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Table 2

Top SNPs for Vitamin B6, Vitamin B12, Folate, and Homocysteine Concentrations

GWAS Meta-analysis
Replication
Four Cohort Meta-analysisc
Concentrations
Chr
SNP
Position (bp)
Genea
Gene Region
Alleles (+/−)
Freq (+)b
N
Effect
SE
p value
Effect
SE
P value
N
Effect
SE
p value
Vitamin B6 (ng/mL)
1rs465474821531374ALPL5′UTRC/T0.501178−1.380.321.21 × 10−8−1.6680.562.08 × 10−111864−1.450.288.30 × 10−18
Vitamin B12 (pg/mL)
19rs60266253898797FUT2exon2A/G0.53292744.208.262.43 × 10−1258.6510.432.19 × 10−10361349.776.472.83 × 10−20
10rs1125436317170699CUBNintron52A/G0.702927−39.169.187.24 × 10−83.6210.940.8153613−21.497.031.11 × 10−6
11rs52693459390069TCN1intron8A/G0.67292736.7610.358.33 × 10−712.8313.240.519361327.628.151.51 × 10−6
Homocysteine (μmol/L)
1rs1801133d11790644MTHFRexon8A/G0.4729651.310.164.36 × 10−13-------
11rs110413217310445SYT9intron3T/C0.102965−0.970.252.42 × 10−60.300.490.2803651−0.700.221.11 × 10−4
Folate (ng/mL)
1rs199959411893482MTHFRd-A/G0.3429310.300.071.12 × 10−7-------
3rs15373464053049PRICKLE23′UTRT/C0.8429310.350.081.01 × 10−6−0.010.190.91336170.290.087.20 × 10−6
aGenes positioned ± 50 kb of the SNP (based on NCBI build 35).
bFrequency is averaged across the three GWAS studies.
cAnalysis of vitamin B6 is from the InCHIANTI and replication study only.
drs1999594 is within 100 kb of MTHFR, r2 = 0.2 with rs1801133.