TABLE 2.
Significant gene-based associations.
| Gene Id | Chrom | Gene contains at least one significant variant from the single-variant GWAS | The gene collapse association p-value is greater than the single-variant association p-value for all variants in the gene | HNPT_EU gene-collapse p-value | UKB gene-collapse p-value | HNPT_EU test statistic | HNPT_EU number of tested variants | HNPT_EU number of rare variants tested | HNPT_EU number of common variants tested | Previous association with triglycerides |
| ZPR1 | 11 | Y | N | 2.39 × 10–42 | 1.17 × 10–75 | 66.88 | 34 | 26 | 8 | * |
| APOA5 | 11 | Y | Y | 1.36 × 10–40 | 1.16 × 10–124 | 52.05 | 25 | 19 | 6 | * |
| BUD13 | 11 | Y | N | 1.13 × 10–37 | 2.82 × 10–53 | 48.04 | 65 | 34 | 31 | * |
| GCKR | 2 | Y | N | 9.75 × 10–23 | 1.26 × 10–38 | 35.39 | 73 | 57 | 16 | * |
| APOC3 | 11 | Y | Y | 2.65 × 10–18 | 2.69 × 10–85 | 28.54 | 18 | 13 | 5 | * |
| LPL | 8 | Y | Y | 5.93 × 10–14 | 1.51 × 10–69 | 22.09 | 106 | 72 | 34 | * |
| NRBP1 | 2 | Y | N | 7.15 × 10–10 | 2.33 × 10–15 | 19.50 | 31 | 29 | 2 | * |
| CSRNP2 | 12 | Y | N | 4.09 × 10–08 | 9.35 × 10–01 | 14.46 | 32 | 25 | 7 | |
| APOA4 | 11 | N | NA | 5.73 × 10–08 | 2.01 × 10–35 | 14.14 | 30 | 20 | 10 | * |
| IFT172 | 2 | N | NA | 6.46 × 10–08 | 7.48 × 10–14 | 17.96 | 118 | 92 | 26 | * |
| BAZ1B | 7 | N | NA | 9.38 × 10–08 | 8.45 × 10–15 | 15.34 | 97 | 67 | 30 | * |
| SIK3 | 11 | Y | N | 3.03 × 10–07 | 1.92 × 10–12 | 13.61 | 321 | 175 | 146 | * |
| MLXIPL | 7 | Y | N | 4.45 × 10–07 | 1.97 × 10–37 | 13.44 | 81 | 56 | 25 | * |
| FNDC4 | 2 | N | NA | 5.03 × 10–07 | 6.35 × 10–12 | 14.72 | 10 | 9 | 1 | * |
| PPM1G | 2 | N | NA | 7.58 × 10–07 | 9.36 × 10–01 | 11.99 | 37 | 29 | 8 | * |
| EIF2B4 | 2 | N | NA | 1.14 × 10–06 | 1.05 × 10–17 | 12.06 | 36 | 26 | 10 | * |
This table shows the statistically significantly associated genes with triglyceride levels in the HNPT_EU and UKB as identified by the SKAT gene-based association analysis. The second column indicates whether the gene contains a variant identified in the single-variant GWAS: this demonstrates whether a gene association would have been undetected based on the single-variant analysis alone. The third column indicates whether the gene-based association is stronger than any single variant association in the gene: “N” indicates that one single-variant association may be driving the gene-based association; “Y” indicates that a combination of variants is driving the association. Genes marked with an “∗” in the last column have a published association with triglycerides. References for those associations can be found in Supplementary Table 6.