Table 2.

Single SNP and component 2-SNP haplotype effects for example replicated 3-SNP haplotypes.

Chr	3-SNP haplotype or logic tree	Tree ORb	Tree Pb	Single SNP	Alternative allele	SNP ORc	SNP Pc	Component 2-SNP haplotype	Pair ORd	Pair Pd
6	(rs3129881 = C) or ((rs375244 = A) and (rs3132947 = G))	3.665	2.3 × 10−24	rs3129881	C	2.227	1.8 × 10−23	rs375244 = A and rs3132947 = G	1.238	7.9 × 10−5
				rs375244	A	0.980	0.715
				rs3132947	G	2.117	1.4 × 10−16
6	((rs9268831 = T) or (rs9269190 = T)) or (rs9270652 = C)	3.075	7.3 × 10−29	rs9268831	T	1.324	1.6 × 10−7	rs9268831 = T or rs9269190 = T	1.633	2.8 × 10−16
				rs9269190	T	1.252	1.3 × 10−4	rs9268831 = T or rs9270652 = C	1.321	2.0 × 10−5
				rs9270652	C	1.109	0.057	rs9269190 = T or rs9270652 = C	1.925	1.2 × 10−18
6	(rs9295704 = C) and ((rs2451752 = A) and (rs2575174 = C))a	0.365	8.9 × 10−15	rs9295704	C	0.669	1.5 × 10−7	rs9295704 = C and rs2451752 = A	0.399	3.2 × 10−14
				rs2451752	A	0.951	0.457	rs9295704 = C and rs2575174 = C	0.638	1.2 × 10−7
				rs2575174	C	0.940	0.393	rs2451752 = A and rs2575174 = C	0.933	0.228
7	((rs12671658 = T) or (rs12702656 = A)) and (rs11768586 = G)a	0.066	3.9 × 10−9	rs12671658	T	1.023	0.682	rs12671658 = T and rs11768586 = G	0.104	1.4 × 10−6
				rs12702656	A	1.039	0.585	rs12702656 = A and rs11768586 = G	0.000	0.953
				rs11768586	G	0.865	0.010
9	(rs4979484 = C) or ((rs13300483 = T) and (rs7028891 = G))a	1.672	3.0 × 10−21	rs4979484	C	1.365	0.005	rs13300483 = T and rs7028891 = G	1.637	1.2 × 10−19
				rs13300483	T	1.584	1.4 × 10−17
				rs7028891	G	1.574	2.8 × 10−17

^aContains no HLA region SNPs.

^b3-SNP haplotype OR and p-value in the combined sample (N = 2,886).

^cSingle SNP ORs and p-values, assuming an additive genetic effect model for the specified alternative allele.

^d2-SNP haplotype ORs and p-values, assuming an additive genetic effect model for the specified haplotype pattern.