Table 1: Genes that are genome-wide significant after CMA and FHS-replicated.
20/29 genes have not been previously associated with the trait in the GWAS Catalog. TOMM40 for TC, ATG2A for BMI, and APOC3 for TG are more significant after CMA than after PASCAL, TWAS, and RVA alone. TOMM40 for LDL, CETP for HDL, and APOC3, LPL, and SLC45A3 for TG have suggestive or genome-wide significant p-values from more than one analysis. The remaining genes are CMA-significant due to a highly significant p-value in one analysis.
| Genes | Trait | CMA p-value | GWAS catalog? | PASCAL p-value | TWAS p-value | RVA p-value | RVA category |
|---|---|---|---|---|---|---|---|
|
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| TOMM40 | LDL | 4.9E-17 | Yes | 1.9E-12 | 7.9E-01 | 1.8E-17 | synonymous |
|
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| TOMM40 | TC | 2.7E-11 | Yes | 1.2E-06 | 2.8E-01 | 2.3E-10 | synonymous |
|
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| ATG2A | BMI | 6.1E-08 | No | 1.8E-01 | 1.8E-07 | 7.5E-04 | downstream |
|
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| AKAP12 | 1.3E-11 | No | 1.0E-01 | 3.1E-16 | NA | NA | |
| CETP | 1.6E-18 | Yes | 9.5E-22 | 8.8E-01 | 1.3E-11 | missense | |
| CPA3 | 3.4E-10 | No | 2.6E-01 | 6.2E-16 | NA | NA | |
| FCER1A | 2.2E-08 | No | 6.6E-01 | 2.8E-16 | NA | NA | |
| GATA2 | HDL | 2.3E-11 | No | 5.5E-01 | 3.9E-21 | NA | NA |
| HERPUD1 | 1.0E-11 | Yes | 8.7E-17 | 1.2E-01 | NA | NA | |
| LINC02458 | 1.0E-08 | Yes | 4.3E-01 | 7.2E-15 | NA | NA | |
| MS4A2 | 5.5E-11 | No | 1.5E-01 | 6.7E-16 | NA | NA | |
| SLC45A3 | 1.8E-12 | Yes | 7.9E-02 | 1.4E-15 | 1.4E-03 | enhancer_DHS | |
|
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| AKAP12 | 2.9E-27 | No | 4.7E-01 | 4.7E-53 | NA | NA | |
| APOA5 | 7.3E-08 | Yes | 2.2E-09 | NA | 4.5E-02 | promoter_CAGE | |
| APOC3 | 2.1E-11 | Yes | 8.0E-09 | NA | 1.0E-04 | plof_ds | |
| CA8 | 8.4E-11 | No | 3.8E-01 | 1.0E-20 | 4.8E-02 | enhancer_CAGE | |
| CPA3 | 3.6E-28 | No | 2.5E-01 | 8.2E-51 | NA | NA | |
| ENPP3 | 4.5E-13 | No | 1.5E-01 | 1.8E-26 | 1.7E-01 | promoter_DHS | |
| FCER1A | 1.7E-18 | No | 8.6E-01 | 1.1E-41 | NA | NA | |
| GATA2 | 6.2E-35 | No | 3.4E-01 | 4.9E-66 | NA | NA | |
| GCSAML | TG | 9.8E-15 | No | 4.8E-01 | 7.9E-28 | NA | NA |
| HDC | 2.4E-28 | No | 3.7E-01 | 4.2E-67 | 4.4E-02 | synonymous | |
| HRH4 | 6.6E-10 | No | 3.7E-01 | 1.6E-16 | 2.0E-02 | missense | |
| LINC02458 | 3.6E-18 | No | 6.3E-01 | 6.5E-37 | NA | NA | |
| LPL | 5.0E-08 | Yes | 4.0E-08 | 2.7E-01 | 5.4E-04 | missense | |
| MS4A2 | 3.1E-34 | No | 7.0E-03 | 2.2E-50 | NA | NA | |
| MS4A3 | 4.9E-18 | No | 6.8E-03 | 7.1E-23 | NA | NA | |
| NTRK1 | 2.3E-07 | No | 2.0E-01 | 1.0E-10 | NA | NA | |
| SLC45A3 | 3.1E-30 | No | 1.9E-01 | 7.5E-56 | 6.5E-05 | enhancer_DHS | |