Table 2

Haplotypic association using the top three SNPs following serial step-wise logistic regression in each cohort is shown (see table 1 and table s8 in the online supplement for further details).

	SNP1	SNP2	SNP3	HAPLOTYPE	F_A	F_U	F_Uexp	OR	95% CI	p	p_perm
UK_risk	rs1269852	rs3906272	rs3129868	CAT	<0.001	<0.001	0.0004	NA	NA	NA	NA
UK_prot	rs1269852	rs3906272	rs3129868	GGG	0.524	0.729	0.7604	0.37	0.31 to 0.44	3.72×10⁻²⁸	1×10⁻⁴
Spanish_risk	rs3130490	rs3129768	rs3117213	ACA	0.004	<0.001	0.001	NA	NA	NA	NA
Spanish_prot	rs3130490	rs3129768	rs3117213	CAC	0.506	0.688	0.6849	0.443	0.36 to 0.55	2.22×10⁻¹³	1×10⁻⁴
Filipino_risk	rs9271366	rs2571391	rs2507987	GAT	0.273	0.092	0.1485	3.45	2.24 to 5.33	5.69×10⁻¹¹	1×10⁻⁴
Filipino_prot	rs9271366	rs2571391	rs2507987	ACA	0.005	0.031	0.0507	NA	NA	NA	NA

F_A, haplotypic frequency in affected SLE cases; F_U, haplotypic frequency in unaffected controls; F_U_exp, expected haplotypic frequency calculated from minor allele frequency of SNPs in controls; NA, not applicable (unable to perform statistical analyses as frequencies too low); p, p value; p_perm, permuted p value (10000 permutations); prot, haplotype comprising all three protective alleles; risk, haplotype comprising all three risk alleles; SLE, systemic lupus erythematosus; SNP, single nucleotide polymorphism.