Table 1.
Genome-wide scan of DNA methylation for an association with fasting glucose concentrations (as a continuous variable)
| Chr | CpG site§ | Position | Discovery | Validation | Meta − analysis | CpG context | Gene | Gene region | |||
|---|---|---|---|---|---|---|---|---|---|---|---|
| Effect†a (95% CI) | Effect a (95% CI) | p | Effect (95% CI) | p | pQ¥ | ||||||
| chr1 | cg14476101 | 120,255,992 | − 0.50 (− 0.66, − 0.35) | − 1.08 (− 1.79, − 0.38) | 0.003 | − 0.53 (− 0.68, − 0.38) | 4.37E − 12 | 0.111 | S Shore | PHGDH | Body |
| chr1 | cg19693031 | 145,441,552 | − 1.11 (− 1.30, − 0.93) | − 1.93 (− 2.55, − 1.30) | < 0.0026 | − 1.18 (− 1.36, − 1.00) | 1.10E − 38 | 0.013 | OpenSea | TXNIP | 3'UTR |
| chr2 | cg00765233* | 235,877,260 | − 1.11 (− 1.49, − 0.74) | − 2.70 (− 5.67, 0.28) | 0.075 | − 1.14 (− 1.51, − 0.77) | 1.92E − 09 | 0.294 | OpenSea | SH3BP4 | 5'UTR |
| chr4 | cg06690548 | 139,162,808 | − 0.50 (− 0.70, − 0.31) | − 0.74 (− 1.70, 0.23) | 0.132 | − 0.51 (− 0.70, − 0.32) | 9.65E − 08 | 0.638 | OpenSea | SLC7A11 | Body |
| chr8 | cg00345025 | 743,875 | − 0.79 (− 1.09, − 0.49) | − 0.46 (− 1.65, 0.73) | 0.444 | − 0.77 (− 1.06, − 0.48) | 2.35E − 07 | 0.594 | N Shore | Intergenic | |
| chr9 | cg14148209* | 7,543,165 | − 1.65 (− 2.16, − 1.13) | − 0.25 (− 3.52, 3.01) | 0.877 | − 1.61 (− 2.12, − 1.11) | 3.93E − 10 | 0.402 | OpenSea | Intergenic | |
| chr10 | cg01391548* | 97,068,696 | − 0.70 (− 0.96, − 0.44) | − 0.53 (− 1.28, 0.23) | 0.167 | − 0.68 (− 0.92, − 0.43) | 6.21E − 08 | 0.675 | OpenSea | Intergenic | |
| chr10 | cg02556345 | 124,181,965 | − 0.88 (− 1.22, − 0.54) | − 0.57 (− 1.89, 0.76) | 0.398 | − 0.86 (− 1.19, − 0.53) | 2.60E − 07 | 0.648 | OpenSea | PLEKHA1 | Body |
| chr10 | cg08994060 | 6,214,026 | − 0.64 (− 0.88, − 0.39) | − 0.69 (− 1.71, 0.32) | 0.179 | − 0.64 (− 0.87, − 0.40) | 1.02E − 07 | 0.915 | OpenSea | PFKFB3 | Body |
| chr10 | cg26262157 | 6,214,079 | − 0.68 (− 0.94, − 0.43) | − 0.89 (− 1.85, 0.08) | 0.070 | − 0.70 (− 0.94, − 0.45) | 2.09E − 08 | 0.685 | OpenSea | PFKFB3 | Body |
| chr11 | cg00574958 | 68,607,622 | − 2.92 (− 3.62, − 2.23) | − 2.26 (− 4.05, − 0.46) | 0.014 | − 2.83 (− 3.48, − 2.19) | 7.60E − 18 | 0.494 | N Shore | CPT1A | 5'UTR |
| chr11 | cg11588197 | 128,391,494 | − 0.74 (− 1.02, − 0.47) | 0.33 (− 0.56, 1.22) | 0.462 | − 0.65 (− 0.91, − 0.38) | 1.34E − 06 | 0.022 | N Shore | ETS1 | Body |
| chr11 | cg17058475 | 68,607,737 | − 1.44 (− 1.94, − 0.95) | − 1.30 (− 2.63, 0.02) | 0.054 | − 1.42 (− 1.89, − 0.96) | 1.48E − 09 | 0.845 | N Shore | CPT1A | 5'UTR |
| chr12 | cg10877979 | 131,569,407 | − 1.31 (− 1.77, − 0.85) | − 0.52 (− 3.81, 2.76) | 0.753 | − 1.29 (− 1.75, − 0.84) | 3.03E − 08 | 0.637 | N Shelf | GPR133 | Body |
| chr13 | cg19750657 | 38,935,967 | 0.69 (0.44, 0.94) | 0.04 (− 1.17, 1.24) | 0.951 | 0.66 (0.41, 0.91) | 1.53E − 07 | 0.293 | OpenSea | UFM1 | 3'UTR |
| chr20 | cg00872151 | 59,964,387 | − 2.36 (− 3.23, − 1.48) | − 0.80 (− 4.86, 3.26) | 0.697 | − 2.29 (− 3.14, − 1.43) | 1.62E − 07 | 0.456 | N Shore | CDH4 | Body |
| chr21 | cg06500161* | 43,656,587 | 0.83 (0.53, 1.12) | 1.69 (0.43, 2.94) | 0.009 | 0.87 (0.59, 1.15) | 1.68E − 09 | 0.184 | S Shore | ABCG1 | Body |
| chr21 | cg08309687** | 35,320,596 | − 0.52 (− 0.71, − 0.32) | − 1.11 (− 2.12, − 0.10) | 0.032 | − 0.54 (− 0.73, − 0.35) | 3.42E − 08 | 0.254 | OpenSea | Intergenic | |
| chr21 | cg17648210 | 46,352,817 | 1.41 (0.88, 1.93) | 1.14 (− 2.45, 4.73) | 0.530 | 1.40 (0.88, 1.92) | 1.16E − 07 | 0.883 | Island | Intergenic | |
Chr Chromosome, CI Confidence interval, CpG CpG dinucleotide, Effect Effect size; UTR Untranslated region. Numbers in bold face are statistically significant
§ Annotation used R v.0.6.0.IlluminaHumanMethylation450kanno.ilmn12.hg19: Annotation for Illumina's 450 k methylation arrays
† Each effect size of the CpGs in the discovery stage was at the epigenome-wide significance level (p < 1E-007)
a Effect size adjusted by age and leukocyte heterogeneities (CD8+CD28−CD45RA− T cell, naïve CD8 T cell, plasma blast, CD4+ T cell, natural killer cell, monocyte, and granulocyte)
¥ p value for Cochran’s Q
* Enhancer associated
** Enhancer and promoter associated