Conditional analyses were performed with GCTA software26 using full meta-analysis summary level statistics and a European reference panel (ALSPAC mothers cohort; n = 8,890) to determine the number of independent signals present in regions identified in our meta-analysis. For each region of interest, we re-ran the meta-analysis conditioning on our SNP with the lowest p-value. The next signal was identified from the conditional meta-analysis results, and included in the second conditional meta-analysis. This process was repeated in an iterative fashion until no residual signal remained below a threshold of p < 5 × 10−8 (see Figure S1 and S2). For 15q25.1, we also employed an additional strategy, conditioning on missense SNP rs16969968 first. The entire process was also repeated using an alternative sample (Netherlands Twin Register) as the LD reference panel (n = 7,000), and similar results obtained.
