Table 1.
SNPs associated with cups of coffee consumed per day among coffee consumers
| Locus | Index SNPa | Closest Gene | EA/ NEA |
EAF EUR/AA |
Stage 1b EUR n ≤ 91,462 |
Stage 2 b | Trans-Ethnic Meta-Analysisc |
|||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EUR n ≤ 30,062 |
AA n ≤ 7,964 |
|||||||||||||
| β (SE) | P | β (SE) | P | β (SE) | P | β (SE) | Log10BF | Post Prob |
n | |||||
| 2p24 | rs1260326 | GCKR | T/C | .41/.17 | −0.04 (0.01) | 1.06 ×10−07 | −0.03 (0.01) | 0.02 | −0.01 (0.03) | 0.77 | −0.04 (0.01) | 6.48 | 0.07 | 129,417 |
| 4q22 | rs1481012 | ABCG2 | A/G | .89/.95 | 0.06 (0.01) | 1.13 ×10−06 | 0.03 (0.02) | 0.11 | 0.16 (0.05) | 1.27 ×10−03 | 0.06 (0.01) | 6.08 | 0.23 | 126,019 |
| 7p21 | rs4410790 rs6968554 |
AHR | T/C A/G |
.37/.52 .39/.33 |
−0.14 (0.01) −0.13 (0.01) |
1.48 ×10−57 2.54 ×10−57 |
−0.05 (0.01) −0.07 (0.01) |
1.66 ×10−04 2.78 ×10−10 |
−0.09 (0.02) −0.05 (0.02) |
2.37 ×10−06 0.02 |
−0.10 (0.01) −0.10 (0.01) |
58.87 69.69 |
0.96 1.00 |
116,674 124,849 |
| 7q11.23 | rs7800944 | MLXIPL | T/C | .72/.67 | −0.05 (0.01) | 7.82 ×10−09 | −0.06 (0.02) | 4.20 ×10−04 | −0.02 (0.02) | 0.37 | −0.05 (0.01) | 8.83 | 0.09 | 116,417 |
| 7q11.23 | rs17685 | POR | A/G | .29/. 19 | 0.07 (0.01) | 9.06 ×10−14 | 0.05 (0.01) | 1.01 ×10−03 | 0.07 (0.03) | 7.55 ×10−03 | 0.07 (0.01) | 15.12 | 0.08 | 115,465 |
| 11p13 | rs6265 | BDNF | T/C | .19/.07 | −0.05 (0.01) | 3.40 ×10−07 | −0.03 (0.01) | 0.07 | −0.05 (0.04) | 0.25 | −0.04 (0.01) | 5.76 | 0.10 | 127,828 |
| 15q24 | rs2470893 rs2472297 |
CYP1A1, CYP1A2 |
T/C T/C |
.31/.06 .24/.06 |
0.12 (0.01) 0.15 (0.01) |
6.89 ×10−44 6.45 ×10−47 |
0.09 (0.01) 0.11 (0.01) |
9.92 ×10−11 3.26 ×10−16 |
0.20 (0.07) 0.19 (0.05) |
4.23 ×10−03 8.62 ×10−05 |
0.12 (0.01) 0.14 (0.01) |
57.79 62.77 |
1.00 0.97 |
113,273 116,272 |
| 17q11.2 | rs9902453 | EFCAB5 | A/G | .54/.80 | −0.04 (0.01) | 2.26 ×10−06 | −0.03 (0.01) | 9.13 ×10−03 | −0.04 (0.03) | 0.17 | −0.03 (0.01) | 6.29 | 0.05 | 126,819 |
Abbreviations: EA, effect allele; NEA, non-effect allele; EAF, effect allele frequency; EUR, European ancestry; AA, African American ancestry; SE, standard error; BF, Bayes-factor, Post Prob, posterior probability
Genic SNPs are in bold-face.
Effect coefficients (SE), representing cups/day per effect allele, and corresponding P-values from stage 1 fixed-effects meta-analysis (columns 6, 7) and stage 2 fixed-effects meta-analyses (columns 8-11).
Effect coefficients (SE), representing cups/day per effect allele, from random-effects meta-analysis of all stage 1 and stage 2 studies (column 12). Log10BF (column 13) and corresponding posterior probabilities (column 14) from trans-ethnic meta-analysis of all stage 1 and stage 2 studies. A posterior probability > 0.5 suggests heterogeneity in allelic effects.