowest –log10 p-values was 10.56 and 4.96 for high and low QSNP, respectively. This suggests that QSNP is appropriately indexing discordance in SNP level effects across genetically correlated indicators.
