Targeted set association analysis. The 3,346 SNPs identified in the first round of analysis as associating with expression traits in cis at an FDR < 0.1 were picked for a second round of analysis. To assess the significance of the resulting set of expression traits detected as associated with this set of SNPs, sets of randomly selected SNPs of size 3,346 with MAF distributions identical to the original set were generated. All sets of SNPS were then analyzed using the same method described above for genome-wide associations.
