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

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

Gene rs# Nominal P Effectc Chr Coded allele Coded allele frequency Genetic Modelg Typeh
GNMT rs1051218e 2.14E-04 -0.57 6 T 3% D 3'
DNMT3B rs2424914 2.16E-03 0.30 20 G 45% R I
SLC25A32 rs3134297e 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'
  1. aModel adjusted for age, smoking, and residuals of plasma folate, plasma vitamin B-6, and plasma vitamin B-12; forward strand allele shown;
  2. bNo FDR-adjusted P values reached False Discovery Rate significance threshold of 0.05.
  3. cEffect represents per genotype change in Alu element methylation standard deviation.
  4. dNo sparse data (fewer than 5 individuals per category) for any genotype categories of these SNPs.
  5. eSNP maps to more than one gene (rs1051218 also maps to PEX6, rs3134297 also maps to WDSOF1/DCAF13).
  6. fNo lower quality SNPs.
  7. gD:Dominant; R:Recessive; A:Additive; O:Overdominant.
  8. h5':5' region; 3':3' region; CN:Coding nonsynonymous; CS:Coding synonymous; I:Intronic.