Folate network genetic variation, plasma homocysteine, and global genomic methylation content: a genetic association study

Table 3 The most statistically significant associations (P ≤ 0.005) between single nucleotide polymorphisms and the Alu methylation phenotype a, b, d, f

Gene	rs#	Nominal P	Effect^c	Chr	Coded allele	Coded allele frequency	Genetic Model^g	Type^h
GNMT	rs1051218^e	2.14E-04	-0.57	6	T	3%	D	3'
DNMT3B	rs2424914	2.16E-03	0.30	20	G	45%	R	I
SLC25A32	rs3134297^e	2.20E-03	0.65	8	C	20%	R	5'
DNMT3B	rs2424922	2.21E-03	0.30	20	C	45%	R	CS
DNMT3B	rs6058891	2.21E-03	0.30	20	C	45%	R	CS
MTHFD1L	rs1738574	2.39E-03	0.24	6	T	45%	O	I
AHCYL2	rs1665105	3.87E-03	0.16	7	T	44%	A	3'
SARDH	rs129886	3.92E-03	-0.60	9	T	19%	R	3'

^aModel adjusted for age, smoking, and residuals of plasma folate, plasma vitamin B-6, and plasma vitamin B-12; forward strand allele shown;
^bNo FDR-adjusted P values reached False Discovery Rate significance threshold of 0.05.
^cEffect represents per genotype change in Alu element methylation standard deviation.
^dNo sparse data (fewer than 5 individuals per category) for any genotype categories of these SNPs.
^eSNP maps to more than one gene (rs1051218 also maps to PEX6, rs3134297 also maps to WDSOF1/DCAF13).
^fNo lower quality SNPs.
^gD:Dominant; R:Recessive; A:Additive; O:Overdominant.
^h5':5' region; 3':3' region; CN:Coding nonsynonymous; CS:Coding synonymous; I:Intronic.

ISSN: 1471-2350