Table 3.
Fine-mapping results
| Locus | Variant | Function | Gene | CADD | Finnish enrichm. | MAF | Traits (P-value) |
|---|---|---|---|---|---|---|---|
| PCSK9 | rs11591147-T | missense | PCSK9 | 10.4 | 3.10 | 0.033 |
CE 18:2;0 (2e-14), 3 SMs: SM 34:1;2 (2e-19), c3 (1e-14), c8 (2e-13) |
| GCKR | rs1260326-T | missense | GCKR | 13.2 | 1.07 | 0.349 |
2 DAGs: DAG 18:1;0_18:2;0 (1e-12), 16 TAGs: TAG 50:4;0 (4e-22), c2 (4e-13), c3 (1e-17) |
| SMIM13 | rs1292311927-T* | splice_region | ELOVL2 | 22.9 | FIN-specific | 0.004 | c6 (2e-7) |
| LPL | rs268-G | missense | LPL | 21.3 | 1.01 | 0.023 | 3 TAGs: TAG 54:4;0 (1e-9) |
| LIPC | rs201563586-A* | missense | LIPC | 24.9 | FIN-specific | 0.002 | c2 (8e-8) |
| rs113298164-T | missense | LIPC | 24.1 | 4.41 | 0.017 |
5 PCs: PC 18:0;0_18:2;0 (1e-12), PC O-16:2;0/18:0;0 (3e-12), 5 PEs: PE 16:0;0_20:4;0 (4e-47), c2 (3e-62), c3 (2e-7), c4 (2e-10), c5 (4e-15), c7 (2e-7), c10 (1e-10) |
|
| LCAT | rs4986970-T | missense | LCAT | 23.2 | 0.83 | 0.028 | c7 (1e-16) |
| ABHD3 | rs1253048206-G* | intergenic | 11.8 | 0.017 | c2 (3e-6) | ||
| rs186249276-T* | missense | ABHD3 | 23.7 | 29.64 | 0.004 | c2 (4e-19), c3 (5e-12) | |
| APOE | rs7412-T | missense | APOE | 26.0 | 0.56 | 0.053 | 5 CEs: CE 18:2;0 (2e-14), c3 (3e-23), c6 (2e-18), c7 (2e-53), c8 (2e-65), c11 (4e-14) |
| rs429358-C | missense | APOE | 16.7 | 1.29 | 0.189 | 2 CEs: CE 20:2;0 (9e-12), c7 (1e-29), c9 (8e-12) | |
| SPHK2 | rs61751862-C* | missense | SPHK2 | 22.1 | 2.45 | 0.031 | c8 (6e-16) |
| LINC01722 | rs61738161-A* | missense | SPTLC3 | 18.0 | 2.24 | 0.086 | 3 Cers: Cer 42:2;2 (3e-17), c8 (7e-19) |
| HNF4A | rs1800961-T | missense | HNF4A | 21.4 | 1.41 | 0.052 | 2 CEs: CE 18:3;0 (1e-10), c2 (1e-10) |
| AGPAT3 | rs62229686-T* | missense | AGPAT3 | 16.3 | 1.44 | 0.039 | c3 (7e-17) |
Locus gene name in italic, variant rsid-minor allele, *variants reaching only low PIP (<0.1) in UKB, function variant function from VEP, gene gene name from VEP in italic, MAF minor-allele frequency, Finnish enrichm. Finnish enrichment calculated as ratio of MAF between our Finnish data and non-Finnish-non-Swedish-non-Estonian European samples in gnomAD v2.1. Bolded if >2. Variants not detected outside Finland in gnomAD are marked as FIN-specific.
Variants with a CADD score >10 and a high PIP (>0.9) in GeneRISK are listed. Traits for which the variant reaches a high PIP are listed and, in the case of multiple species of a lipid class, the number of species and the species for which the variant reaches the lowest P-value are given. Two-sided P-values calculated using a linear-mixed-model (uv) and canonical correlation analysis (mv) are reported.