Gene–methylation interactions: discovering region-wise DNA methylation levels that modify SNP-associated disease risk

Table 1 The SNPs selected for the current analyses, along with the names of the nearest genes (if any), and the measures of association (relative risks (RR), 95% confidence intervals (CI), and p values; taken from Tables 1–3 in Ref. [24])

SNP	Locus	Minor allele^a	MAF^a	RR	95% CI	p value	Cleft subtype^b
rs12543318	8q21.3	c	0.31	1.51	1.31–1.75	4.46e ⁻⁸	CLO
rs987525	8q24	a	0.19	1.85	1.63–2.10	1.47e ⁻¹⁹	CLP
rs560426	ABCA4	g	0.44	1.24	1.10–1.41	3.91e ⁻⁴	CLP
rs3758249	FOXE1	t	0.36	0.78	0.69–0.88	8.18e ⁻⁵	CLP
rs642961	IRF6	a	0.23	1.60	1.36–1.87	1.41e ⁻⁸	CLO
rs7078160	KIAA1598	a	0.17	1.33	1.15–1.53	1.04e ⁻⁴	CLP
rs13041247	MAFB	c	0.41	0.67	0.59–0.76	2.32e ⁻⁹	CLP
rs227731	NOG1	g	0.47	0.74	0.64–0.85	3.8e ⁻⁵	CPO
rs742071	PAX7	t	0.38	1.52	1.31–1.75	3.74e ⁻⁸	CLO
rs8001641	SPRY2	g	0.54	0.79	0.70–0.90	2.05e ⁻⁴	CLP
rs7590268	THADA	g	0.25	1.27	1.12–1.46	3.96e ⁻⁴	CLP
rs1873147	TPM1	g	0.27	1.31	1.13–1.53	5.82e ⁻⁴	CLO

^aThe minor allele and its frequency (MAF) for the Norwegian population were taken from Table 1 in the Appendix of Ref. [24]
^bThe cleft subtype (CLO, CPO, or CLP) for which the association was the strongest

ISSN: 1868-7083