To estimate the joint effects of the two independently associated PTPN2 SNPs from the 18p11 region (rs1893217 and rs478582), we performed a 2-d.f. test by simply entering both genotypes into the logistic regression model as numerical indicator variables coded 0, 1 or 2 (in other words, as multiplicative allelic effects), representing the number of occurrences of the minor alleles A and A. When compared with the basic model, this 2-d.f. likelihood ratio test corresponds to the ‘locus-based’ score test described in ref. 11.
