Table 4.
Significant differentially methylated CpGs for type 2 diabetes as originally identified in blood and replicated in the Lifelines type 2 diabetes EWAS sample in blood (n = 198)
| Illumina ID | CHR | MAPINFO | Gene name | Location in gene | Location in CpG island | Mean methylation (%) | Model 1 | Model 1 + BMI | ||
|---|---|---|---|---|---|---|---|---|---|---|
| Delta methylation (%) | p value | Delta methylation (%) | p value | |||||||
| cg06500161a | 21 | 43656587 | ABCG1 | Body | Shore | 60.9 | 3 | 2.9 × 10−7 | 2.39 | 3 × 10−4 |
| cg24531955a | 8 | 23154691 | LOXL2 | 3′UTR | Open sea | 25.4 | −1.99 | 1.6 × 10−4 | −1.63 | 6 × 10−3 |
| cg19693031 | 1 | 145441552 | TXNIP | 3′UTR | Open sea | 69.5 | −3.6 | 2.5 × 10−4 | −2.68 | 1.5 × 10−2 |
| cg02711608a | 19 | 47287964 | SLC1A5 | 1stExon | Shelf | 20.1 | −1.81 | 3.2 × 10−4 | −1.26 | 2.7 × 10−2 |
| cg11024682a | 17 | 17730094 | SREBF1 | Body | Shelf | 44.6 | 1.88 | 5.5 × 10−4 | 1.04 | 8 × 10−2 |
| cg07960624 | 8 | 119208486 | SAMD12 | 3′UTR | Open sea | 39.7 | −2.3 | 4.8 × 10−3 | −1.59 | 9 × 10−2 |
| cg03497652 | 16 | 4751569 | ANKS3 | Body | Open sea | 55.5 | 1.86 | 9.7 × 10−3 | 1.79 | 3 × 10−2 |
| cg19266329 | 1 | 145456128 | POLR3GL b | – | Open sea | 60.9 | −1.77 | 1 × 10−2 | −0.98 | 0.20 |
| cg22909677 | 6 | 109172312 | ARMC2 | 5′UTR | Shelf | 80.4 | 1.11 | 1.2 × 10−2 | 1.04 | 0.07 |
| cg08309687a | 21 | 35320596 | ATP5O b | – | Open sea | 56.7 | −2.61 | 1.5 × 10−2 | −0.92 | 0.36 |
| cg26804423a | 7 | 8201134 | ICA1 | Body | Open sea | 63.8 | 1.39 | 1.5 × 10−2 | 0.78 | 0.23 |
| cg13199639 | 6 | 33360495 | KIFC1 | Body | Shore | 11.7 | −0.91 | 1.9 × 10−2 | −0.49 | 0.34 |
| cg15962267 | 5 | 138612986 | SNHG4 | Body | Shelf | 69.9 | −1.29 | 2.9 × 10−2 | −0.79 | 0.22 |
| cg03725309a | 1 | 109757585 | SARS | Body | Shore | 17.9 | −1.06 | 3.4 × 10−2 | −0.72 | 0.19 |
| cg10919522a | 14 | 74227441 | C14orf43 | 5′UTR | Shore | 31.4 | −1.42 | 4 × 10−2 | −0.42 | 0.56 |
No CpGs originally identified in other tissues were replicated in the present study looking at methylation in blood
Delta methylation is based on β values; p values are from analyses based on M values
Abbreviations: CHR, chromosome; MAPINFO, position on the chromosome; Shore, 0–2 kb from CpG island; Shelf, 2–4 kb from CpG island; Open sea, more than 4 kb from CpG island
Significant p values below 9.6 × 10−4 based on Bonferroni calculation
aCpGs also found to be associated with BMI in recently published EWAS [42]
bClosest genes were POLR3GL (108 bp downstream) and ATP5O (32,438 bp upstream)