Genomic SEM was used to perform SNP-level tests of heterogeneity (QSNP; Supplementary Information section 3.5.1; Supplementary Data 1–2) to investigate whether each SNP had consistent, pleiotropic effects on the seven input phenotypes that effectively only operate via EXT. If the EXT loci really index a shared genetic externalizing liability, we would expect to identify heterogeneity mostly in regions of the genome not associated with EXT. In the absence of heterogeneity, it is expected that a given SNP’s GWAS effects on the input phenotypes will scale proportionally to the factor loadings24 (see Supplementary Information section 3.5.2). The genome-wide QSNP analysis was adequately powered (mean χ(1)2 = 1.864; Extended Data Fig. 2), and at one-sided QSNP P < 5×10−8, we identified 160 QSNP loci (Supplementary Information section 3.5.1). Importantly, only eight of these 160 loci overlapped with EXT loci (~1% = 8/579) (Figure 2; Supplementary Table 9). Reassuringly, we identified 3.6 times more EXT loci than QSNP loci (579/160). Using a less stringent significance threshold by focusing specifically on the 579 EXT loci, only 7% (41/579) were significant for QSNP (one-sided QSNP
