Top results (P−5) from CMH test of allele frequencies in main effect and transgenerational effect models.

SNPs with P−5 in the EMA discovery sample are listed. The model type (Model) and SNP identity (SNP) are shown. For each SNP, the closest annotated genes are indicated as well as relative SNP position to those genes (Nearest Gene(s) and Location). P-values (CMH P-value) and odds ratios (CMH OR) are shown for a Cochran-Mantel-Haenszel test of pair-type counts in case vs. control pairs from the EMA discovery cohort. In order to show that our models under investigation are not driven by proband main effects (in maternal main effect model) or both maternal and proband main effects (in transgenerational effect models), a comparison between multinomial models is shown (LRT P-value). Replication datasets were imputed to allow maximum coverage of SNPs across different platforms. Replication was performed on trios; results were then combined across replication datasets using random-effects meta-analysis (Rep. P-value, Rep. OR). *Indicates that a merged Rep. P-value and OR are presented rather than the meta-analyzed statistic.