Pair-wise marker-marker linkage disequilibrium (LD) was assessed using the D' and r2 statistic in Haploview 3.31 (Barrett et al., 2005). Many of the traits studied were correlated and there was substantial LD across GABRA2 (see Figure 1). As a result the effective number of statistical tests done was substantially less than the actual number of tests. To take account of both of these factors we estimated the effective number of tests by utilizing permutations in QTDT. Since QTDT only implements permutations for the “within” test, we cannot do this for the “total” test (but see below). Two p-values are available from the permutation routine; one p-value which corrects for all tests done, p_corrected, and another p-value for each trait/marker combination singly, p_uncorrected. If all traits and markers were uncorrelated then a permutation procedure would yield a p-value equivalent to a Bonferroni correction; that is, p_corrected = 1 – (1-p_uncorrected)^n where n denotes the number of tests done. An estimate of the effective number of independent “within” tests is hence n_effective = log(1-p_corrected)/log(1-p_uncorrected), approximately 110 (compared with 242 non-independent tests in
