Table 2.

Genome-wide significant variants^† for circulating total HCY, CYSTA and SAH levels.

						Meta-analysis			Affymetrix Axiom			Illumina 1M/1M Duo			Illumina Omni1			Illumina OncoArray
rsID	Chr	Position (BP)	Gene	Allele Eff/Ref	Eff allele freq	Beta	S.E.	P	Beta	S.E.	P	Beta	S.E.	P	Beta	S.E.	P	Beta	S.E.	P	Phet
tHCY
rs35976024	2	86003971	ATOH8	A/G	0.32	−0.10	0.02	4.89E-08	−0.10	0.05	0.06	−0.11	0.02	2.11E-06	−0.11	0.05	0.04	−0.04	0.09	0.62	0.91
CYSTA
rs28391580	15	38033956		T/C	0.27	−0.24	0.04	2.82E-08	−0.24	0.10	0.02	−0.22	0.06	1.62E-04	−0.34	0.11	0.001	−0.18	0.11	0.11	0.75
rs28416399	15	38028526		G/A	0.27	−0.24	0.04	2.97E-08	−0.24	0.10	0.02	−0.22	0.06	1.75E-04	−0.34	0.11	0.001	−0.18	0.11	0.11	0.74
rs765683	15	38018791		T/C	0.30	−0.23	0.04	3.20E-08	−0.27	0.10	0.01	−0.18	0.06	1.21E-03	−0.35	0.10	0.001	−0.21	0.11	0.05	0.53
rs4924190	15	38017922		T/C	0.25	−0.24	0.04	3.30E-08	−0.23	0.10	0.03	−0.22	0.06	2.69E-04	−0.39	0.11	3.26E-04	−0.17	0.11	0.12	0.52
rs11856650	15	38025137		A/G	0.27	−0.23	0.04	3.75E-08	−0.24	0.10	0.02	−0.22	0.06	2.24E-04	−0.34	0.11	0.001	−0.18	0.11	0.11	0.74
rs8023982	15	38021714		A/G	0.27	−0.23	0.04	4.08E-08	−0.24	0.10	0.02	−0.22	0.06	2.23E-04	−0.33	0.11	0.001	−0.18	0.11	0.11	0.76
SAH
rs139435405	14	36655451		C/T	0.75	0.23	0.04	1.95E-08	0.27	0.09	0.002	0.19	0.05	5.43E-04	0.27	0.08	0.001	N/A	N/A	N/A	0.62
rs149119426	14	36656744		T/C	0.63	0.23	0.04	4.26E-08	0.20	0.09	0.02	0.20	0.06	3.73E-04	0.30	0.08	2.02E-04	N/A	N/A	N/A	0.61
Biomarker PC1
rs12665366	6	541907	EXOC2	G/A	0.12	−0.35	0.06	2.33E-08	−0.44	0.15	0.003	−0.26	0.08	0.001	−0.43	0.16	0.005	−0.80	0.26	0.002	0.18

Abbreviation: Chr, chromosome. S.E., standard error. PC, principal component. tHCY, total Homocysteine. CYSTA, Cystathionine. SAH, S-adenosylhomocysteine. P_het. P_{heterogeneity.}

^†Variants identified in at least three arrays.