LD between markers should be considered when using SNP data to search for disease or trait association. Thus, SNPs exhibiting trait association in our primary analysis that were also in close proximity to one another were tested to see if they were in LD with each other. Pair-wise LD coefficients were computed using the program LDMAX, which is part of the GOLD computer package [5]; results are reported using the normalized coefficient D' = D/|D|max, where D = p11 - p1 p2, p11 is the frequency for the haplotype containing allele 1 at both markers, pi is the frequency of allele 1 at the ith marker of the pair, and |D|max is the maximum possible (absolute) value of D given the marker allele frequencies.
