Table 3. Differentially methylated genes.
| Subcutaneous adipose tissue | |||||||
| Gene | Target ID | Distance to TSS(base pairs) | Mean type 2 diabetic (%) | Mean non-diabetic (%) | Difference(% points) | P | Padj |
| ZNF668 | cg09765256 | −3 | 3.4±0.5 | 2.6±0.5 | 0.8 | <0.0001 | 0 |
| HSPA2 | cg01520924 | 12.1±1.6 | 14.8±1.6 | −2.7 | <0.0001 | 0 | |
| C8orf31 | cg04612566 | 27 | 35.1±6.0 | 26.9±5.4 | 8.1 | <0.0001 | 0 |
| CD320 | cg23963136 | 266 | 1.4±0.4 | 1.9±0.3 | −0.5 | <0.0001 | 0 |
| SFT2D3 | cg11206634 | −198 | 67.9±3.7 | 74.5±3.6 | −6.6 | 0.0001 | 0 |
| TWIST1 | cg22498251 | −415 | 10.6±0.8 | 12.6±0.8 | −1.9 | 0.0001 | 0 |
| MYO5A | cg23287547 | 769 | 2.6±0.4 | 3.4±0.5 | −0.8 | 0.0001 | 0 |
| SULT1A1 | cg18530748 | 22 | 6.3±1.2 | 4.7±1.3 | 1.5 | 0.0001 | 0.1 |
| PRRX2 | cg04713521 | 618 | 4.7±1.1 | 2.8±1.1 | 1.9 | 0.0002 | 0.9 |
| TGFA | cg07004820 | 479 | 3.0±0.4 | 4.2±0.3 | −1.2 | 0.0002 | 0.9 |
| WDR8 | cg13501117 | 60 | 4.7±0.5 | 5.4±0.5 | −0.6 | 0.0002 | 0.9 |
| ERCC6 | cg14343062 | 504 | 3.2±0.7 | 1.8±0.6 | 1.4 | 0.0003 | 1.0 |
| HNF4A | cg19717150 | 437 | 75.2±3.8 | 70.5±3.6 | 4.6 | 0.0003 | 1.0 |
| ZDHHC8 | cg25650110 | 98 | 4.2±0.6 | 5.6±0.6 | −1.4 | 0.0003 | 1.0 |
| CDKN2A | cg12840719 | 12.6±1.9 | 16.6±2.1 | −4.0 | 0.0003 | 1.0 | |
| GNB5 | cg14120436 | 67 | 36.2±6.0 | 43.0±5.7 | −6.8 | 0.0003 | 1.0 |
| CREBL2 | cg09819033 | −200 | 1.7±0.4 | 2.5±0.3 | −0.8 | 0.0004 | 1.0 |
| TMEM79 | cg14500718 | −1283 | 20.7±5.1 | 28.9±3.9 | −8.2 | 0.0004 | 1.0 |
| VGLL1 | cg12384303 | −424 | 58.4±3.6 | 69.4±4.8 | −11.0 | 0.0005 | 1.0 |
| KITLG | cg18422443 | −148 | 1.9±0.4 | 2.5±0.5 | −0.6 | 0.0005 | 1.0 |
| Skeletal muscle | |||||||
| Gene | Target ID | Distance to TSS (base pairs) | Mean T2D (%) | Mean non-T2D (%) | Difference (% points) | P | Padj |
| IL8 | cg16468729 | 190 | 48.1±7.1 | 37.3±8.9 | 10.8 | 0.0001 | 0.0003 |
| GZMB | cg08766149 | 131 | 85.3±2.1 | 88.3±2.4 | −3.0 | 0.0001 | 0.4 |
| MTUS1 | cg22807551 | −992 | 10.4±3.8 | 7.8±3.7 | 2.6 | 0.0002 | 0.4 |
| PNOC | cg03642518 | 354 | 55.5±3.5 | 52.3±4.1 | 3.2 | 0.0004 | 0.9 |
| PDGFD | cg07748540 | 270 | 4.8±1.3 | 3.4±0.9 | 1.5 | 0.0005 | 0.9 |
| KLF2 | cg04898512 | −656 | 89.7±1.2 | 88.2±1.5 | 1.5 | 0.0006 | 0.9 |
| ZNF160 | cg12586262 | 22 | 13.5±2.8 | 9.9±1.9 | 3.6 | 0.0006 | 0.9 |
| PCBP3 | cg23272214 | −32 | 85.8±2.8 | 88.1±2.5 | −2.3 | 0.0007 | 1.0 |
| CDR2 | cg23142935 | 630 | 3.3±1.8 | 2.6±1.6 | 0.7 | 0.0010 | 1.0 |
| TEKT4 | cg05723825 | 243 | 54.6±5.4 | 59.2±4.9 | −4.6 | 0.0014 | 1.0 |
| DHCR24 | cg10073091 | 604 | 13.4±2.2 | 15.3±2.6 | −2.0 | 0.0014 | 1.0 |
| ADAM17 | cg24320643 | 321 | 14.1±3.3 | 11.2±3.1 | 2.9 | 0.0017 | 1.0 |
| SCARA3 | cg26847866 | 500 | 52.0±6.8 | 61.1±5.6 | −9.1 | 0.0017 | 1.0 |
| KLHL12 | cg04462209 | 321 | 3.7±1.4 | 2.8±1.4 | 0.9 | 0.0017 | 1.0 |
| SRPK2 | cg00950418 | −122 | 3.5±1.2 | 4.5±1.6 | −1.1 | 0.0018 | 1.0 |
| AMN | cg09616556 | −348 | 65.8±2.9 | 69.8±3.0 | −3.9 | 0.0018 | 1.0 |
| FOLR3 | cg07676849 | −1106 | 58.6±6.8 | 50.9±6.2 | 7.7 | 0.0021 | 1.0 |
| PTPN1 | cg15864184 | −17 | 10.6±3.7 | 7.0±3.2 | 3.5 | 0.0025 | 1.0 |
| CDH13 | cg00806490 | 295 | 10.1±2.7 | 13.1±1.5 | −3.0 | 0.0026 | 1.0 |
| PIGR | cg02105856 | 23 | 38.7±2.4 | 30.6±2.3 | 8.1 | 0.0027 | 1.0 |
The 20 CpG sites with the lowest P-values for the intra-pair methylation difference between type 2 diabetic and non-diabetic twins are shown for subcutaneous adipose tissue and skeletal muscle. The total number of differentially methylated CpG sites, without correction for multiple testing, was 1,458 in subcutaneous adipose tissue and 789 in skeletal muscle. Each CpG site is identified with Illumina probe target ID. The CpG site location is given as the base pair distance to transcription start site (TSS) if available. Data are shown as mean±standard deviation. P adj-values are corrected for multiple testing (26,850 tests).