Subsequently, association with ALS for SNPs from the replicated cis SNP-transcript pairs was tested in the GWAS replication data by logistic regression using gender, dummy-coded nationality and the first two EIGENSTRAT principal components (these were significantly correlated to case/control status) as covariates. Association test results were clumped based on LD (r2 >0.5) using PLINK, so that SNP p values could be obtained for independent eQTLs. eQTLs with a replication pGWAS <0.05 after Bonferroni correction for the number of independent (LD-based clumped) loci were considered to be significant (Figure 1).
