PMC full text:
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) | ||||||||||||||||||
| 1 | rs4654748 | 21531374 | ALPL | 5′UTR | C/T | 0.50 | 1178 | −1.38 | 0.32 | 1.21 × 10−8 | −1.668 | 0.56 | 2.08 × 10−11 | 1864 | −1.45 | 0.28 | 8.30 × 10−18 | |
| Vitamin B12 (pg/mL) | ||||||||||||||||||
| 19 | rs602662 | 53898797 | FUT2 | exon2 | A/G | 0.53 | 2927 | 44.20 | 8.26 | 2.43 × 10−12 | 58.65 | 10.43 | 2.19 × 10−10 | 3613 | 49.77 | 6.47 | 2.83 × 10−20 | |
| 10 | rs11254363 | 17170699 | CUBN | intron52 | A/G | 0.70 | 2927 | −39.16 | 9.18 | 7.24 × 10−8 | 3.62 | 10.94 | 0.815 | 3613 | −21.49 | 7.03 | 1.11 × 10−6 | |
| 11 | rs526934 | 59390069 | TCN1 | intron8 | A/G | 0.67 | 2927 | 36.76 | 10.35 | 8.33 × 10−7 | 12.83 | 13.24 | 0.519 | 3613 | 27.62 | 8.15 | 1.51 × 10−6 | |
| Homocysteine (μmol/L) | ||||||||||||||||||
| 1 | rs1801133d | 11790644 | MTHFR | exon8 | A/G | 0.47 | 2965 | 1.31 | 0.16 | 4.36 × 10−13 | - | - | - | - | - | - | - | |
| 11 | rs11041321 | 7310445 | SYT9 | intron3 | T/C | 0.10 | 2965 | −0.97 | 0.25 | 2.42 × 10−6 | 0.30 | 0.49 | 0.280 | 3651 | −0.70 | 0.22 | 1.11 × 10−4 | |
| Folate (ng/mL) | ||||||||||||||||||
| 1 | rs1999594 | 11893482 | MTHFRd | - | A/G | 0.34 | 2931 | 0.30 | 0.07 | 1.12 × 10−7 | - | - | - | - | - | - | - | |
| 3 | rs153734 | 64053049 | PRICKLE2 | 3′UTR | T/C | 0.84 | 2931 | 0.35 | 0.08 | 1.01 × 10−6 | −0.01 | 0.19 | 0.913 | 3617 | 0.29 | 0.08 | 7.20 × 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.
