Table 3.
List of the four identified risk variants associated with FPG either at genome-wide significant p-values (<1.8E-08) or at nominal p-values of 1.0 < E-06.
| SNP: Effect Allele: Trait | Gene: functional consequences | Phase | Effect SizeR | P-valueR | Effect SizeDM | P-valueDM |
|---|---|---|---|---|---|---|
| rs1002487: C#, FPG | RPS6KA1: intronic | Discovery | 8.315 | 1.64E-08 | 8.297 | 1.58E-08 |
| Replication | 3.442 | 3.7E-04 | 3.509 | 2.15E-04 | ||
| Meta | 6.551 | 5.72E-11 | 6.652 | 2.89E-11 | ||
| rs487321: A#, FPG | CADPS: intronic | Discovery | 6.133 | 1.53E-07 | 6.161 | 1.23E-07 |
| Replication | 3.955 | 2.25E-06 | 3.88 | 3.033E-06 | ||
| Meta | 7.047 | 1.83E-12 | 7.031 | 2.054E-12 | ||
| rs707927: G@,$, FPG | VARS, VWA7: intron in VARS, 2 Kb upstream of VWA7 | Discovery | 0.9453 | 8.24E-06 | 0.9262 | 1.19E-05 |
| Replication | 0.6375 | 8.25E-05 | 0.6503 | 3.18E-05 | ||
| Meta | 5.928 | 3.074E-09 | 6.033 | 1.61E-09 | ||
| rs12600570: T@, FPG | DHX58: intronic | Discovery | 0.8166 | 7.49E-06 | 0.8374 | 4.11E-06 |
| Replication | 0.3892 | 4.67E-03 | 0.3682 | 5.65E-03 | ||
| Meta | 5.142 | 2.715E-07 | 5.186 | 2.15E-07 | ||
| The following associations with HbA1c are shown in this table for the sake of completion; HbA1c associations are not considered significant except in the case of RPS6KA1. | ||||||
| rs1002487: C#, HbA1C | RPS6KA1: intronic | Discovery | 7.367 | 4.91E-08 | 7.186 | 9.649E-08 |
| Replication | 1.811 | 2.71E-03 | 1.875 | 0.00115 | ||
| Meta | 5.784 | 7.27E-09 | 5.896 | 3.71E-09 | ||
| rs487321: A#, HbA1C | CADPS: intronic | Discovery | 2.387 | 2.47E-03 | 2.38 | 2.44E-03 |
| Replication | 1.893 | 2.77E-04 | 1.826 | 3.82E-04 | ||
| Meta | 4.723 | 2.32E-06 | 4.569 | 3.18E-06 | ||
| rs707927: G@, HbA1C | VARS, VWA7: intron in VARS, 2 Kb upstream of VWA7 | Discovery | 0.5632 | 5.43E-04 | 0.5502 | 6.96E-04 |
| Replication | 0.3689 | 1.63E-04 | 0.3799 | 8.33E-05 | ||
| Meta | 5.088 | 3.61E-07 | 5.181 | 2.21E-07 | ||
| rs12600570: T@, HbA1C | DHX58: intronic | Discovery | 0.31 | 2.82E-02 | 0.3344 | 1.76E-02 |
| Replication | 0.194 | 1.98E-02 | 0.1805 | 2.81E-02 | ||
| Meta | 3.179 | 1.47E-03 | 3.178 | 1.48E-03 | ||
EffectSize, Effect size represents beta value for discovery and replication phases, and Z-score for meta-analysis. R-regular correction: Corrected for age, sex and the top 10 principal components that resulted from the Principal Components Analysis of the genotype data; DM: Corrected for diabetes medication in addition to the regular correction.
#association with the trait was observed under the genetic model based on recessive mode of inheritance; @association with the trait was observed under the genetic model based on additive mode of inheritance.
$Upon performing inverse normal transformation on the FPG values, the p-values for association of the marker rs707927 with FPG improved in the discovery phase; the values were (p-value = 1.26E-07; effect size = 0.3314) which upon further correction for diabetes medication were (p-value = 2.72E-07; effect size = 0.3226).