Table 3.

Table 3 focuses on results achieving genome-wide significance in large samples. We use a significance threshold of 5×10⁻⁸ (reference ¹⁹⁸). Most associations achieving this level of significance are secure but some may ultimately prove not to be. Included are SNPs with p < 5×10⁻⁸ that were evaluated in samples of a minimum of around 10,000 cases and 10,000 controls. Discovery sample sizes reflect the primary samples for which full GWAS were conducted. In most cases, discovery P values were > 5×10⁻⁸ but met a threshold (typically 1×10⁻⁵) for inclusion in replication efforts. In some instances, simultaneous publications based upon overlapping samples were considered “discovery”. Where this occurred, providing samples of roughly equivalent sizes, the most significant primary GWAS findings are given; otherwise, the largest discovery samples are favored. For many studies, it was not possible to extract the exact sample size used for each locus so the sample sizes above are approximate. P-values and ORs are from the meta-analysis with the largest sample sizes. If two meta-analyses based on overlapping samples reported similar results, the “discovery” study is cited. The genes nearest each locus are provided but etiological variants are generally unknown, and it remains likely that some of the associations do not alter the function of the designated genes (e.g., ITIH3-ITIH4 where multiple correlated SNPs span many genes, and TCF4-CCDC68 where statistically independent associations occur in TCF4 and closer to CCDC68). In the TCF4-CCDC68 example, it may be that both associations point to the same functional element but, it is also possible that independent etiological variants occur in adjacent genes.

For the SCZ loci attributed to Steinberg et al., ¹⁹⁵ no discovery sample size is listed because the initial P values were modest and, as the authors conducted multiple follow-up analyses, there is no obvious discovery sample. At the MHC, the International Schizophrenia Consortium ⁶⁹ is designated discovery as it was the only primary GWAS for which genome-wide significance at the MHC was obtained. Steinberg et al. is cited for the meta-analysis at the MHC as it reported the most significant MHC association. ¹⁹⁵ The most significant SNP at the MHC across the two studies is not identical, and the one listed is that from Steinberg et al. Multiple statistically independent SNPs have been reported at the MHC. ^58,186 We note that genome-wide significance had been reported in BIP for ANK3¹⁹⁹ but not in a larger mega-analysis including the same samples. ⁵⁹ Others have reported genome-wide significance for composite phenotype studies of ITIH3-ITIH4²⁰⁰ (but see reference ²⁰¹) and CACNA1C ²⁰² but in samples smaller than required for inclusion in the above table.

ALCcon means alcohol consumption. The rs671 association was in East Asian samples. The ADH1B locus was also associated with ALC.

NDcon means nicotine consumption (as maximal cigarettes per day, continuous). NDinit means smoking initiation (ever versus never began smoking). NDsc means smoking cessation (whether regular smokers had quite at time of interview).