Chiu et al. [2009] used an extension of a generalized estimating equations approach to conduct linkage disequilibrium (LD) mapping with a sliding window of 100 SNPs in a region containing 1,561 SNPs located between 28,000 and 40,000 cM on 6p21. They also tested for interactions between these SNPs and both shared epitope (SE) alleles and sex. In the single-SNP analysis, 251 out of 1,561 SNPs had a p-value ≤3.2×10−5 (the Bonferroni corrected significance level). There was a significant interaction between the SE allele number and the estimated disease locus at 32.6 cM. However, there was no interaction between sex and the estimated disease locus.
