Table 1.

P value of pathway- and gene-level tests with risk of overall, ER+ and ER− breast cancer

Gene	Chromosome	Number of total SNPsa	Number of effective SNPsa	P value
				Overall	ER+	ER−
Pathway	—	37658	10688	0.006	0.16	0.046
Pathway excluding top gene	—	37498	10623	0.54	—	0.85
AKT1	14	348	146	0.90	0.70	0.16
AKT2	19	392	90	0.61	0.06	0.14
AKT3	1	1794	289	0.06	0.42	0.36
BRAF	7	1101	153	0.67	0.65	0.63
CAB39	2	877	173	0.24	0.35	0.51
CAB39L	13	1111	348	0.75	0.004	0.96
DDIT4	10	114	39	0.76	0.43	0.98
EEF2K	16	486	125	0.87	0.60	0.31
EIF4B	12	332	76	0.48	0.43	0.39
EIF4E	4	517	86	0.82	0.02	0.27
EIF4E1B	5	247	129	0.55	0.052	0.35
EIF4E2	2	421	109	0.63	0.12	0.72
EIF4EBP1	8	286	82	0.38	0.95	0.55
EIF4G1	3	190	72	0.39	0.49	0.29
FIGF	X	276	91	0.20	0.87	0.19
HIF1A	14	406	111	0.17	0.032	0.95
IGF1	12	477	125	0.10	0.38	0.41
INS	11	100	59	0.76	0.36	0.77
MAPK1	22	892	154	0.63	0.29	0.53
MAPK3	16	111	47	0.82	0.60	0.79
MLST8	16	143	71	0.48	0.83	0.49
MTOR	1	1163	192	0.032	0.08	0.62
PDPK1	16	235	72	0.37	0.55	0.48
PGF	14	204	98	0.71	0.63	0.55
PIK3CA	3	562	100	0.84	0.86	0.74
PIK3CB	3	660	105	0.09	0.32	0.27
PIK3CD	1	585	215	0.39	0.14	0.31
PIK3CG	7	347	99	0.88	0.58	0.27
PIK3R1	5	640	221	0.08	0.21	0.64
PIK3R2	19	218	68	0.13	0.33	0.61
PIK3R3	1	797	144	0.72	0.21	0.15
PIK3R5	17	830	339	0.13	0.10	0.69
PPM1A	14	460	94	0.24	0.73	0.73
PRKAA1	5	346	75	0.43	0.37	0.13
PRKAA2	1	589	137	0.97	0.43	0.18
PRKAB1	12	191	63	0.77	0.95	0.23
PRKAB2	1	268	64	0.06	0.78	0.68
PRKAG1	12	109	41	0.16	0.32	0.39
PRKAG2	7	2953	1239	0.53	0.48	0.98
PRKAG3	2	160	65	0.00003b	0.09	0.17
RHEB	7	530	158	0.35	0.75	0.87
RICTOR	5	990	169	0.35	0.11	0.31
RPS6	9	225	57	0.86	0.45	0.75
RPS6KA1	1	408	132	0.47	0.10	0.18
RPS6KA2	6	4147	1622	0.09	0.69	0.11
RPS6KA3	X	417	101	0.045	0.16	0.001
RPS6KA6	X	541	95	0.14	0.43	0.04
RPS6KB1	17	340	72	0.77	0.85	0.67
RPS6KB2	11	117	48	0.96	0.99	0.55
RPTOR	17	4113	1110	0.75	0.94	0.82
STK11	19	205	94	0.37	0.64	0.10
STRADA	17	386	78	0.86	0.69	0.78
STRADB	2	186	38	0.09	0.006	0.65
TSC1	9	492	107	0.14	0.28	0.57
TSC2	16	301	146	0.915	0.32	0.49
ULK1	12	283	104	0.28	0.34	0.51
ULK2	17	656	152	0.97	0.80	0.13
ULK3	15	118	49	0.70	0.92	0.67
VEGFA	6	229	102	0.69	0.96	0.12
VEGFB	11	121	42	0.74	0.96	0.14
VEGFC	4	915	206	0.71	0.86	0.76

^aFor each candidate gene, its start and end chromosomal positions plus 10 kb upstream and 10 kb downstream were determined using the UCSC Genome Browser. SNPs within each gene region were extracted from The Root Consortium GWAS data and defined as ‘total SNPs’. ‘Effective SNPs’ means the remaining SNPs after excluding the SNPs with MAF < 0.01 and the SNPs with a lower MAF in every pair of SNPs with correlation r² ≥ 0.8.

^bOnly P value for PRKAG3 remained significant after Bonferroni correction.