After quality control, there were 1,307 ALS cases and 1,835 controls in the GWAS replication set with genotypes for 266,492 SNPs (Table S2). 577 cis eQTL SNPs were tested for association in the GWAS replication data. Using linkage disequilibrium-based clumping of association results [28], 322 independent clumps could be formed. This number of clumps was used for Bonferroni correction, as these clumps designate independent loci. Table 1 shows clumps with a nominal pGWAS <0.05 in the replication set. Ultimately, we identified 1 cis eQTL, comprising 8 SNP-transcript pairs, which was significantly replicated, and the transcript of which mapped to gene CYP27A1. The results for this locus are listed in Table S3, also indicating that the explained variance of gene expression that is achieved by the linear models ranged from 48–65%. The relationships between the SNPs and gene-expression levels are shown in Figure S3.
