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 discovery and replication sets and was associated with susceptibility to ALS in the joint GWAS data; however, no association with ALS was found in the GWAS replication set alone (Table 2).
