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Table 2 The most statistically significant associations (P ≤ 0.005) between single nucleotide polymorphisms and the plasma homocysteine phenotype a, e

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

Gene Name rs# Nominal P Effectc Chr. Coded allele Coded allele frequency Genetic Modelg SNP Typeh
FTCD rs2277820 3.09E-04b 7.22% 21 T 26% O I
SLC19A1 rs1051266 4.16E-04b 5.04% 21 A 44% A CN
SLC19A1 rs1131596 4.31E-04b 5.03% 21 C 44% A 5'
SLC19A3 rs13007334 4.61E-04b 6.89% 2 C 46% O I
SLC19A1 rs4819130 5.65E-04b 4.94% 21 C 44% A I
MTHFD1L rs11754661d 1.51E-03 49.98% 6 A 7% R I
DNMT1 rs2228611 2.42E-03 -6.44% 19 G 49% D CS
ALDH1L1 rs3772424 2.52E-03 6.14% 3 A 20% D I
GGH rs4617146 2.55E-03 5.31% 8 T 19% A I
CELF1 rs4752843 2.74E-03 -5.72% 11 C 14% A I
SLC19A1 rs12482346 3.02E-03 4.08% 21 T 44% A I
SLC19A1 rs2297291 3.39E-03 6.07% 21 A 41% D I
TCN2 rs4820886 3.41E-03 -17.30% 22 G 13% R I
TCN2 rs9621049 3.41E-03 -17.30% 22 T 13% R CN
GLDC rs7848919 3.52E-03 5.70% 9 G 32% D 3'
SARDH rs2502741f 3.60E-03 6.60% 9 A 50% D I
SLC19A1 rs1051298 3.68E-03 3.98% 21 T 44% A 3'
CBS rs6586282 4.06E-03 -5.80% 21 T 18% O I
FOLH1 rs202673 4.08E-03 -19.30% 11 G 14% R I
MTHFD1 rs1950902f 4.19E-03 -5.18% 14 T 16% A CN
  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. bFDR-adjusted P values reached False Discovery Rate significance threshold of 0.05.
  3. cEffect is shown as percent change in plasma homocysteine levels.
  4. dSparse data (fewer than 5 individuals per category) for some genotype categories.
  5. eNo SNPs map to more than one gene.
  6. fLower quality SNP.
  7. gD:Dominant; R:Recessive; A:Additive; O:Overdominant.
  8. h5':5' region; 3':3' region; CN:Coding nonsynonymous; CS:Coding synonymous; I:Intronic.