Fig. 1

Natural logarithm of the odds ratios (ORs) for the different combinations of MHC and non-MHC genotypes. All ORs were calculated relative to a group consisting of the same MHC genotype and with the genotypes (0,0) at all non-MHC loci involved in the comparison – see text. The MHC genotypes, in order of increasing disease-risk (Fig. S2), are presented on the x-axis (as columns) and the genotypes at non-MHC loci are presented on the y-axis (as rows). The values for ln(OR) and the z-scores for each comparison are represented as numbers at the points of intersection of the column and row for any two haplotypes. Comparisons with a z-score (|z|< 1) are shaded in yellow; comparisons with a z-score (1 ≥|z|< 2) are shaded in either pale blue (negative) or pale red (positive); comparisons with a z-score (2 ≥ z < 3) are shaded in light red; comparisons with a z-score (3 ≥ z < 4) are shaded in red; comparisons with a z-score (z ≥ 4) are maroon. Specific combinations having marginal totals of less than15 total representations in the WTCCC are indicated by (na). Adjustment for multiple comparisons [45] only impacted the significance of z-scores less than 2.5