Table 2.

Annotation of independent genome-wide significant associations for MCI-MRS and BAIBA in HCHS/SOL sample set B.

							Effect allele frequency in Hispanic/Latino ancestry
Outcome	Variant	Chromosome	Position (hg38)	Eff. allele	Non-eff. allele	R2	European	African	Amerindian	Beta	p value	Gene	Annotation
MCI-MRS (n = 3890)	rs37371	5	35040125	G	A	0.995	0.920	0.983	0.412	0.232	1.76E-15	AGXT2	intron
	rs344515	5	35025665	A	G	0.994	0.621	0.633	0.876	−0.192	1.80E-14	AGXT2	intron
BAIBA (n = 3863)	rs16899972	5	34998673	A	C	1.000	0.509	0.287	0.475	0.287	4.75E-38	AGXT2	missense
	rs183958240	5	35002671	G	A	0.947	0.010	0.010	0.031	−0.811	1.81E-12	AGXT2	missense
	rs13174311	5	35032240	T	C	0.998	0.355	0.100	0.023	−0.321	4.13E-32	AGXT2	intron
	rs180749	5	35033500	A	G	1.000	0.990	0.816	0.908	1.423	1.63E-192	AGXT2	missense
	rs37369	5	35037010	T	C	0.998	0.070	0.639	0.576	0.385	1.93E-51	AGXT2	splice donor
	rs140156063	5	35037031	A	G	0.998	0.010	0.012	0.019	1.148	6.00E-14	AGXT2	missense
	rs37370	5	35039381	T	C	1.000	0.921	0.984	0.414	−0.892	3.59E-210	AGXT2	intron
	rs11613331	12	242301	A	G	0.997	0.515	0.236	0.036	0.168	5.59E-12	SLC6A13	intron

Independent associations were identified by sequential conditional analysis.

MCI mild cognitive impairment, MRS metabolomic risk score, AF allele frequency.

P values were computed based on the score test.

R² provides the imputation quality of the genetic variant in the HCHS/SOL dataset.