Table 2.
Replication of rs9349379 eQTL effects in human coronary arteries (hCA) from GTEx
| Exon | Exon length (bp) | Beta (SE) | P-value | Variance explained (%) |
|---|---|---|---|---|
| 6 (5’UTR) | 141 | −0.084 (0.13) | 0.51 | – |
| 7 (5’UTR) | 56 | −0.11 (0.13) | 0.39 | – |
| 7.8 | 520 | −0.15 (0.12) | 0.22 | – |
| 8 | 165 | −0.31 (0.13) | 0.017 | 3.4 |
| 9 | 81 | −0.19 (0.13) | 0.14 | – |
| 10 | 168 | −0.35 (0.13) | 0.0065 | 3.1 |
| 10.11 | 207 | −0.30 (0.13) | 0.022 | 3.9 |
| 11 | 322 | −0.35 (0.13) | 0.0074 | 2.8 |
| 12 | 248 | −0.40 (0.13) | 0.0019 | 5.0 |
| 13 | 157 | −0.28 (0.13) | 0.029 | 3.0 |
| 14a | 240 | −0.17 (0.13) | 0.20 | – |
| 5′-14b | 184 | 0.095 (0.13) | 0.47 | – |
| 3′-14c | 56 | −0.25 (0.13) | 0.059 | – |
| 15 | 62 | −0.25 (0.13) | 0.058 | – |
| 16 | 141 | −0.27 (0.13) | 0.042 | 2.3 |
| 17 | 77 | −0.31 (0.13) | 0.017 | 3.5 |
| 18 (3’UTR) | 779 | −0.25 (0.13) | 0.055 | – |
We analysed by linear regression the association between genotypes at rs9349379 (additive model) and normalized levels of PHACTR1 exon expression. Expression levels were corrected for the length of the exons (Materials and methods). Effect sizes (Beta) and standard errors (SE) are in standard deviation units. The direction of the effect size is for the G-allele, associated with increased coronary artery disease risk. We analyzed data from 122 hCA samples (NAA = 48, NAG = 57, NGG = 17). The frequency of the G-allele was 37%. When significant (P-value < 0.05), we provided the percentage of PHACTR1 exon expression variation explained by genotypes at rs9349379. aThe full exon 14; bpart of exon 14 which is specific to the short PHACTR1 transcript; cpart of exon 14 which is present in all PHACTR1 transcripts (see Additional file 5 for details)