Table 1.

P-values of alternative effect, mediation effect, and total effect for genes with most significant total effect (FDR < 1%) using the asthma data. Ch, chromosome; Q_S, test with only SNP-set, the SNP-only model; Q_SG, test with both SNP set and gene expression (without interaction), the main effect model; Q_SGC, test with SNP set, gene expression, and their cross-product interactions, the full model; Q_omb, omnibus test for Q_S (if applicable), Q_SG, and Q_SGC

				Alternative effect			Mediation effect			Total effect
Probe	Gene	Ch	Number of eQTL	$Q_{omb}^{AE}$	$Q_{SG}^{AE}$	$Q_{SGC}^{AE}$	$Q_{omb}^{ME}$	$Q_{SG}^{ME}$	$Q_{SGC}^{ME}$	$Q_{omb}^{TE}$	$Q_S^{TE}$	$Q_{SG}^{TE}$	$Q_{SGC}^{TE}$
219003_s_at	MANEA	6	159	2.9 × 10−4	2.6 × 10−4	2.8 × 10−4	0.0079	0.0076	0.0082	4.8 × 10−7	2.1 × 10−6	2.9 × 10−7	2.8 × 10−7
225523_at	MRPL53	2	175	5.7 × 10−4	5.8 × 10−4	6.2 × 10−4	0.055	0.053	0.060	1.9 × 10−6	1.0 × 10−5	5.2 × 10−6	1.0 × 10−6
226996_at	LYCAT	2	193	0.19	0.18	0.18	4.7 × 10−4	4.6 × 10−4	5.0 × 10−4	5.2 × 10−6	0.0065	4.0 × 10−6	6.0 × 10−5
230261_at	ST8SIA4	5	185	0.012	0.012	0.013	1.9 × 10−4	2.0 × 10−4	2.0 × 10−4	6.3 × 10−6	0.0020	4.1 × 10−6	1.4 × 10−4
222422_s_at	NDFIP1	5	48	0.11	0.11	0.11	0.0011	0.0010	0.0012	6.4 × 10−6	0.0031	4.0 × 10−6	4.1 × 10−5
1554193_s_at	MANEA	6	67	0.0017	0.0018	0.0020	0.012	0.011	0.012	9.0 × 10−6	6.0 × 10−5	4.8 × 10−6	1.4 × 10−5
229319_at	—	6	148	0.29	0.29	0.28	2.9 × 10−4	3.0 × 10−4	3.0 × 10−4	1.2 × 10−5	0.018	7.5 × 10−6	6.70 × 10−5
209815_at	PTCH1	9	13	0.92	0.91	0.93	1.0 × 10−5	1.8 × 10−5	1.3 × 10−5	1.6 × 10−5	0.32	8.5 × 10−6	2.2 × 10−4