TABLE 2.
Summary of GWA discovery meta-analysis of associations at P < 1 × 10−6 and second-stage analysis1
| Discovery GWA (n = 2138) |
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| Model 12 |
Model 23 |
Model 34 |
Second-stage analysis (n = 265)5 |
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| SNP | Chr | Nearest gene | Allele (effect/ noneffect) | Allele frequency (effect) | β ± SE | P value | β ± SE | P value | β ± SE | P value | OR (95% CI) | P value |
| rs964184 | 11 | ZNF259 | G/C | 0.15 (0.002) | 0.23 ± 0.04 | 5.91 × 10−8 | 0.14 ± 0.04 | 0.001 | 0.13 ± 0.04 | 0.002 | 1.06 (0.63, 1.75) | 0.83 |
| rs4645543 | 8 | KCNK9 | T/C | 0.04 (0.003) | −0.42 ± 0.08 | 2.00 × 10−7 | −0.35 ± 0.08 | 5.69 × 10−6 | −0.35 ± 0.08 | 1.60 × 10−5 | 0.98 (0.42, 2.30) | 0.97 |
| rs2199565 | 8 | KCNK9 | T/G | 0.04 (0.003) | −0.42 ± 0.08 | 2.04 × 10−7 | −0.35 ± 0.08 | 5.65 × 10−6 | −0.35 ± 0.08 | 1.59 × 10−5 | 0.99 (0.43, 2.30) | 0.99 |
| rs7018214 | 8 | KCNK9 | C/T | 0.04 (0.002) | −0.39 ± 0.08 | 6.44 × 10−7 | −0.33 ± 0.07 | 1.14 × 10−5 | −0.33 ± 0.08 | 2.54 × 10−5 | 1.05 (0.43, 2.53) | 0.92 |
| rs2108622 | 19 | CYP4F2 | T/C | 0.3 (0.001) | 0.16 ± 0.03 | 8.78 × 10−7 | 0.16 ± 0.03 | 2.90 × 10−7 | 0.16 ± 0.03 | 9.68 × 10−7 | 1.17 (0.75, 1.84) | 0.49 |
| rs12609820 | 19 | CYP4F2 | C/T | 0.31 (0.004) | 0.16 ± 0.03 | 1.00 × 10−6 | 0.16 ± 0.03 | 3.06 × 10−7 | 0.16 ± 0.03 | 2.10 × 10−6 | 1.20 (0.76, 1.90) | 0.44 |
| rs2192574 | 2 | CTNAA2 | C/T | 0.11 (0.001) | 0.28 ± 0.06 | 1.82 × 10−6 | 0.28 ± 0.06 | 1.49 × 10−6 | 0.29 ± 0.06 | 8.23 × 10−7 | 0.85 (0.46, 1.55) | 0.59 |
| rs4852146 | 2 | CTNAA2 | C/T | 0.33 (0.007) | 0.18 ± 0.04 | 2.08 × 10−6 | 0.19 ± 0.04 | 1.42 × 10−7 | 0.18 ± 0.04 | 3.23 × 10−6 | 0.97 (0.62, 1.51) | 0.89 |
| rs6862909 | 5 | CDO1 | T/G | 0.01 (0.0002) | −0.81 ± 0.19 | 1.41 × 10−5 | −0.96 ± 0.18 | 1.24 × 10−7 | −0.94 ± 0.19 | 7.69 × 10−7 | 41.3 (1.29, 1322) | 0.03 |
| rs6862071 | 5 | CDO1 | T/A | 0.01 (0.0001) | −0.94 ± 0.22 | 2.29 × 10−5 | −1.14 ± 0.22 | 1.35 × 10−7 | −1.09 ± 0.23 | 1.73 × 10−6 | 63.1 (1.48, 2687) | 0.03 |
| rs4122275 | 5 | CDO1 | A/G | 0.02 (0.001) | −0.68 ± 0.17 | 4.76 × 10−5 | −0.81 ± 0.16 | 4.31 × 10−7 | −0.78 ± 0.17 | 3.90 × 10−6 | 7.50 (0.98, 57.4) | 0.05 |
Additive allele mode. Chr, chromosome; GWA, genome-wide association; SNP, single-nucleotide polymorphism.
Analyses adjusted for age, sex, and study-specific covariates (e.g., study site, population stratification by principal components, when applicable) (P < 10−6). Association coefficients are shown as βs ± SEs; β represents the change in circulating phylloquinone (ln-nmol/L) per each additional copy of the effect allele.
Analyses adjusted for age, sex, circulating triglycerides, and study-specific covariates (e.g., study site, population stratification by principal components, when applicable). Association coefficients are shown as βs ± SEs; β represents the change in circulating phylloquinone (ln-nmol/L) per each additional copy of the effect allele.
Analyses adjusted for age, sex, circulating triglycerides, vegetable intake, and study-specific covariates (e.g., study site, population stratification by principal components, when applicable). Association coefficients are shown as βs ± SEs; β represents the change in circulating phylloquinone (ln-nmol/L) per each additional copy of the effect allele.
Second-stage covariates determined by the model with the strongest P value from discovery GWA. Association coefficients are shown as ORs and 95% CIs for having high (>1.0 nmol/L) circulating phylloquinone concentrations, per each additional copy of the effect allele.