Table 2.
List of CpG sites with differential methylation at a p value < 0.01 in newborn cord blood DNA per 400 g of weight gain/week in early pregnancy (from 0 to 18 weeks), the ALSPAC cohort (n = 88)
| Chr a | Gene name | CpG site | Position b | Coef c . (se) | p value | q value | |
|---|---|---|---|---|---|---|---|
| 11 |
Matrix metallopeptidase 7 |
MMP7_E59 |
101906629 |
0.072 |
(0.016) |
1.55E-05 |
0.023 |
| 11 |
Potassium channel, subfamily K, member 4 |
KCNK4_P171 |
63815280 |
0.060 |
(0.014) |
4.57E-05 |
0.034 |
| 19 |
Janus kinase 3 |
JAK3_P1075 |
17820875 |
0.034 |
(0.008) |
7.13E-05 |
0.036 |
| 11 |
Transient receptor potential cation channel, subfamily M, member 5 |
TRPM5_E87 |
2400764 |
0.072 |
(0.020) |
0.0003 |
0.065 |
| 12 |
Protein tyrosine phosphatase, non-receptor type 6 |
PTPN6_E171 |
6926172 |
0.042 |
(0.011) |
0.0003 |
0.065 |
| 4 |
Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 |
NFKB1_P496 |
103641022 |
0.058 |
(0.016) |
0.0002 |
0.065 |
| 1 |
Absent in melanoma 2 |
AIM2_E208 |
157313063 |
0.015 |
(0.004) |
0.0003 |
0.065 |
| 17 |
Ecotropic viral integration site 2A |
EVI2A_E420 |
26672423 |
0.039 |
(0.010) |
0.0002 |
0.065 |
| 17 |
Septin 9 |
SEPT9_P58 |
72827686 |
0.034 |
(0.010) |
0.0005 |
0.077 |
| 15 |
Interleukin 16 |
IL16_P93 |
79262162 |
0.037 |
(0.011) |
0.0006 |
0.077 |
| 9 |
PALM2-AKAP2 protein |
PALM2_AKAP2_P183 |
111582227 |
0.025 |
(0.007) |
0.0005 |
0.077 |
| 20 |
DNA (cytosine-5-)-methyltransferase 3 beta |
DNMT3B_P352 |
30813500 |
0.040 |
(0.012) |
0.0005 |
0.077 |
| 13 |
5-hydroxytryptamine (serotonin) receptor 2A |
HTR2A_E10 |
46368166 |
0.011 |
(0.003) |
0.0008 |
0.096 |
| 6 |
RAB32, member RAS oncogene family |
RAB32_P493 |
146906028 |
0.038 |
(0.011) |
0.0009 |
0.098 |
| 22 |
Breakpoint cluster region (BCR) |
BCR_P422 |
21852130 |
0.024 |
(0.007) |
0.0010 |
0.103 |
| 9 |
Transmembrane protein with EGF-like and two follistatin-like domains 1 |
TMEFF1_P234 |
102275304 |
0.042 |
(0.013) |
0.0016 |
0.146 |
| 11 |
Transient receptor potential cation channel, subfamily M, member 5 |
TRPM5_P721 |
2401572 |
0.053 |
(0.017) |
0.0017 |
0.148 |
| 10 |
ATP-binding cassette, sub-family C (CFTR/MRP), member 2 |
ABCC2_E16 |
101532577 |
0.078 |
(0.025) |
0.0018 |
0.148 |
| 12 |
v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog |
KRAS_E82 |
25295039 |
0.042 |
(0.014) |
0.0021 |
0.155 |
| 11 |
Tumor susceptibility gene 101 |
TSG101_P139 |
18505204 |
0.045 |
(0.015) |
0.0022 |
0.155 |
| 11 |
Solute carrier family 22 (organic cation transporter), member 18 |
SLC22A18_P216 |
2877311 |
0.032 |
(0.011) |
0.0021 |
0.155 |
| 20 |
v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) |
SRC_P164 |
35406338 |
0.051 |
(0.017) |
0.0027 |
0.177 |
| 6 |
Major histocompatibility complex, class II, DO beta |
HLA_DOB_P1114 |
32893876 |
0.014 |
(0.004) |
0.0027 |
0.177 |
| X |
Biglycan |
BGN_P333 |
152413272 |
0.027 |
(0.009) |
0.0030 |
0.181 |
| 2 |
Interleukin 1, beta |
IL1B_P829 |
113311656 |
0.029 |
(0.009) |
0.0030 |
0.181 |
| 11 |
Cathepsin D (lysosomal aspartyl peptidase) |
CTSD_P726 |
1742524 |
0.033 |
(0.011) |
0.0034 |
0.192 |
| 7 |
Carboxypeptidase A4 |
CPA4_P961 |
129719269 |
0.020 |
(0.007) |
0.0035 |
0.192 |
| 22 |
Breakpoint cluster region (BCR) |
BCR_P346 |
21852206 |
0.021 |
(0.007) |
0.0036 |
0.192 |
| 16 |
PYD and CARD domain containing |
PYCARD_E87 |
31121665 |
0.023 |
(0.008) |
0.0038 |
0.192 |
| 17 |
Homeo box B2 |
HOXB2_P99 |
43977490 |
0.040 |
(0.014) |
0.0038 |
0.192 |
| 17 |
v-crk sarcoma virus CT10 oncogene homolog (avian) |
CRK_P721 |
1307015 |
0.043 |
(0.015) |
0.0039 |
0.192 |
| 22 |
Seizure related 6 homolog (mouse)-like |
SEZ6L_P299 |
24895181 |
0.031 |
(0.011) |
0.0044 |
0.208 |
| 19 |
Kallikrein 11 |
KLK11_P103 |
56223205 |
0.022 |
(0.008) |
0.0046 |
0.210 |
| X |
ELK1, member of ETS oncogene family |
ELK1_E156 |
47394808 |
0.025 |
(0.009) |
0.0058 |
0.255 |
| 2 |
CDC-like kinase 1 |
CLK1_P538 |
201438205 |
0.036 |
(0.013) |
0.0064 |
0.263 |
| 6 |
Solute carrier family 22 (organic cation transporter), member 2 |
SLC22A2_P109 |
160600058 |
0.021 |
(0.008) |
0.0064 |
0.263 |
| 19 |
Apolipoprotein C-II |
APOC2_P377 |
50140706 |
0.015 |
(0.006) |
0.0067 |
0.263 |
| X |
Dyskeratosis congenita 1, dyskerin |
DKC1_P276 |
153644068 |
0.030 |
(0.011) |
0.0066 |
0.263 |
| 20 |
v-src sarcoma (Schmidt-Ruppin A-2) viral oncogene homolog (avian) |
SRC_P297 |
35406205 |
0.025 |
(0.009) |
0.0080 |
0.300 |
| 10 |
N-acetyltransferase 2 |
NAT2_P11 |
18293024 |
0.012 |
(0.004) |
0.0079 |
0.300 |
| 8 |
PTK2 protein tyrosine kinase 2 |
PTK2_P735 |
142081249 |
0.022 |
(0.008) |
0.0085 |
0.312 |
| 1 |
CD34 antigen |
CD34_P339 |
206151645 |
0.021 |
(0.008) |
0.0092 |
0.330 |
| 4 |
Interleukin 8 |
IL8_P83 |
74825056 |
0.051 |
(0.019) |
0.0098 |
0.334 |
| 11 | Progesterone receptor | PGR_P790 | 100507255 | 0019 | (0.007) | 0.0096 | 0.334 |
aChromosome. bChromosomal position based on NCBI human reference genome assembly Build 36.1.
cRegression coefficient using linear mixed models. All models adjusted for child’s sex and maternal age at child’s birth and the inclusion of a PCR plate random batch effect.
Suffixes denote the Illumina probe identity (P = within promoter, E = within first exon).
Probes shown in bold displayed >5% difference in methylation.