Figure S1. Comparison of association between measured fasting plasma glucose at 2nd
trimester (Z-score) and DNAm at cg12083122 (X-axis) with association between GRS10
(Z-score) and DNAm at cg12083122 (Y-axis). Error bars represent 95% intervals
assuming a normal distribution. Red diagonal line indicates alignment of association that
are consistent in effect sizes and direction, supporting here that maternal glycemia is
negatively associated with methylation at cg12083122.
Figure S2. Genomic region of LEP from ENCODE, including genomic location, CpG
islands, H3K markers, DNase Hypersensitivity Cluster, and Transcription Factors binding
sites. All CpG sites annotated around LEP available on 450k HumanMethylation chip are
represented on this figure at their genomic position; colors of CpG sites represent
methylation levels in cell line GM12878 (orange is for fully methylated, purple is for
partially methylated and dark blue is for unmethylated). The CpG highlighted in light
blue (cg12083122) was the primary site of interest for our analyses. The five SNPs
genotyped for our study in proximity of leptin promoter are also represented in this figure
at their genomic position. Black rectangles indicate CpG regions analysed in previous
studies that have investigated methylation levels near LEP region with name of first
author, as referenced in the Discussion.
Table S1. 21 SNPs known to be associated with fasting glucose (in non-pregnant populations, some were replicated in pregnancy)
SNP
CHR
Gene
rs560887
rs10885122
rs6235
rs1260326
rs10811661
rs1371614
rs7903146
rs7936247
rs7651090
rs6943153
rs11920090
rs2191349
2
10
5
2
9
2
10
11
3
7
3
7
rs4502156
15
rs4841132
rs11708067
rs11605924
rs6113722
rs174550
rs9368222
rs3802177
rs11603334
8
3
11
20
11
6
8
11
G6PC2
ADRA2A
PCSK1
GCKR
CDKN2A/B
DPYSL5
TCF7L2
MTNR1B
IGF2BP2
GRB10
SLC2A2
DGKB/TMEM195
FAM148B/VPS13
C/C2CD4A/B
PPP1R3B
ADCY5
CRY2
FOXA2
FADS1
CDKAL1
SLC30A8
ARAP1
Raising
Gen3G
fasting
allele
glucose
frequency
allele
N
β
SE
P value
R²
GRS10
C
G
G
C
A
A
T
T
C
T
A
A
0.68
0.88
0.71
0.53
0.83
0.24
0.32
0.38
0.30
0.30
0.84
0.55
475
467
476
475
465
467
467
375
467
467
467
465
0.097
0.068
0.067
0.063
0.052
0.040
0.036
0.027
0.023
0.023
0.019
0.011
0.022 9.06E-06
0.033
0.04
0.023
0.005
0.020
0.002
0.029
0.08
0.025
0.11
0.022
0.11
0.025
0.29
0.023
0.31
0.024
0.33
0.028
0.49
0.021
0.61
0.041
0.009
0.017
0.020
0.007
0.005
0.006
0.003
0.002
0.002
0.001
0.001
y
y
y
y
y
y
y
y
y
y
-
T
0.56
460
0.008
0.021
0.69
<0.001
-
T
T
A
C
A
T
G
C
0.07
0.78
0.46
0.95
0.71
0.26
0.73
0.86
475
466
466
466
467
461
466
466
0.006
-0.001
-0.002
-0.003
-0.006
-0.009
-0.015
-0.038
0.043
0.026
0.021
0.049
0.024
0.025
0.024
0.031
0.89
0.98
0.92
0.96
0.79
0.72
0.52
0.22
<0.001
<0.001
<0.001
<0.001
<0.001
<0.001
0.001
0.003
-
Reference
SNP in
literature
LD
(R²)
Dupuis/HAPO
Dupuis
Manning/HAPO rs13179048 0.7
Dupuis/HAPO
rs780094 0.93
Scott
Manning
Dupuis
rs4506565 0.92
Dupuis/HAPO
Scott
Scott
Dupuis
Dupuis
Dupuis
Associated
with fasting
glucose in
pregnancy?
Yes
No
Yes
Yes
No
No
No
Yes
No
No
No
No
rs11071657 0.31
No
Manning/HAPO
Dupuis
Dupuis
Scott
Dupuis
Scott
Dupuis
rs11558471 0.96
Manning/Scott
-
Yes
No
No
No
No
No
No
No
Dupuis is for Dupuis et al. Nat Gen 2010. HAPO is for Hayes et al. Diabetes 2013. Manning is for Manning et al. Nat Gen 2012. Scott is for Scott. et al. Nat Gen 2012. CHR: Chromosome.
N: Number of participants included in linear regressions. β: Estimated effect of SNPs fasting glucose at 2 nd trimester in Gen3G. SE: Standard error of the effect. R2: Coefficient of
determination, indicate percentage of the variance in fasting glucose levels that is explained by the SNP. No covariables were included in regressions. GRS: Genetic Risk Score. LD: Linkage
Disequilibrium. In GRS10 column, yes (y) indicates SNPs included in GRS10 – we included all SNPs in GRS21. P values <0.05 are bold and P values <0.15 are italic.
Table S2. Linear regressions between 16 sites of DNAm levels of LEP gene in cord
blood cells and leptin levels in cord blood
CpG
CHR
cg14734794
cg03084214
cg12782180
cg07464571
cg00840332
cg19594666
cg26814075
cg13381984
cg00666422
cg12083122*
cg23753947
cg25435800
cg25730670
cg16683741
cg18603538
cg24862443
7
7
7
7
7
7
7
7
7
7
7
7
7
7
7
7
Genomic
Mean ± SD of
location
raw DNAm
(built 37)
127879920 93.90 ± 1.07
127880619 91.99 ± 1.43
127880932 32.13 ± 5.45
127881001 29.02 ± 4.00
127881269 10.64 ± 2.81
127881280 22.48 ± 5.42
127881298 29.32 ± 5.30
127881344 29.55 ± 5.12
127881440 61.99 ± 4.09
127883819 93.52 ± 1.15
127889701 92.39 ± 1.16
127890193 89.44 ± 2.74
127891366 93.50 ± 1.05
127891959 90.83 ± 1.73
127894591 86.14 ± 2.52
127896859 92.91 ± 1.06
β
SE
P value
0.02
0.09
-0.14
-0.09
-0.04
-0.10
-0.07
-0.06
-0.09
-0.17
-0.08
-0.04
-0.03
-0.16
-0.14
0.05
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.07
0.79
0.18
0.04
0.20
0.54
0.14
0.29
0.42
0.17
0.01
0.26
0.53
0.64
0.02
0.04
0.42
N = 170 for each regression.* Indicates the CpG we selected for our analyses. CHR: Chromosome. SD: standard
deviation. β: association of DNAm levels in cord blood cells with neonatal circulating leptin levels. SE: Standard
error. P values <0.05 are bold.
Table S3. Regressions between 16 sites of DNAm levels of LEP gene in cord blood cells
and fasting glucose at 2nd trimester
CpG
CHR
cg14734794
cg03084214
cg12782180
cg07464571
cg00840332
cg19594666
cg26814075
cg13381984
cg00666422
cg12083122*
cg23753947
cg25435800
cg25730670
cg16683741
cg18603538
cg24862443
7
7
7
7
7
7
7
7
7
7
7
7
7
7
7
7
Genomic
location
(built 37)
127879920
127880619
127880932
127881001
127881269
127881280
127881298
127881344
127881440
127883819
127889701
127890193
127891366
127891959
127894591
127896859
Mean ± SD of
raw DNAm
β
SE
P value
93.90 ± 1.07
91.99 ± 1.43
32.13 ± 5.45
29.02 ± 4.00
10.64 ± 2.81
22.48 ± 5.42
29.32 ± 5.30
29.55 ± 5.12
61.99 ± 4.09
93.52 ± 1.15
92.39 ± 1.16
89.44 ± 2.74
93.50 ± 1.05
90.83 ± 1.73
86.14 ± 2.52
92.91 ± 1.06
0.29
-0.06
-0.20
-0.03
-0.04
-0.36
-0.25
-0.07
-0.22
-0.43
-0.29
0.19
-0.19
-0.13
-0.05
0.11
0.24
0.24
0.23
0.24
0.23
0.23
0.23
0.23
0.24
0.24
0.23
0.24
0.24
0.23
0.24
0.23
0.23
0.78
0.39
0.91
0.87
0.13
0.29
0.76
0.36
0.07
0.21
0.41
0.41
0.57
0.84
0.64
N = 173 participants included for each regression.* Indicates the CpG we selected for our analyses. CHR:
Chromosome. SD: standard deviation. β: association between maternal fasting glucose on DNAm levels in cord
blood cells of neonates. SE: Standard error. P values <0.05 are bold and P values <0.15 are italic.
Table S4. Regressions between DNAm levels of LEP gene in cord blood cells at cg12083122
and selected SNPs in and around LEP
SNPs on
LEP gene
CHR
Genomic
position
(built 37)
rs7799039
rs28954080
rs2167270
rs4731426
rs4236625
7
7
7
7
7
127878783
127880698
127881349
127882070
127883695
Distance
Sample
from
MAF
cg12083122
5036
3121
2470
1749
124
0.43
0.09
0.34
0.44
0.10
N
β
SE
P value
R2
159
155
169
172
170
-0.09
-0.03
0.13
0.07
<0.01
0.12
0.17
0.11
0.11
0.17
0.43
0.88
0.26
0.52
1.00
0.004
<0.001
0.008
0.002
<0.001
CHR: Chromosome. MAF: Minor Allele Frequency. N: number of participants included in the
regressions. β: Estimated association between SNPs on DNAm levels in cord blood cells of
neonates. SE: Standard error. R2: Coefficient of determination, indicated percentage of the
variance in DNAm levels that is explained by the SNP.