Table 1 Genome-wide significant loci associated with metabolites.

Metabolites	sex	−log P	SNP	Chr.	Gene	Allele	MAF	Residue change
asparagine	all	14.19	rs8012505	14	ASPG	C > G	0.127	S344R
phenylalanine	all	12.54	rs118092776	12	PAH	C > T	0.047	R53H
proline	all	14.88	rs5747933	22	PRODH	G > T	0.148	T275N
glycine	all	50.66	rs1047891	2	CPS1	C > A	0.152	T1406N
formate	all	8.34	rs1801133	1	MTHFR	C > T	0.397	A222V
Chr., chromosome; MAF, minor allele frequency
MAFs of SNPs investigated in this study
			MAF
Gene			ASPG	PAH	PRODH	CPS1	MTHFR	MYLK
Allele			C > G	C > T	G > T	C > A	C > T	G > A
Non-synonymous variant			S344R	R53H	T275N	T1406N	A222V
ToMMo			0.127	0.047	0.148	0.152	0.397	0.020
CSHL- HAPMAP	HapMap-JPT	Japan	0.852^*1			0.153	0.360	0.017
	HapMap-HCB	China	0.909^*1			0.159	0.512	0.058
	HapMap-CEU	European (Utah, USA)	0.817^*1			0.295	0.310	0.808
	HapMap-YRI	Sub-Saharan African	0.567^*1			0.283	0.093	0.044
	HAPMAP-ASW	African ancestry in Southwest USA.				0.388	0.112	0.214
1000 GENOMES (pilot 1)	YRI_low_coverage_panel		0.051			0.186	0.119	0.008
	CEU_low_coverage_panel		0.175		0.083	0.300	0.275	0.800
	CHB + JPT_low_coverage_panel		0.117	0.025	0.158	0.100	0.433	0.042

MAFs of HAPMAP and 1000GENOMES are obtained from NCBI dbSNP database (http://www.ncbi.nlm.nih.gov/SNP/).
*1: Definition of the minor allele for ASPG in CSHL-HAPMAP seems to be opposite to that in 1000GENOMES or our study.

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