Skip to main content
. Author manuscript; available in PMC: 2020 May 1.
Published in final edited form as: Diabetologia. 2017 Jan 26;60(4):645–655. doi: 10.1007/s00125-016-4203-1

Table 3.

The association of the 48 differentially methylated CpG sites with CIR, BMI and diabetes risk in later life

 CpG  Gene/CpG island  CIR
  BMI
  Diabetes risk
Effect (SD/SD) 95% CI p value Effect (%/SD) 95% CI p value HR (/SD) 95% CI p value
cg24049468 AK3 −0.088 −0.162, −0.013 0.02* 0.9 −2.1, 4.0 5.7 × 10−1 1.13 0.82, 1.45 0.44
cg25949304 PCDHGA4 0.080 0.010, 0.150 0.03* −3.0 −5.7, −0.3 3.1 × 10−2* 0.93 0.66, 1.21 0.63
cg04645534 STC1 0.072 0.002, 0.141 0.05* −4.5 −7.2, −1.8 1.3 × 10−3* 0.97 0.67, 1.27 0.85
cg16426215 chr16:56709677–56709953 0.123 −0.004, 0.249 0.06 −2.9 −7.6, 2.0 2.4 × 10−1 0.95 0.40, 1.49 0.84
cg09674170 CLDN9 −0.076 −0.161, 0.008 0.08 1.0 −2.4, 4.5 5.6 × 10−1 1.18 0.70, 1.32 0.39
cg06717221 ATP8B3 −0.065 −0.137, 0.007 0.08 −3.1 −5.9, −0.3 3.2 × 10−2* 1.01 0.81, 1.56 0.94
cg12140144 PRDM16 0.074 −0.015, 0.163 0.10 6.0 2.4, 9.8 1.2 × 10−3* 2.12 1.74, 2.50 9.7 × 10−5*
cg20941258 TDGF1 0.053 −0.033, 0.139 0.23 2.6 −0.8, 6.2 1.3 × 10−1 1.37 1.01, 1.73 0.08
cg24996440 chr2:3583550–3584833 0.049 −0.039, 0.137 0.28 −3.0 −6.3, 0.5 8.9 × 10−2 0.85 0.49, 1.20 0.36
cg17186803 SCN4B 0.058 −0.050, 0.166 0.29 6.2 1.5, 10.7 8.9 × 10−3* 1.25 0.77, 1.72 0.37
cg08911291 chr9:44118137–44120175 0.044 −0.041, 0.129 0.31 3.3 −0.1, 6.8 5.5 × 10−2 1.47 1.09, 1.85 0.05*
cg07464358 - −0.062 −0.184, 0.060 0.32 9.2 4.3, 14.4 2.3 × 10−4* 1.21 0.71, 1.71 0.45
cg20769177 WNT9B 0.031 −0.038, 0.101 0.38 −0.7 −3.3, 2.0 6.0 × 10−1 1.11 0.77, 1.45 0.55
cg05772155 chr10:65800729–65801528 −0.029 −0.096, 0.038 0.40 −1.6 −4.1, 1.0 2.2 × 10−1 0.94 0.68, 1.19 0.62
cg10772621 chr19:54411376–54411968 0.029 −0.041, 0.100 0.41 −4.9 −7.4, −2.4 2.3 × 10−4* 0.98 0.69, 1.27 0.89
cg07993743 WNT9B 0.027 −0.042, 0.097 0.44 −1.0 −3.7, 1.8 5.0 × 10−1 1.02 0.70, 1.35 0.89
cg15618978 TRIM59 0.030 −0.055, 0.116 0.49 2.5 −1.1, 6.3 1.7 × 10−1 0.99 0.61, 1.37 0.96
cg04350311 ELFN2 0.027 −0.052, 0.106 0.51 4.2 1.1, 7.5 9.2 × 10−3* 0.94 0.59, 1.29 0.73
cg03862414 PLEKHH3 −0.026 −0.105, 0.053 0.52 1.5 −1.7, 4.8 3.7 × 10−1 1.07 0.76, 1.43 0.71
cg15833797 LHX3 −0.025 −0.102, 0.052 0.52 0.1 −2.9, 3.2 9.5 × 10−1 1.09 0.72, 1.41 0.61
cg14381623 LHX3 0.021 −0.045, 0.087 0.53 2.0 −0.7, 4.7 1.6 × 10−1 1.07 0.78, 1.37 0.64
cg08414676 SORD −0.023 −0.097, 0.052 0.55 −1.3 −4.1, 1.6 3.7 × 10−1 1.01 0.71, 1.32 0.93
cg08370430 chr17:12927455–12928747 −0.021 −0.097, 0.056 0.60 −1.1 −4.1, 1.9 4.6 × 10−1 0.98 0.67, 1.30 0.91
cg04413090 SBK1 0.018 −0.054, 0.091 0.62 5.3 2.4, 8.4 4.1 × 10−4* 1.08 0.78, 1.38 0.62
cg20345234 chr10:65800729–65801528 −0.017 −0.086, 0.052 0.63 −2.3 −4.9, 0.3 8.7 × 10−2 0.99 0.70, 1.28 0.96
cg16482344 LINC00839 0.017 −0.052, 0.086 0.63 −1.7 −4.3, 1.0 2.1 × 10−1 0.96 0.69, 1.23 0.77
cg24503407 PM20D1 0.017 −0.055, 0.090 0.64 −1.0 −3.6, 1.7 4.8 × 10−1 0.99 0.69, 1.29 0.94
cg21192468 LHX3 −0.013 −0.077, 0.051 0.69 2.3 −0.4, 5.0 9.5 × 10−2 1.04 0.76, 1.32 0.79
cg26671988 chr5:102090439–102091241 −0.015 −0.092, 0.063 0.71 1.2 −1.9, 4.5 4.5 × 10−1 1.17 0.84, 1.50 0.35
cg27073142 SORD −0.012 −0.080, 0.056 0.73 −1.7 −4.2, 0.9 2.1 × 10−1 1.10 0.81, 1.42 0.52
cg25629768 LMNB2 −0.014 −0.097, 0.068 0.73 1.3 −1.9, 4.5 4.4 × 10−1 1.13 0.79, 1.46 0.49
cg15183961 ANKRD20A2 −0.014 −0.097, 0.068 0.73 4.4 1.4, 7.6 4.4 × 10−3* 1.12 0.82, 1.38 0.47
cg12875241 GPR143 0.011 −0.056, 0.079 0.74 0.7 −2.0, 3.4 6.2 × 10−1 1.03 0.74, 1.31 0.87
cg20749955 PPP1R3B 0.012 −0.060, 0.084 0.75 −4.0 −6.6, −1.2 4.7 × 10−3* 0.96 0.64, 1.28 0.81
cg08292290 GLRX5 0.013 −0.072, 0.098 0.76 −3.5 −6.4, −0.5 2.2 × 10−2* 1.09 0.73, 1.45 0.65
cg25952247 LHX3 0.009 −0.056, 0.074 0.78 −0.2 −2.9, 2.5 8.6 × 10−1 0.97 0.69, 1.25 0.83
cg14105781 TBL1X −0.019 −0.154, 0.117 0.79 3.9 −1.4, 9.4 1.5 × 10−1 0.91 0.11, 1.21 0.75
cg00509616 GCOM1 −0.012 −0.097, 0.074 0.79 3.9 0.6, 7.5 2.3 × 10−2* 1.25 0.87, 1.64 0.25
cg27222147 CACNA1C 0.018 −0.113, 0.149 0.79 −3.0 −7.5, 1.7 2.1 × 10−1 0.66 0.38, 1.45 0.14
cg06268875 PIEZ02 0.008 −0.066, 0.083 0.82 −1.2 −3.9, 1.6 3.9 × 10−1 0.93 0.63, 1.23 0.65
cg14732789 chr20:29534910–29535208 −0.009 −0.096, 0.078 0.84 −3.7 −7.0, −0.4 2.9 × 10−2* 1.30 0.95, 1.64 0.14
cg21172615 LHX3 −0.007 −0.082, 0.068 0.86 2.5 −0.5, 5.6 1.1 × 10−1 1.01 0.66, 1.36 0.94
cg14605520 LHX3 0.005 −0.071, 0.080 0.90 0.7 −2.2, 3.7 6.4 × 10−1 1.03 0.70, 1.36 0.86
cg05806645 PPP1R3B 0.004 −0.066, 0.073 0.91 −2.8 −5.4, 0.0 5.0 × 10−2* 1.18 0.85, 1.50 0.33
cg13700073 FSCN2 −0.004 −0.080, 0073 0.93 −2.3 −5.4, 0.8 1.4 × 10−1 0.97 0.63, 1.31 0.86
cg13427473 - 0.002 −0.078, 0.081 0.97 −3.6 −6.4, −0.6 1.9 × 10−2* 1.02 0.69, 1.35 0.91
cg00762450 ANKRD20A4 −0.001 −0.081, 0.078 0.97 3.5 0.4, 6.8 2.8 × 10−2* 1.26 0.93, 1.59 0.17
cg15796459 SHROOM2 −0.001 −0.12.6, 0.125 0.99 −2.9 −7.4, 1.7 2.2 × 10−1 1.69 1.16, 2.21 0.05

CpG position is given in a chromosome:base pair format

A CpG is assigned to a gene if it is located within the gene region; if it is not within a gene region, the start/stop of the CpG island is given

The effect size of CIR is shown as the SD difference in CIR per SD difference in M-value. The effect size of BMI is shown as the per cent difference in BMI (expressed as a multiplier) per SD of M-value.

The HR for development of diabetes is shown per SD of M-value. The 95% CI of effects/HRs are shown in the adjacent columns

All associations were adjusted for age, sex and proportion of the American Indian ancestry of the offspring, as well as for the mother’s age when the child was born, array batch and four PCs (the four most significant PCs were calculated from genome-wide methylation data). CIR was additionally adjusted for BMI and HOMA-IR of the offspring. All the models were further corrected for intrauterine exposure to diabetes

*

p ≤ 0.05