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

From: Genetic variants in the MRPS30 region and postmenopausal breast cancer risk

Ranka Rs numberb Chromosome Position MAFc Alleled Combined test P-valuee Combined test FDRf Main effect test P-valueg Main effect test rankh 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
  1. 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.