| SNP Names | Position relative to the gene | Position on the Vista Plot | Conserved noncoding? |
| ApoA1/A5.6350 | 3' to ApoA5 | 6350 | Yes |
| ApoA1/A5.6427 | 3' to ApoA5 | 6427 | Yes |
| ApoA1/A5.6444 | 3' to ApoA5 | 6444 | Yes |
| ApoA1/A5.18685 | 3' to ApoA5 | 18685 | No |
| ApoA1/A5.27106 | 3' to ApoA5 | 27106 | Yes |
| ApoA1/A5.27339 | 3' to ApoA5 | 27339 | Yes |
| ApoA1/A5.27573 | 3' to ApoA5 | 27573 | No |
| ApoA1/A5.34529 | 3' to ApoA5 | 34529 | No |
| ApoA1/A5.86306 |
exon 3 of ApoA5, 3' UTR |
86306 | Yes |
| ApoA1/A5.87446 | intron 2 of ApoA5 | 87446 | No |
| ApoA1/A5.88027 |
exon 2 of ApoA5, CGA (Arg) or CCA (Pro) |
88027 | No |
| ApoA1/A5.88199 | 5' to ApoA5 | 88199 | No |
| ApoA1/A5.89327 | 5' to ApoA5 | 89327 | No |
| ApoA1/A5.100435 | 5' to ApoA5 | 100435 | No |
| ApoA1/A5.140612 | 5' to ApoA1, intron of KIAA0999 | 140612 | Yes |
| ApoA1/A5.149559 | 5' to ApoA1, intron of KIAA0999 | 149559 | No |
| ApoA1/A5.149587 | 5' to ApoA1, intron of KIAA0999 | 149587 | Yes |
| ApoA1/A5.159922 | 5' to ApoA1, intron of KIAA0999 | 159922 | Yes |
| ApoA1/A5.160065 | 5' to ApoA1, intron of KIAA0999 | 160065 | No |
| ApoA1/A5.160426 | 5' to ApoA1, intron of KIAA0999 | 160426 | Yes |
| ApoA1/A5.160975 | 5' to ApoA1, intron of KIAA0999 | 160975 | Yes |
| ApoA1/A5.163113 | 5' to ApoA1, intron of KIAA0999 | 163113 | No |
| ApoA1/A5.163423 | 5' to ApoA1, intron of KIAA0999 | 163423 | No |
| ApoA1/A5.165530 | 5' to ApoA1, intron of KIAA0999 | 165530 | No |
| ApoA1/A5.166036 | 5' to ApoA1, intron of KIAA0999 | 166036 | Yes |
| ApoA1/A5.166623 | 5' to ApoA1, intron of KIAA0999 | 166623 | No |
| ApoA1/A5.170537 | 5' to ApoA1, intron of KIAA0999 | 170537 | Yes |
| ApoA1/A5.170728 | 5' to ApoA1, intron of KIAA0999 | 170728 | No |
| ApoA1/A5.171286 | 5' to ApoA1, exon of KIAA0999 | 171286 | Yes |
| ApoA1/A5.185036 | 5' to ApoA1, intron of KIAA0999 | 185036 | No |
| ApoA1/A5.185055 | 5' to ApoA1, intron of KIAA0999 | 185055 | No |