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Most significant haplotypes associated with resistance to nine Xoo strains.
The two most significant haplotypes within the LD block are shown in the plot.
It should be mentioned that the most significant haplotypes (A-G and G-A) found by Washizuka et al. [ 5] were rare haplotypes, which could be more easily influenced by the small sample size (199 patients vs. 221 controls).
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The two most significant haplotype associations concurred with the single locus associations.
A region of 7.7 kb drove the most significant haplotype-specific methylation, and overlies a region containing putative enhancer sequence.
The most significant haplotype combination was with the TLR5 G22A SNP, without the two protective TLR5 SNPs (C100T and T1844C) and with the two TLR4 SNPs (A1571T and G1807A) (p<0.0001).
In the adjusted global analysis the most significant haplotype in all three data sets consisted of two SNPs (rs2056974-rs2473316) (unrelated p = 0.007, family p = 0.004, and combined p = 0.006) (Figure 1c, Table 3).
In the adjusted global test the most significant haplotype in the unrelated and combined data sets consisted of three SNPs (rs353644-rs353630-rs7937602; p = 0.002 and p = 9.1×10−5, respectively; Figure 1a; Table 1).
In the adjusted global analysis the most significant haplotype in all three data sets (unrelated, family and combined) consisted of three SNPs (rs1414275-rs11588376-rs1016140) (p = 0.02, p = 0.04, and p = 0.008, respectively) (Figure 1b, Table 2).
In the adjusted global analysis the most significant haplotype in all three data sets consisted of three SNPs (rs12409415-rs2056225-rs2243158) (unrelated p = 0.008, family p = 3.2×10−5, and combined p = 0.004) (Figure 1d, Table 4).
In the adjusted global analysis the most significant haplotype in the family and combined data sets consisted of three SNPs (rs2287047-rs997049-rs3917299) (unrelated p = 0.001, family p = 0.02, and combined p = 0.02) (Figure 1e, Table 5).
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