In addition to testing SNP markers to determine whether a single SNP could directly influence the SHAS phenotype, a number of smoking and drinking phenotypes were analyzed by including them as covariates when modeling their relationship with SHAS. Three of these phenotypes (average number of cigarettes per day, the maximum amount drank in one day, and the average number of drinks consumed on days the subject consumed alcohol) improved the overall peak LOD score compared to the model without covariates. The other tested phenotypes (number of days the subject drank in the last week, amount consumed 24 hours prior to challenge, number of days of smoking in a month, and number of cigarettes smoked on days where the subject smoked), lowered the peak LOD score presumably because these phenotypes are correlated with the SHAS score. All LOD scores are shown in the Table 3 below.
