The polygenic analyses indicated significant gene-environment interaction effects with parental knowledge and peer deviance, and we used set-based analyses to probe whether the individual top SNPs contributing to our polygenic scores were themselves enriched for gene-environment interaction. We examined this question using the set of top SNPs (p ≤ 0.0001) from the ALSPAC GWAS. We selected this relatively stringent p-value threshold in view of the computing resources required to perform the permutation analyses described below. Of the 311 SNPs meeting this threshold in ALSPAC, 279 (90%) were available in FinnTwin12. We pruned by LD in the FinnTwin12 sample in order to reduce the set to include only independent (r2 < 0.50) SNPs, which resulted in 76 SNPs. Because LD calculations should be made on independent individuals, we used a randomly-selected sample of independent individuals in the FinnTwin12 sample (n = 634) for this purpose. We then permuted the phenotypic and covariate information for these individuals 100,000 times while keeping the genotypic information (LD) unchanged. For each of these permuted datasets, we examined gene-environment interaction effects for parental knowledge and peer
