Table 3.

Haplotype Analysis of Promoter SNPs rs12914489 and rs16958477 with Missense Variants R141L and G153D

Haplotype*	Estimated Haplotype Frequency			P†	OR (95% CI)†
	ES	Controls	Combined
GAGG	0.400	0.282	0.340	0.0005	1.70 (1.26–2.29)
GCGG	0.284	0.209	0.246	0.014	1.51 (1.09–2.09)
GCTG	0.120	0.215	0.169	0.0004	0.50 (0.34–0.73)
AAGG	0.140	0.059	0.098	0.0001	2.56 (1.55–4.24)
GCGA	0.010	0.163	0.088	3.9 × 10−14	0.05 (0.02–0.15)
Total	0.954	0.928	0.941	1.7 × 10−17‡

^*The four SNPs included in the haplotype analysis are rs12914489, rs16958477, rs1048661 (R141L) and rs3825942 (G153D). Only haplotypes with a frequency over 5% in the combined samples were shown.

^†Obtained from the haplotype-specific test using Haploview. The OR was calculated for each of the haplotypes compared with all the other haplotypes. The Bonferroni corrected significance level was 0.01 (0.05/5). Significant SNPs are highlighted in bold.

^‡Obtained from the omnibus test with PLINK.