In addition to our genome-wide screen for eQTLs associated with sporadic ALS, we specifically examined possible relevant cis effects in two previously associated loci (gene UNC13A and chromosome 9p21.2) [7], [12]. The detection of cis effects might fine-map these loci. For the UNC13A locus (SNP rs12608932), multiple-testing correction was applied for 41 possible SNP-transcript pairs in cis (as determined by a genomic distance of <500kb between the SNP and a probe’s midpoint). One SNP-transcript pair had a nominal p value <0.05, the transcript of which mapped to gene PGLS (pEQTL = 0.01). However, when using a 5% Benjamini-Hochberg FDR for the locus as multiple-testing correction, no SNP-transcript pairs reached statistical significance. For the chromosome 9p21.2 locus, we looked for cis eQTLs within a 130kb LD block comprising previously associated SNPs (rs2814707 and rs3849942). Multiple-testing correction for the testing of 328 SNP-transcript pairs was applied using a 5% FDR. Two SNP-transcript pairs reached the threshold for statistical significance and were associated with C9orf72 isoform a expression levels (Table 2 and Figure S4). SNP rs1565948 modulated C9orf72 gene expression in both eQTL
