We use the R package Variant Annotation59 to functionally annotate the SNPs and indels. We considered only the relationship between the marker and its target gene in a cis-eQTL signal and not the functional property of the SNP in relation to other genes. For example, the relationship for a cis-eQTL signal between a SNP located outside the transcribed region of the target gene X was marked as “none” even if the SNP sat in the intron of gene Y. For a small proportion of the markers, no functional annotation was available.
