Analyses of single marker and pairwise effects of candidate loci for rheumatoid arthritis using logistic regression and random forests.

Single-marker and pairwise interaction analysis using LR Single-marker analysis showed highly significant disease association with rs2476601 ( p = 2 × 10 -8 ), and nominally significant effects for rs237025 ( p = 0.003) and CT60 ( p = 0.038) in both the median-replaced and the imputed data sets (see Figure 2a and 2c ).

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One rare single-nucleotide polymorphism (SNP), HugotSNP8ms2 (minor allele frequency <0.05), showed nominally significant deviations from HWE in the controls ( p = 0.008) and in the full sample ( p = 0.006) due to an overrepresentation of rare homozygotes, which might be the result of chance or genotyping error.

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