Initially, all SNPs were excluded from analysis if the minor allele was not present at least six times in the sample group, translating to an MAF cutoff of 0.04. All significant observations that had p-values below the threshold and that met the MAF cutoff requirement were exported and the list was evaluated based on the following criteria: (1) Associations that were present on the exon or transcript list that were actually due to the opposing level were moved to the appropriate list. Specifically, a study-wide significant transcript level association was reported if the p-value achieved the threshold requirements, the affected transcript contained >2 exons, and >40% of exons contained in a transcript were significantly associated at exon-level study-wide significance level. Consistent with those rules, transcripts containing <2 exons associating with genotype that were study-wide significant and/or <40% of exons within a transcript were affected were removed and allowed on the exon-level list if they achieved exon-level study-wide significance. (2) Using stepwise linear regression (STATA/IC 10.0) associations were removed that were redundant due to LD between SNPs. Specifically, following inclusion of
