Table 2.

Differentially methylated CpG sites associated with ln(total urinary arsenic levels) at $p_{\text{FDR}}<0.05$, sorted by chromosome and position.

CpG	Chromosome	Positiona	Gene	Feature category	$p$-Value	$p_{\mathrm{FDR}}$	$p_{\mathrm{Bonferroni}}$	Median methylation (%)b	Mean difference in % methylation (95% CI)c
cg12106731	1	36023279	NCDN; KIAA0319L	TSS200; TSS1500	$1.24\times {10}^{-7}$	0.014	0.098	0.60	0.04 (0.02, 0.05)
cg07317306	1	110314824	Intergenic	—	$9.79\times {10}^{-7}$	0.041	0.773	17.75	0.50 (0.31, 0.69)
cg18616702	1	150523808	ADAMTSL4; MIR4257	5′UTR; TSS1500	$2.35\times {10}^{-8}$	0.004	0.019	22.45	0.80 (0.50, 1.10)
cg04940901	3	52418250	DNAH1	Body	$1.96\times {10}^{-7}$	0.017	0.155	71.58	0.97 (0.60, 1.33)
cg06690548	4	139162808	SLC7A11	Body	$9.56\times {10}^{-10}$	0.001	0.001	96.24	$-0.49$ ($-0.66$, $-0.32$)
cg01538969	6	30624636	DHX16	Body	$7.09\times {10}^{-7}$	0.035	0.559	57.05	1.31 (0.80, 1.82)
cg14827056	8	141550539	EIF2C2	Body	$2.14\times {10}^{-7}$	0.017	0.169	88.76	0.58 (0.35, 0.81)
cg09280971	9	73036509	Intergenic	—	$4.63\times {10}^{-7}$	0.028	0.365	31.54	0.64 (0.40, 0.89)
cg14595618	10	71135446	HK1	Body	$7.63\times {10}^{-7}$	0.035	0.602	39.52	1.29 (0.76, 1.82)
cg27178850	11	9039431	Intergenic	—	$4.66\times {10}^{-7}$	0.028	0.367	69.43	0.82 (0.51, 1.13)
cg03036214	15	63640658	CA12	Body	$1.23\times {10}^{-6}$	0.048	0.967	56.18	1.30 (0.78, 1.82)
cg00500428	16	3074502	HCFC1R1; THOC6	TSS1500; Body	$1.83\times {10}^{-7}$	0.017	0.144	5.61	$-0.31$ ($-0.43$, $-0.19$)
cg03497652	16	4751569	ANKS3	Body	$1.49\times {10}^{-9}$	0.001	0.001	74.34	1.57 (1.08, 2.06)
cg07021906	16	87866833	SLC7A5	Body	$9.19\times {10}^{-7}$	0.040	0.725	82.02	0.85 (0.51, 1.20)
cg12116137	17	1576449	PRPF8	Body	$1.22\times {10}^{-7}$	0.014	0.096	77.19	1.33 (0.83, 1.84)
cg21369801	17	80202961	CSNK1D	Body; 3′UTR	$3.96\times {10}^{-7}$	0.028	0.312	77.81	1.17 (0.73, 1.62)
cg20493718	17	80202979	CSNK1D	Body; 3′UTR	$1.04\times {10}^{-8}$	0.002	0.008	97.47	0.35 (0.20, 0.50)
cg08059112	19	2294887	LINGO3	5′UTR	$6.19\times {10}^{-7}$	0.034	0.488	56.18	0.89 (0.54, 1.24)
cg22294740	19	2294961	LINGO3	5′UTR	$8.78\times {10}^{-9}$	0.002	0.007	55.92	1.84 (1.20, 2.48)
cg20509831	19	58866362	A1BG-AS1; A1BG; ZNF497	Body, TSS1500; 3′UTR	$6.45\times {10}^{-7}$	0.034	0.509	28.10	0.89 (0.53, 1.25)

Note: —, no data; BMI, body mass index; CI, confidence interval; GED, General Education Diploma.

^aGRCh37/hg19 assembly.

^bPercent methylation calculated $\text{Beta-value}\times 100$.

^cEffect size estimate from limma models of Beta-values [i.e., mean difference in percent methylation for each unit change in ln(total urinary arsenic levels)] adjusted for age, sex, BMI, self-reported smoking status, education ($<\mathrm{high\hspace{0.17em}school}$, high school graduate or GED, $>\text{high\hspace{0.17em}school}$), study center (Arizona, Oklahoma, North and South Dakota), estimated glomerular filtration rate, and cell-type proportion estimates.