We used the Single Nucleotide Polymorphism Spectral Decomposition (SNPSpD) test, a simple correction for multiple testing of SNPs in LD with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. The user-friendly Web interface (http://gump.qimr.edu.au/general/daleN/SNPSpD/) (Nyholt, 2004) provides the effective number of independent marker loci and experiment-wide significance threshold required to keep Type I error rate at 5%. For this study, including 11 SNPs, the effective number of independent marker loci is 5 and the experiment-wide significance threshold was 0.01.
