one SNP, rs10938397 on 4p12, could not be compared between meta-analyses because there was no corresponding proxy SNP. Of the 78 variants catalogued, 29 had matching SNPs on the Affymetrix 6.0 array. For the 49 SNPs not present, proxies (45 r2 > 0.8; 4 r2 > 0.7) were identified using SNP Annotation and Proxy Search V2.1 (Johnson et al. 2008). Following removal of seven duplicate proxies and six variants from Willer et al. for which no proxies were available (r2 > 0.7), 65 SNPs remained. Haploview version 4.10 was used to determine phase and corresponding proxy alleles (Barrett et al. 2005; Barrett 2009). In order to avoid bias due to correlated effects, SNP pruning (r2 > 0.8) was performed using PLINK v. 1.07p (Purcell et al. 2007). Of the 56 remaining SNPs, 19 met genome-wide significance criteria in the two meta-analyses. The additional 37 were included as they were the next top SNPs reported (p < 0.05). Although our SNP selection threshold was more liberal than the traditional genome-wide significance threshold, it was more conservative than other models of complex disease risk prediction (Evans et al. 2009; Purcell et al. 2009). Supplemental Table 1 details information on the 78 catalogued
