Table 2.
Breast-cancer risk associations and Bayesian false-discovery probability (BFDP, bold text indicates BFDP < 0.8) of individual SNPs with p values < 0.05 in adjusted dominant and recessive logistic regression models*, sorted by ORb
| SNP | Nearest gene | Chromosome, position (GRCh38.p13), and referent/variant alleles | ORa (95% CI) | p value ORa | ORb (95% CI) | p value ORb | BFDP for ORb Prior probability for effect (β ≠ 0) | ||
|---|---|---|---|---|---|---|---|---|---|
| 0.1 | 0.05 | 0.01 | |||||||
| dominant | |||||||||
| rs7300641# | TPH2 | chr12:71,974,791: C:A | 1.046 (1.005–1.089) | 0.0290 | 1.071 (1.025–1.119) | 0.0023 | 0.3113 | 0.4883 | 0.8326 |
| rs1386492# | TPH2 | chr12:71,968,485: A:G | 1.046 (1.005–1.089) | 0.0282 | 1.070 (1.024–1.118) | 0.0026 | 0.3393 | 0.5202 | 0.8496 |
| rs1473473$ | TPH2 | chr12:72,010,598: A:G | 1.050 (1.009–1.094) | 0.0168 | 1.066 (1.020–1.114) | 0.0042 | 0.4562 | 0.6391 | 0.9022 |
| rs4760751§ | TPH2 | chr12:71,984,138: G:A | 1.040 (0.997–1.084) | 0.0698 | 1.066 (1.018–1.116) | 0.0064 | 0.5240 | 0.6992 | 0.9237 |
| rs1487276$ | TPH2 | chr12:72,011,279: G:A | 1.050 (1.008–1.093) | 0.0184 | 1.065 (1.019–1.113) | 0.0049 | 0.4855 | 0.6658 | 0.9121 |
| rs1386489§ | TPH2 | chr12:71,955,510: A:G | 1.040 (0.998–1.085) | 0.0635 | 1.065 (1.017–1.115) | 0.0072 | 0.5509 | 0.7214 | 0.9310 |
| rs1487281§ | TPH2 | chr12:71,986,242: A:C | 1.036 (0.994–1.081) | 0.0950 | 1.062 (1.014–1.112) | 0.0101 | 0.6267 | 0.7799 | 0.9486 |
| rs7299582§ | TPH2 | chr12:71,962,534: A:G | 1.037 (0.994–1.081) | 0.0915 | 1.062 (1.014–1.112) | 0.0101 | 0.6267 | 0.7799 | 0.9486 |
| rs17110627 | TPH2 | chr12:71,996,615: G:A | 0.967 (0.931–1.005) | 0.0844 | 0.958 (0.919–0.998) | 0.0412 | 0.8461 | 0.9207 | 0.9837 |
| recessive | |||||||||
| rs10857561 | MAPK8 | chr10:48,400,595: G:A | 1.118 (1.056–1.184) | 0.0001 | 1.106 (1.039–1.177) | 0.0016 | 0.2344 | 0.3926 | 0.7710 |
| rs7075976 | MAPK8 | chr10:48,406,234: A:G | 1.064 (1.015–1.116) | 0.0097 | 1.064 (1.010–1.120) | 0.0193 | 0.7110 | 0.8385 | 0.9644 |
| rs2129575 | TPH2 | chr12:71,946,293: C:A | 0.932 (0.859–1.012) | 0.0932 | 0.907 (0.830–0.991) | 0.0314 | 0.7572 | 0.8682 | 0.9717 |
| rs17110627 | TPH2 | chr12:71,996,615: G:A | 0.940 (0.868–1.018) | 0.1268 | 0.905 (0.829–0.987) | 0.0235 | 0.7246 | 0.8475 | 0.9666 |
| rs13515 | MAPK1 | chr22:21,761,597: G:A | 0.930 (0.840–1.031) | 0.1678 | 0.886 (0.792–0.991) | 0.0341 | 0.7713 | 0.8769 | 0.9738 |
BFDP Bayesian false-discovery probability, OR Odds ratio, CI Confidence interval
Chromosome and position (GRCh38.p13): For example, chr9:91,426,574: A:G indicates chromosome 9, base pair location 91,426,574, referent allele A, variant allele G;
aAdjusted for study, reference age and eight principal components
bAdjusted for study, reference age, parity, breast feeding, smoking status, current intake of estrogen-progesterone MHT, and eight principal components
*Supplementary table S3 provides an overview of all models for the main analysis
#, $, §, %, and † mark SNPs that are pairwise linked (r2 > 0.95) in controls: # rs7300641 and rs1386492; $ rs1473473 and rs1487276; § rs4760751, rs1386489, rs1487281, and rs7299582