Table 2.

Top 20 CpG sites based on smallest p-value demonstrating cord blood methylation differences in cotinine concentration levels from maternal plasma samples among nonsmoking pregnant women in the newborn epigenetic study ($n=79$).

CpG Site	Mapped Gene	Chr	beta	SE	Unadjusted p-value	Adjusted p-value	UCSC Referenced Gene Description
cg11407598		19	$-0.76$	0.08	$1.71\times {10}^{-22}$	$6.59\times {10}^{-17}$
cg09199225	AGER	6	1.38	0.16	$6.16\times {10}^{-19}$	$1.19\times {10}^{-13}$	Advanced glycosylation end product-specific receptor
cg05396900	PRKG1	10	0.44	0.05	$5.00\times {10}^{-18}$	$6.42\times {10}^{-13}$	Protein kinase, cGMP-dependent, type I
cg19810457	MAPK9	5	$-0.63$	0.07	$1.95\times {10}^{-17}$	$1.72\times {10}^{-12}$	Mitogen-activated protein kinase 9
cg15570148	FHIT	3	0.30	0.04	$2.23\times {10}^{-17}$	$1.72\times {10}^{-12}$	Fragile histidine triad
cg01588993		12	$-0.40$	0.05	$4.44\times {10}^{-17}$	$2.85\times {10}^{-12}$
cg01417692	MOBKL2C	1	$-0.11$	0.01	$1.44\times {10}^{-16}$	$7.67\times {10}^{-12}$
cg06432426		2	$-0.31$	0.04	$1.75\times {10}^{-16}$	$7.67\times {10}^{-12}$
cg06567155	SLC25A15	13	$-0.51$	0.06	$1.79\times {10}^{-16}$	$7.67\times {10}^{-12}$	Solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15
cg06998640		12	$-0.10$	0.01	$2.23\times {10}^{-16}$	$8.59\times {10}^{-12}$
cg01373721	TIMM23	10	0.13	0.02	$8.40\times {10}^{-16}$	$2.94\times {10}^{-11}$	Translocase of inner mitochondrial membrane 23 homolog (yeast)
cg27413290	ZC3H3	8	$-0.55$	0.07	$1.86\times {10}^{-15}$	$5.97\times {10}^{-11}$	Zinc finger CCCH-type containing 3
cg14189245	C11orf10|FEN1	11	0.46	0.06	$2.14\times {10}^{-15}$	$6.34\times {10}^{-11}$	Flap structure-specific endonuclease 1
cg09719342	STK32A	5	$\begin{array}{c}-0.93\end{array}$	0.12	$3.50\times {10}^{-15}$	$9.64\times {10}^{-11}$	Serine/threonine kinase 32A
cg20490386	CTDP1	18	$-0.11$	0.01	$3.87\times {10}^{-15}$	$9.94\times {10}^{-11}$	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1
cg14992144	GHRL|GHRLOS	3	0.26	0.03	$8.35\times {10}^{-15}$	$2.01\times {10}^{-10}$	Ghrelin opposite strand RNA conserved region|ghrelin opposite strand/antisense RNA|ghrelin/obestatin prepropeptide
cg02913918	CACNA1E	1	$-0.17$	0.02	$2.19\times {10}^{-14}$	$4.96\times {10}^{-10}$	Calcium channel, voltage-dependent, R type, alpha 1E subunit
cg07052606	DCTPP1	16	0.27	0.04	$4.20\times {10}^{-14}$	$8.98\times {10}^{-10}$	dCTP pyrophosphatase 1
cg25660646	BSG	19	0.32	0.04	$4.85\times {10}^{-14}$	$9.84\times {10}^{-10}$	Basigin (Ok blood group)
cg04007792	DLGAP2	8	$-0.09$	0.01	$6.18\times {10}^{-14}$	$1.19\times {10}^{-9}$	Discs, large (Drosophila) homolog-associated protein 2

Note: Top 20 CpG sites are based on adjusted p-values, which are listed from smallest p-value to largest p-value. Beta coefficients and p-values were obtained using beta regression (see “Methods” section). Results for all FDR-significant CpGs are provided in Excel Table S1. Table 2 and Excel Table S1 show results for all FDR-significant CpGs. Model-based estimates were derived from beta regression investigating the association between methylation of umbilical cord blood from infants and secondhand smoke exposure from maternal plasma cotinine. These models were adjusted for race/ethnicity, mother’s age at delivery, maternal education, and parity, as well as technical covariates (e.g., plate, row, column), and Houseman-estimated cell proportions. The resulting p-values were corrected using Benjamini and Hochberg’s FDR method, with CpG sites with FDR $<0.05$ considered statistically significant. Exposure contrasts for the coefficients indicate change in relation to $1\text{-unit ng}/\mathrm{mL}$ increase in cotinine from maternal plasma. “Chr” makes reference to the chromosome number. FDR, false discovery rate; UCSC, University of California, Santa Cruz.