Identified gene interactions.

Six pairs of SNPs that represented interacting loci. Chr: chromosome and cytoband information. Nearest Gene: When the nearest annotated gene was >500 kb away from the SNPs, it was not listed. The trend p-values were obtained with the shared controls. The validation of allelic effect for loci with original trend p-values>0.05 is not presented. Validation status: Unavailable, data unavailable for validation; PPR, p-value of the proxy replication; Meta-analysis, susceptibility locus found by meta-analysis studies after the WTCCC study; Not significant, validation was not significant (P>0.05); Known region, a susceptibility region that was known at the time of the WTCCC study; PLV, p-value of the local validation. The last five columns contain the interaction results. Pure interaction p-values were obtained with the shared controls. Two-locus p-value (expanded): two-locus LRT p-value according to the search situation, and the two-locus p-values and the corresponding corrected p-values for the final significance were obtained in the expanded control analysis.
*Bonferroni corrected P<0.05. Because all of these loci were obtained in the simultaneous searches, in which the two-locus tests took account of all effects of the two loci, therefore the main effects and the interaction effects were examined in the validation analyses, and the following criterion was used to determine the validation status of each locus: (1) if the pure interaction effect was validated (i.e. P<0.05), both of the loci and their interaction effect were validated, irrespective of the validations of the main effects; (2) if the pure interaction effect was not validated, then the validation status of a locus was determined by the validation of its main effect.