Table 2.
Genes discovered and replicated by the joint test or interaction only test
| Trait | Gene | CHR | Alcohol* | Test | N.discovery† | cMAF Range‡ | p.discovery | N.replication† | p.replication | |
|---|---|---|---|---|---|---|---|---|---|---|
| LPL | 8 | Both | Joint | 5 | 0.036 | − 0.040 | 8.76E-22 | 5 | 4.25E-21 | |
| APOC3 | 11 | Both | Joint | 3 | 0.001 | − 0.001 | 2.82E-06 | 2 | 4.62E-06 | |
| HDL-C | CD300LG | 17 | Both | Joint | 5 | 0.031 | − 0.055 | 2.64E-12 | 6 | 5.94E-10 |
| LIPG | 18 | Both | Joint | 5 | 0.014 | − 0.019 | 7.65E-17 | 5 | 4.09E-11 | |
| ANGPTL4 | 19 | Both | Joint | 5 | 0.024 | − 0.031 | 2.34E-20 | 5 | 5.53E-09 | |
| HNF4A | 20 | Both | Joint | 5 | 0.031 | − 0.034 | 3.37E-10 | 5 | 3.20E-07 | |
| CELSR2 | 1 | Both | Joint | 5 | 0.079 | − 0.093 | 1.63E-10 | 6 | 3.21E-08 | |
| MYBPHL | 1 | Both | Joint | 5 | 0.044 | − 0.051 | 7.26E-09 | 6 | 6.49E-06 | |
| PCSK9 | 1 | Both | Joint | 5 | 0.050 | − 0.055 | 3.16E-62 | 6 | 9.06E-11 | |
| LDL-C | APOB | 2 | Both | Joint | 5 | 0.174 | − 0.226 | 5.33E-18 | 6 | 1.20E-15 |
| LPA | 6 | RegDrink | Joint | 5 | 0.096 | − 0.147 | 2.28E-05 | 6 | 3.7E-04 | |
| APOH | 17 | Both | Joint | 5 | 0.074 | − 0.081 | 1.11E-05 | 6 | 1.18E-05 | |
| BCAM | 19 | Both | Joint | 5 | 0.120 | − 0.166 | 1.49E-18 | 6 | 1.77E-37 | |
| CBLC | 19 | Both | Joint | 5 | 0.084 | − 0.104 | 7.48E-22 | 6 | 1.64E-35 | |
| LPL | 8 | Both | Joint | 5 | 0.036 | − 0.040 | 8.55E-19 | 5 | 7.30E-16 | |
| APOA4 | 11 | Both | Joint | 5 | 0.019 | − 0.024 | 8.83E-09 | 6 | 3.77E-09 | |
| APOA5 | 11 | Both | Joint | 5 | 0.025 | − 0.033 | 8.93E-07 | 5 | 2.3E-04 | |
| TG | APOC3 | 11 | Both | Joint | 3 | 0.001 | − 0.001 | 2.09E-10 | 3 | 7.92E-08 |
| MAP1A | 15 | Both | Joint | 5 | 0.129 | − 0.166 | 1.70E-06 | 6 | 4.30E-05 | |
| CD300LG | 17 | Both | Joint | 5 | 0.031 | − 0.055 | 1.39E-09 | 6 | 5.26E-08 | |
| ANGPTL4 | 19 | Both | Joint | 5 | 0.024 | − 0.031 | 1.33E-24 | 5 | 3.56E-15 | |
| SMC5 | 9 | CurDrink | Interaction | 4 | 0.001 | − 0.002 | 6.65E-06 | 4 | 0.013§ | |
Both indicates the gene-lipid pair was identified through using both current and regular drinker as the alcohol consumption variable.
N.discoery and N.replication represent the number of studies included in the respective meta-analyses.
cMAF Range represents the cumulative minor allele frequency for variants aggregated in the genes across studies involved in discovery phase for that gene.
SMC5-current drinking interaction on TG levels just missed the Bonferroni corrected threshold of significance (p = 0.0125) for replication but reached nominal significance.
Significant threshold for replication was set as p < 0.0017 for joint test and p < 0.0125 for interaction test using Bonferroni correction.