Genetic variants in the MRPS30 region and postmenopausal breast cancer risk

Table 1 Top 20 SNPs identified by combined test for main effect and interaction with clinical trial interventions

Rank^a	Rs number^b	Chromosome	Position	MAF^c	Allele^d	Combined test P-value^e	Combined test FDR^f	Main effect test P-value^g	Main effect test rank^h	Gene
1	rs1219648	10q26	123336180	0.42	G/A	6.45E-09	3.21E-05	3.90E-10	1	FGFR2
2	rs2981579	10q26	123327325	0.44	A/G	7.76E-09	1.94E-05	2.78E-09	2	FGFR2
3	rs3750817	10q26	123322567	0.37	T/C	5.61E-08	9.32E-05	9.02E-08	5	FGFR2
4	rs11200014	10q26	123324920	0.41	A/G	1.08E-07	0.000135	3.40E-09	3	FGFR2
5	rs2420946	10q26	123341314	0.42	T/C	1.56E-07	0.000156	1.49E-08	4	FGFR2
6	rs2981582	10q26	123342307	0.41	A/G	5.25E-07	0.000437	9.99E-08	6	FGFR2
7	rs7705343	5p12	44915334	0.42	G/A	5.88E-05	0.0419	0.000355	11	MRPS30
8	rs13159598	5p12	44841683	0.42	G/A	0.000136	0.0846	0.000425	13	MRPS30
9	rs11746980	5p12	44935642	0.43	C/T	0.000240	0.133	0.000511	16	MRPS30
10	rs9790879	5p12	44813635	0.43	A/G	0.000244	0.122	0.000963	19	MRPS30
11	rs2330572	5p12	44776746	0.43	C/A	0.000294	0.133	0.00129	22	MRPS30
12	rs7555040	1p33	47641903	0.13	G/A	0.000336	0.140	0.002483	26	Unknown
13	rs4415084	5p12	44698272	0.43	T/C	0.000400	0.153	0.000436	14	MRPS30
14	rs994793	5p12	44779004	0.43	G/A	0.000417	0.148	0.00184	23	MRPS30
15	rs2218080	5p12	44750087	0.44	C/T	0.000446	0.148	0.00274	30	MRPS30
16	rs7795554	7p21	12159269	0.36	C/T	0.000498	0.155	0.00353	40	Unknown
17	rs7519783	1q32	198951680	0.27	G/A	0.000904	0.265	0.229	1160	Unknown
18	rs1499111	4q28	129691789	0.22	T/C	0.00115	0.318	0.0736	431	Unknown
19	rs719278	3q11	98887302	0.40	A/G	0.00122	0.320	0.238	1204	EPHA6
20	rs1232355	3q26	88073313	0.05	C/T	0.00132	0.329	0.179	942	Unknown

^aRank, rank of SNPs based on combined test P-value; ^bRs number, SNP identification (rs) number in dbSNP database; ^cMAF, minor allele frequency in the study population; ^dAllele, minor/major allele; ^eCombined test P-value, P-value based on the simultaneous test with 5 df; ^fCombined test FDR, FDR based on the simultaneous test with 5 df; ^gMain effect P-value, P-value based on main effect test only; ^hMain effect rank, rank of SNPs based on main effect P-value.