Table 1.
Information about differentially methylated sites (DMSs) that showed significant correlation with gene expression and association with nearby SNPs
| CpG site | Gene | Methylation changes | Gene expression changes | mQTL analysis | ||
|---|---|---|---|---|---|---|
| methylation difference (adjusted P-value) | correlation coefficient (adjusted P-value) | mQTL-SNP | maximum methylation difference (adjusted P-value) | |||
| discovery | replication | |||||
| chr14.24801071 | ADCY4* | −0.17 (6.60e−03) | −0.17 (1.44e−02) | −0.40 (2.15e−04) | rs11158632 | 0.18 (2.75e-02) |
| chr14.24801073 | ADCY4* | −0.17 (4.00e−02) | −0.19 (2.50e−02) | −0.29 (1.28e−02) | rs12891732 | 0.15 (1.29e-02) |
| chr10.49673509 | ARHGAP22* | −0.11 (6.52e−03) | −0.09 (3.74e−03) | −0.32 (4.25e−03) | rs9663790 | 0.12 (1.14e-02) |
| chr6.91007306 | BACH2* | −0.13 (8.67e−03) | −0.10 (6.24e−03) | 0.32 (4.60e−03) | rs2174281 | 0.14 (4.39e-02) |
| chr1.95393371 | CNN3* | −0.18 (1.47e−03) | −0.11 (3.80e−03) | 0.33 (2.72e−03) | rs859057 | 0.02 (1.91e-02) |
| chr17.56004243 | CUEDC1* | −0.09 (9.65e−05) | −0.05 (1.58e−03) | −0.38 (4.15e−04) | rs1017528 | 0.11 (4.15e-02) |
| chr19.45930589 | ERCC1* | −0.14 (1.84e−10) | −0.05 (1.79e−02) | −0.32 (3.29e−03) | rs11615 | 0.14 (3.07e-02) |
| chr21.40176597 | ETS2* | −0.17 (1.02e−03) | −0.10 (9.91e−04) | 0.24 (4.10e−02) | rs2283639 | 0.39 (3.23e-11) |
| chr11.61596996 | FADS2 | −0.17 (1.61e−02) | −0.14 (2.44e−02) | −0.32 (6.24e−03) | rs174535 | 0.23 (7.59e-03) |
| chr6.150040098 | LATS1 | −0.22 (8.28e−09) | −0.11 (2.27e−04) | 0.44 (4.23e−05) | rs10872646 | 0.24 (3.79e-02) |
| chr5.169694956 | LCP2* | −0.12 (2.58e−04) | −0.05 (4.01e−02) | 0.30 (6.89e−03) | rs2271146 | 0.18 (3.87e-03) |
| chr19.58513473 | LOC100128398 | 0.08 (4.95e−02) | 0.06 (1.26e−02) | −0.33 (2.72e−03) | rs11881126 | 0.14 (1.04e-03) |
| chr10.134166587 | LRRC27* | −0.10 (7.72e−05) | −0.07 (7.98e−06) | −0.31 (4.96e−03) | rs2474339 | 0.08 (2.65e-02) |
| chr13.113656361 | MCF2L* | −0.23 (3.74e−05) | −0.21 (3.72e−02) | 0.39 (3.26e−04) | rs2993282 | 0.25 (3.55e-02) |
| chr19.45351770 | PVRL2 | −0.18 (1.10e−05) | −0.06 (1.32e−02) | −0.42 (9.53e−05) | rs2075642 | 0.20 (8.22e-03) |
| chr19.45351779 | PVRL2 | −0.21 (1.81e−07) | −0.12 (3.44e−03) | −0.39 (2.15e−04) | rs395908 | 0.12 (3.79e-02) |
| chr19.45352168 | PVRL2 | −0.14 (2.62e−02) | −0.15 (1.46e−05) | −0.26 (2.39e−02) | rs4803760 | 0.36 (1.59e-03) |
| chr15.67430536 | SMAD3* | −0.07 (8.35e−04) | −0.09 (8.13e−04) | 0.39 (2.15e−04) | rs1065080 | 0.04 (5.34e-03) |
| chr22.39147165 | SUN2 | −0.11 (3.47e−02) | −0.10 (1.71e−05) | 0.39 (2.15e−04) | rs4821822 | 0.07 (1.54e-02) |
| chr12.50136491 | TMBIM6 | −0.13 (8.59e−03) | −0.10 (4.02e−02) | 0.26 (2.95e−02) | rs1993398 | 0.04 (1.29e-02) |
| chr17.10634582 | TMEM220* | −0.15 (1.11e−03) | −0.13 (1.51e−03) | 0.33 (2.87e−03) | rs406446 | 0.19 (8.05e-03) |
| chr10.73062374 | UNC5B | −0.12 (1.66e−03) | −0.04 (3.79e−03) | −0.29 (1.19e−02) | rs1538894 | 0.13 (5.45e-03) |
| chr6.30883001 | VARS2* | −0.14 (4.36e−03) | −0.21 (3.96e−02) | −0.26 (2.73e−02) | rs2249459 | 0.23 (1.99e-02) |
| chr3.22412739 | ZNF385D | −0.19 (2.19e−03) | −0.23 (9.34e−04) | −0.28 (1.86e−02) | rs9854991 | 0.22 (2.96e-02) |
Genes are listed alphabetically, sites are sorted by genes; columns show adjusted P-values as well as the difference in mean methylation levels between old and young individuals in the discovery and replication cohort; Spearman’s correlation coefficient and maximum difference in median methylation levels between genotypes. * indicates genes for which a literature and database search ((28, 32–41); https://gemex.eurac.edu/bioinf/age/ (42)) yielded significant age-related expression changes.