Table 4. Significant associations.

Disease	SNP ID	Chr	Region (Mb)	Gene	BF2	P2	BF1	P1
CAD	rs7104543	11	120.16–120.24	GRIK4	7.29	10.74	0.71	2.36
RA	rs1010342	4	1.04–1.08	SPON2	6.11	11.98	0.60	2.33
RA	rs11218032	11	120.16–120.24	GRIK4	11.60	14.50	−0.90	0.52
T2D	rs2383208	9	22.12–22.13	CDKN2A, CDKN2B	7.62	8.57	1.96	3.69
CD	rs9268858	6	32.54–32.56	HLA-DRA	5.20	8.27	1.66	3.35
RA	rs1605705	3	7.24–7.28	GRM7	5.76	8.43	1.04	2.82
T1D	rs6578246	11	2.18–2.26	INS-IGF2	4.96	8.52	2.34	4.09
T1D	rs3218256	22	35.87–35.87	IL2RB	4.60	6.47	2.44	4.26

P₂ = −log₁₀ P-value, which is the minimum P-value over 10 independent EM runs, and in each EM run a P-value was computed using logistic regression Equation 8. BF₂ = log₁₀ Bayes factor, which is averaged over 10 independent EM runs, and in each EM run a Bayes factor was computed using our haplotype method. P₁ and BF₁ are P-values and Bayes factors for the single-SNP test, respectively. The coordinates are from NCBI Build 35.