Table 2.

Top associated SNPs for GWAS with log maximum AST, ALT and LFT >2X ULN in LD-MTX subjects (n = 1429).

chr	base pair	ref	alt	rs	Mapped Gene/nearest Gene	MAF	info	genotyped	association in LD-MTX subject
									beta	se	p value
log maximum AST outcome
1	169,586,946	T	C	rs2244526	SELP	0.1	0.92	Imputed	0.12	0.02	3.5E-07
2	28,804,276	T	C	rs13421347	PLB1	0.04	0.98	Genotype	0.17	0.03	4.8E-07
2	156,500,331	G	A	rs72889976		0.04	0.77	Imputed	0.16	0.03	5.5E-07
2	210,593,241	T	G	rs71420769	MAP2	0.03	0.78	Imputed	0.37	0.07	5.6E-07
4	67,601,162	G	A	rs11937537		0.23	0.95	Genotype	0.09	0.02	1.4E-07
12	131,011,393	T	C	rs6486549	RIMBP2	0.39	0.96	Imputed	0.07	0.01	9.8E-08
15	71,810,708	T	C	rs59374539	THSD4	0.02	0.99	Genotype	1.35	0.26	2.2E-07
17	65,706,413	T	A	rs80320525	NOL11	0.05	0.52	Imputed	0.81	0.16	9.4E-07
20	2,580,184	C	A	rs570089265	TMC2	0.02	0.74	Imputed	0.31	0.06	2.6E-07
log maximum ALT outcome
5	31,893,186	TA	T	rs34950471	PDZD2	0.09	0.77	Imputed	0.14	0.03	2.2E-07
9	1,279,510	G	C	rs35602716	DMRT2	0.02	0.83	Imputed	2.13	0.43	8.1E-07
17	2,707,990	C	T	rs76993247	RAP1GAP2	0.02	0.51	Imputed	0.59	0.09	5.0E-10
17	19,759,902	A	C	rs28661593	ULK2	0.03	0.70	Imputed	1.69	0.30	3.6E-08
18	8,723,770	C	T	rs589952	MTCL1	0.02	0.89	Imputed	1.14	0.22	2.0E-07
18	9,888,688	A	G	rs551429	TXNDC2	0.03	0.94	Imputed	1.59	0.30	1.9E-07
LFT > 2X ULN outcome
9	83,760,434	A	G	rs11139045	TLE1	0.03	0.998	Genotype	1.43	0.27	9.4E-08
12	52,994,955	G	A	rs61747192	KRT72	0.13	0.996	Imputed	0.83	0.17	9.9E-07
13	23,577,442	T	C	rs77522295	BASP1P1	0.04	0.998	Genotype	1.24	0.25	5.0E-07

Chr: chromosome; ref: reference allele; alt: alternative allele; MAF: minor allele frequency; info: imputation info score (0–1). All SNP reached suggestive significance level of 10⁻⁶. Genome wide significance was marked bold.