Table 2.

Summary of the discovery phase associations that were tested in the replication study (SHIP-2)

Locus	Index variant	Chr	Biochemical (metabolite)	EA	Beta	SE	P-value
AGMAT	rs10927806	1	4-Guanidinobutanoate	C	0.115	0.044	8.9 × 10−3
ATP13A5	rs55918334	3	Creatinine	G	0.239	0.040	2.8 × 10−9
SLC2A9	rs13129697	4	Urate	T	0.576	0.045	7.7 × 10−35
	rs7675964	4	Allantoin	C	0.209	0.049	2.3 × 10−5
DMGDH	rs248386	5	Dimethylglycine	C	−0.336	0.055	1.4 × 10−9
DPYS	rs80274300	8	3-Ureidopropionate	C	−1.035	0.049	3.1 × 10−82
ABOa	rs9411378	9	N-acetylglucosamine/N-acetylgalactosamine	A	0.032	0.048	0.502
ACADS	rs34673751	12	Ethylmalonate	G	−0.132	0.049	7.3 × 10−3
TYMS/ENOSF1	rs2790	18	Ribonate	A	0.137	0.055	0.013

^aSince information for the index variant (rs201298979) at the ABO locus was not available in the replication study, a proxy variant (rs9411378) that was in high LD (r² = 0.95) with the index variant was used for the replication analysis.

Replication in SHIP-2 could be attempted for 9 of the 14 mQTLs that were identified in the discovery phase (metabolites corresponding to the remaining five mQTLs were not measured in SHIP-2). For each of these nine mQTLs, the most significant variant-metabolite pair identified in the discovery phase was tested in SHIP-2, using salivary metabolite data that were not normalized for osmolality (since SHIP-2 saliva samples represented stimulated saliva).