A total of 274 SNPs had discovery q<0.3, and were included in replication. SNAP analysis indicated that 121 represent LD-independent tests, setting replication significance at 0.05/121=0.0004. Lookup replication and meta-analysis results arranged by chromosome and base pair are also shown for all 28 SNPs with q<0.1 in Table 1. Supplementary Table S1 shows these results for all 274 SNPs with q<0.3. No individual SNP achieved p<0.0004 in any sample. In meta-analysis of the 4 case-control samples, one SNP in a second novel locus, the long noncoding RNA (lncRNA) gene LOC339975 showed a GWS signal (chr. 4q35.2, rs11726136, p=7.52×10−7, q=0.149 in the discovery sample, Figure 3D, and GWS p=4.20×10−8 in meta-analysis of the four case/control samples, Table 1 and Supplementary Table S1). Because of differences in ascertainment and severity of affection, we performed replication analyses including the Australian population sample separately; this signal was not significant when the Australian sample was included (Supplementary Table S1).
