Fig. 2

Lower triangular plots of the natural logarithm of the odds ratios (ORs) for replacing one MHC haplotype by another in different genotypic contexts. For example, at the point of intersection for \((0 \to H + )\) in the 7th column and \((c1 \to H + )\) in the in the 10th row, the value of (0.5) represents the log of the ratio: \(\frac{{OR{\text{ for the transition: }}(c1,0) \to (c1,H + ){\text{ }} = {\text{ }}3.67}}{{OR{\text{ for the transition: }}(H + ,0) \to (H + ,H + ){\text{ }} = {\text{ }}2.17{\text{ }}}}\) or equivalently: \(\frac{{OR{\text{ for the transition: }}(0,c1) \to (0,H + ){\text{ }} = {\text{ }}2.74{\text{ }}}}{{OR{\text{ for the transition: }}(H + ,c1) \to (H + ,H + ){\text{ }} = {\text{ }}1.62}}\). Positive numbers indicate that OR for the replacement transition (indicated by the column) using the 1st companion haplotype (indicated by 1st haplotype of the transition listed in the row) is greater than the same replacement transition using the 2nd companion haplotype (indicated by 2nd haplotype of the transition listed in the row). Conversely, a negative number indicates that the OR for the replacement transition using the 2nd companion haplotype is greater than it is using the 1st companion haplotype. Operationally, these replacement transitions are simply ORs comparing cases to controls for the two genotypes (e.g., \(OR(c1,H + )/OR(c1,0) = 3.67\)). Because of symmetry, this describes either of two, mathematically equivalent, replacement scenarios. The first compares the replacement of (0) by (H +) when the companion haplotype is (c1) to the same replacement when the companion is (H +). The second compares the replacement of (c1) by (H +) when the companion haplotype is (0) to the same replacement when the companion is (H +). Therefore, the interpretation for the meaning of the replacement transitions represented by the rows and column are interchangeable. These two, mathematically equivalent, replacement scenarios (i.e. transitions) can be depicted as follows: . Only transitions for (H +), “extended risk” (ER), “all protective” (AP), (c1), and (0) haplotypes are shown. These transitions are indicated on both the y-axis (as rows) and the x-axis (as columns) and values of ln(OR) for each transition comparison are represented as numbers at the points of intersection of the column and row for any two transitions. Specific combinations having marginal totals of less than15 total representations in the WTCCC are indicated by (na). Comparisons of the OR for the numerator with the OR for the denominator, and which have an absolute z-score > 3.0, are shaded either dark blue (negative) or dark red (positive); comparisons having an absolute z-score = 2.0–3.0 are shaded either light blue (negative) or light red (positive); comparisons having an absolute z-score = 1.0–2.0 are shaded either pale blue (negative) or pale red (positive) yellow; comparisons having absolute z-scores < 1.0 are shaded in yellow. Adjustment for multiple comparisons [45] only impacted the significance of z-scores less than 2.5