Association analysis given linkage.

Shown are all SNPs yielding genome-wide significant p-values with either the quantitative and/or the qualitative antibody phenotype in the SAFHS. The regression coefficients refer to the estimated change in the phenotype for each dose of the rarer SNP allele. For the SAFHS all significant genome-wide results (p≤5.29×10−8) are presented in bold lettering. After correcting for multiple testing during replication in the SADGS (we tested the entire HLA region, with 5689 available SNPs: p≤0.05/5689≈8.79×10−6), there are two significant SNPs in the replication sample. When using the combined sample of both studies (SAFHS+SAFDGS), all SNPs originally significant in the SAFHS discovery sample are highly significant.
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).