Table 3 summarizes the secondary gene-based analysis of all other SNPs genotyped. Three columns of p-values are provided which were obtained used the permutation procedure implemented in PLINK (Purcell et al., 2007): p-value refers to the individual SNP p-value, Set p refers to gene-level p-value, and All sets p refers to individual SNP p-value corrected for all SNPs tested across all genes. SNPs rs2072658 in CHRNB2 and rs6730111 in CHRNA1 had MAF <0.01 so were not included in the PLINK analysis, leaving a total of 224 SNPs. These exploratory tests revealed significant evidence for association of CHRNA10 (set-based empirical p=0.007) and CHRNA4 (p=0.020) with the “dizziness” item. Only SNPs in CHRNA10 (rs2231532) reached experiment-wide significance when corrected for all SNPs tested (all sets p=0.048, Table 3). Nominal p-values for all SNPs tested are available in Supplementary Table 1. A series of graphs in Figure 1 provide an overview of all SNPs tested by chromosome and gene. Each dot plots the −log (p-value) on the y-axis of individual SNPs along their respective chromosomal positions on the x-axis. The dashed horizontal line at −log(0.01) reflects a for p-value of 0.01.
