Table 3.

The Number of Interactions Identified from the WTCCC Data Sets of Seven Diseases under Different Constraints

	BD	CAD	CD	HT	RA	T1D	T2D
C1	10	16	8	7	350	4499	18
C1 & C2	0	0	1	0	0	789	0
C1 & C2 & C3	0	0	1	0	0	91	0

Abbreviations are as follows: BD, bipolar disorder; CAD, coronary artery disease; CD, Crohn disease; HT, hypertension; RA, rheumatoid arthritis; T1D, type 1 diabetes; T2D, type 2 diabetes. C¹ is the significance threshold constraint: the significance threshold is 0.05 for the Bonferroni-corrected interaction p value. C² is the distance constraint: the physical distance between two interacting SNPs is at least 1Mb. This constraint is used to avoid interactions that might be attributed to the LD effects.⁴C³ is the main effect constraint: The single-locus p value should not be less than 10⁻⁶. This constraint is used to see whether there exist strong interactions without significant main effects, because those SNPs with p ≥ 10⁻⁶ are usually filtered out in the typical single-locus scan.