Association analysis, given linkage, conditional on the top SNP.

The top SNP, rs477515/rs2516049, was determined based on analysis of the quantitative antibody trait in the combined sample (SAFHS and SAFDGS). Only the extended HLA region was analyzed. Shown are the SNPs yielding genome-wide significant p-values (p≤5.29×10−8, shown in bold) with either the quantitative and/or the qualitative antibody phenotype in the combined sample. The regression coefficients refer to the estimated change in the phenotype for each dose of the rarer SNP allele.
aSince we used a liability threshold model for analysis of the dichotomous trait (see methods section), the direction of effect on EBNA-1 discrete serostatus is opposite of the sign of the regression coefficient, but is in the same direction as the regression coefficient for the quantitative trait (e.g. for SNP rs204999, the minor allele is associated with a decrease in EBNA-1 antibody level and seronegativity).