Table 5. Genes with a SNP with p<0.001 in cholesterol and lipid-related processes that are significantly enriched in both GWAS.
| Gene Symbol | Chr location (Mb) | No. of SNPs (Harold) | Best p-value (Harold) | No. of SNPs (Lambert) | Best p-value (Lambert) | Best SNP (Harold) | Best SNP (Lambert) | r2 (Harold) |
| APOE | 19 (50) | 5 | <1.00E-10 | 5 | <1.00E-10 | rs8106922 | rs8106922 | 1 |
| APOC1 | 19 (50) | 3 | <1.00E-10 | 3 | <1.00E-10 | rs8106922 | rs8106922 | 1 |
| CLU | 8 (28) | 15 | 1.40E-09 | 14 | 5.19E-08 | rs11136000 | rs11136000 | 1 |
| APOC2 | 19 (50) | 4 | 3.43E-08 | 4 | 2.78E-03 | rs5167 | rs3760627 | 0.373 |
| APOC4 | 19 (50) | 4 | 3.43E-08 | 4 | 2.78E-03 | rs5167 | rs3760627 | 0.373 |
| ABCA7 | 19 (1) | 19 | 1.56E-05 | 17 | 4.24E-03 | rs3764650 | rs3764650 | 1 |
| ABCA1 | 9 (107) | 164 | 5.31E-05 | 169 | 1.30E-02 | rs12686004 | rs12336969 | 0.006 |
| ABCA12 | 2 (216) | 60 | 7.88E-05 | 62 | 1.43E-01 | rs2225064 | rs10206315 | 0.0002 |
| LIPC | 15 (57) | 69 | 1.39E-04 | 64 | 6.34E-03 | rs17269348 | rs1077834 | 0.001 |
| ATP8A1 | 4 (42) | 64 | 1.82E-04 | 61 | 1.25E-01 | rs3811769 | rs9291220 | 0.105 |
| ATP8B4 | 15 (48) | 91 | 1.89E-04 | 86 | 1.69E-03 | rs8041340 | rs2009833 | 0.105 |
| MALL | 2 (110) | 6 | 2.46E-04 | 3 | 4.37E-01 | rs12998618 | rs11240790 | 0.725 |
| ATP8A2 | 13 (25) | 154 | 1.06E-03 | 153 | 2.46E-04 | rs3117849 | rs10492697 | 0.001 |
| OSBPL7 | 17 (43) | 19 | 2.85E-04 | 19 | 3.07E-02 | rs11079797 | rs11652164 | 0.047 |
| SCARB1 | 12 (124) | 24 | 3.00E-04 | 25 | 6.94E-02 | rs4765622 | rs6488950 | 0.042 |
| VPS4B | 18 (59) | 16 | 3.30E-04 | 15 | 1.89E-03 | rs8094406 | rs8091623 | 0.144 |
| ABCG1 | 21 (42) | 99 | 1.51E-03 | 95 | 4.64E-04 | rs4148084 | rs1044317 | 0.015 |
| LIPG | 18 (43) | 19 | 5.20E-04 | 19 | 8.97E-03 | rs12604221 | rs2000813 | 0.046 |
| OSBPL9 | 1 (59) | 13 | 5.66E-04 | 12 | 3.81E-01 | rs856614 | rs1770791 | 0.005 |
| PCTP | 17 (51) | 18 | 1.60E-02 | 19 | 6.01E-04 | rs2960060 | rs8079126 | 0.000 |
| SLC27A4 | 9 (130) | 7 | 8.19E-02 | 7 | 6.20E-04 | rs3003600 | rs7019382 | 0.028 |
| NPC1 | 18 (19) | 15 | 4.60E-02 | 15 | 6.25E-04 | rs1808579 | rs12970899 | 0.172 |
| APOA1 | 11 (116) | 6 | 7.62E-04 | 5 | 2.22E-01 | rs12718464 | rs509712 | 0.0002 |
| APOC3 | 11 (116) | 4 | 7.62E-04 | 3 | 2.68E-01 | rs12718464 | rs10047459 | 0.335 |
| APOA4 | 11 (116) | 4 | 7.62E-04 | 3 | 3.00E-01 | rs12718464 | rs1263167 | 0.0001 |
| AGTR1 | 3 (149) | 51 | 8.83E-04 | 50 | 1.32E-02 | rs7647223 | rs4681444 | 0.006 |
| SOAT1 | 1 (177) | 25 | 2.79E-02 | 25 | 9.94E-04 | rs2492778 | rs4652366 | 0.015 |
Genes included are those that have a SNP with p<0.001 in the Harold GWAS, and are in the lipid-related processes significantly enriched in both GWAS (Table 4). APOC1, APOC2 and APOC4 are not included in the enrichment analysis (Tables 3 and 4) since they are in LD with APOE. APOA1 and APOA4 share the same best SNP and are therefore counted as the same gene in the enrichment analyses. Two genes, CLU and APOA4, are found in both cholesterol and immune-related GO processes. The category-wide set-based analysis allows for such dependence between genes. Genes contributing to the enrichment signal from Harold et al. are in bold, genes contributing to the signal from Lambert et al. are in italic and genes contributing to the signal in both are in bold italic.