TABLE II.

The odds ratios (95% CIs) of 11 SNPs estimated from allele frequencies reported by Parkes et al. [2007] in an initial scan (stage 1) and replication study (stage 2)

Chr	SNP	Stage 1 OR	Stage 2 OR	GZW	MLE	ZP	UMVCUE
5p13	rs17234657	1.55 (1.38, 1.74)	1.16 (1.05, 1.29)	1.55	1.39	1.39	1.16
5p13	rs9292777	1.38 (1.26, 1.51)	1.34 (1.21, 1.49)	1.38	1.37	1.37	1.39
10q24	rs10883365	1.27 (1.17, 1.38)	1.18 (1.02, 1.37)	1.26	1.24	1.24	1.16
18p11	rs2542151	1.35 (1.21, 1.50)	1.15 (1.00, 1.32)	1.32	1.27	1.25	1.15
5q33	rs13361189	1.51 (1.30, 1.76)	1.38 (1.20, 1.59)	1.46	1.46	1.45	1.40
3p21	rs9858542	1.26 (1.15, 1.38)	1.17 (1.02, 1.34)	1.21	1.22	1.21	1.17
5q33	rs4958847	1.35 (1.20, 1.53)	1.36 (1.19, 1.56)	1.26	1.36	1.35	1.35
5q23	rs10077785	1.29 (1.16, 1.43)	1.19 (1.04, 1.36)	1.20	1.25	1.22	1.19
1q24	rs12035082	1.22 (1.12, 1.33)	1.14 (0.99, 1.31)	1.15	1.19	1.17	1.15
21q22	rs2836754	1.22 (1.12, 1.33)	1.15 (1.01, 1.32)	1.11	1.19	1.16	1.16
1q31	rs10801047	1.38 (1.18, 1.61)	1.47 (1.29, 1.68)	1.09	1.42	1.39	1.44

Columns 1–4: SNPs are ranked in order of stage 1 statistical significance. Columns 5–8: The one-stage correction of Ghosh et al. [2008] (GZW), the two-stage MLE, corrected MLE of Zhong and Prenctice [2008], and our UMVCUE for the ith ranked stage 1 SNP's true odds ratio. MLE, maximum likelihood estimator; SNP, single-nucleotide polymorphism.