Table 1. Genome-wide SNPs most strongly associated with piperaquine IC₅₀s.

Locus	Chr.	Position	Gene ID	Gene description	N/S	Alteration	p value
L13	13	2,504,560	PF3D7_1362500	exonuclease, putative	N	p.Glu415Gly	2.69 × 10−9
L12-01	12	418,346	PF3D7_1208900	conserved Plasmodium protein, unknown function	S	p.981Pro	4.80 × 10−8
L13	13	2,728,402	PF3D7_1368700	mitochondrial carrier protein, putative	N	p.Asn252Asp	2.33 × 10−7
L13	13	2,512,415	PF3D7_1362700	conserved Plasmodium protein, unknown function	S	p.687Asn	6.25 × 10−7
L13	13	2,519,091	PF3D7_1362800	conserved Plasmodium protein, unknown function	N	p.Gly202Asp	2.12 × 10−6
L13	13	2,447,146	PF3D7_1361000	arginine methyltransferase 5, putative (PRMT5)	N	p.Asn40Ser	3.96 × 10−6
L04-01	4	904,088	PF3D7_0420000	zinc finger protein, putative	S	p.213Leu	7.67 × 10−6
L14-01	14	2,411,942	PF3D7_1458700	conserved Plasmodium protein, unknown function	N	p.Arg25Lys	1.27 × 10−5
L14-01	14	2,395,752	PF3D7_1458300	conserved Plasmodium protein, unknown function	N	p.Ile301Phe	2.03 × 10−5
L13	13	2,542,366	PF3D7_1363300	mitochondrial ribosomal protein L9 precursor, putative	N	p.Thr28Ile	2.48 × 10−5
L12-02	12	1,787,279	PF3D7_1242000	conserved Plasmodium protein, unknown function	N	p.Ser518Asn	2.90 × 10−5
L04-01	4	865,807	PF3D7_0419400	conserved Plasmodium protein, unknown function	S	p.2423Ile	3.05 × 10−5
L06-01	6	866,478	PF3D7_0621100	conserved Plasmodium protein, unknown function	N	p.Asp1144Glu	4.04 × 10−5
L12-01	12	407,838	PF3D7_1208800	zinc finger protein, putative	N	p.Ser438Asn	4.56 × 10−5
L13	13	2,656,558	PF3D7_1366400	rhoptry protein (Rhop148)	N	p.Lys836Asn	5.02 × 10−5
L14-01	14	2,385,550	PF3D7_1457900	conserved Plasmodium protein, unknown function	S	p.3324Thr	8.00 × 10−5
L04-01	4	865,709	PF3D7_0419400	conserved Plasmodium protein, unknown function	N	p.Leu2391Ile	8.96 × 10−5
L13	13	2,746,936	PF3D7_1369100	conserved Plasmodium protein, unknown function	N	p.Leu430Arg	8.98 × 10−5

Significant SNPs (Bonferroni-corrected p≤8.6×10⁻⁷, boldface) and suggestive SNPs (p≤10⁻⁴) associated with piperaquine IC₅₀s, according to increasing p value, are shown. For each SNP, we list the locus name; chromosome number (Chr.); nucleotide position; gene ID; gene description; whether the SNP is nonsynonymous (N) or synonymous (S); encoded amino-acid alteration; and association p value.