Susceptibility to CAP related to haplotypes encompassing SFTPA1, SFTPA2 and SFTPD When haplotypes encompassing both SFTPA genes were studied, we observed 39 of the 64 expected haplotypes, and only 14 haplotypes had frequencies higher than 1% (data not shown). The most common SFTPA1-SFTPA2 haplotype, 6A 2 -1A 0 , was underrepresented in patients (P = 0.0005, OR = 0.77; 95% CI 0.66 to 0.90), whereas 6A 3 -1A was overrepresented (P = 0.0007, OR = 3.92; 95% CI 1.63 to 10.80) (see Table 3 ). Both differences remained significant after Bonferroni correction. For the observed odd-ratios, the powers of the tests with a significance level of 1% were 87.76% and 84.04% for the haplotypes 6A 2 -1A 0 and 6A 3 -1A respectively. On the other hand, dominant and recessive logistic regression models showed a significant dominant effect on CAP susceptibility for haplotypes 6A 3 -1A and 6A-1A 1 and a recessive effect for haplotype 6A 2 -1A 0 (see Table 3 ). We also intended to analyze whether phased variants encompassing the three genes were involved in susceptibility to CAP. Only 68 of the 128 expected haplotypes were observed, and 16 of them had a frequency over 1%. Chromosomes containing C-6A 2 -1A 0 were decreased in patients when compared with controls (P = 0.00001, OR = 0.62; 95% CI 0.50 to 0.77), a difference that remained significant after Bonferroni correction. C-6A 2 -1A 0 was also significantly associated with protection against CAP in a dominant model (see Table 3 ).