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.