Table 3 Odds ratios, 95% confidence intervals, and FDR correction P-value as the interaction effect of each pair of polymorphism on breast cancer risk.

Locus 1	Locus 2	Control^a (N = 941)		Case^a (N = 959)		Adj OR^b	Permutation P interaction	FDR P interaction^c
Locus 1	Locus 2	N	%	N	%	(95% CI)	Permutation P interaction	FDR P interaction^c
NPAS2	RORA
rs3820787	rs1482057						0.001	0.114
AA	One increment of A	296	31.46	290	30.24	0.82 (0.57–1.18)
AG	One increment of A	458	48.67	466	48.59	0.93 (0.71–1.22)
GG	One increment of A	178	18.92	193	20.13	2.52 (1.51–4.19)
CUL1	RORA
rs758880	rs1482057						0.002	0.129
GG	One increment of A	253	26.89	261	27.22	0.69 (0.48–1.01)
GA	One increment of A	478	50.80	491	51.20	1.19 (0.91–1.56)
AA	One increment of A	202	21.47	199	20.75	1.75 (1.08–2.81)
CLOCK	CUL1
rs11133373	rs758880						0.001	0.114
GG	One increment of A	421	44.74	360	37.54	0.80 (0.64–1.00)
CG	One increment of A	416	44.21	474	49.43	0.99 (0.80–1.21)
CC	One increment of A	97	10.31	116	12.10	1.84 (1.13–3.00)

OR: Odds ratios, 95% CI: 95% confidence intervals, FDR: false discovery rate.
^aNumber of subjects in each group with successful genotyping data
^bOdd ratio after adjustment by age at time of diagnosis or interview, educational level, number of pregnancies, age at birth of first child, body mass index, age at menarche, alcohol consumption, smoking, use of female hormone treatment, and family history of breast cancer in first degree relatives.
^cP interaction after adjustment by false discovery rate method. P < 0.2 was considered noteworthy.

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