Table2:

The top 3 most significant associations with response to ICI under dominant logistic regression models^a

SNPs	Reported Genes	Chromosome position	Major/Minor allele	Anti-CTLA-4 (N Controls= 78, N Cases= 135 ) (N total= 213)		Anti-PD-1 (N Controls= 88, N Cases= 81) (N total= 169)		Combined therapy (N Controls= 33, N Cases= 10) (N total= 43)
				OR (95%CI)	p-value	OR (95%CI)	p-value	OR (95%CI)	p-value
rs10488631	TNPO3, IRF5	chr7:128954129	T/C	1.14(0.52-2.49)	0.74	1.20(0.55-2.60)	0.63	31.19(1.62-597.9)	0.02
rs17388568	IL2, ADAD1, IL21	chr4:122408207	G/A	NA	NA	0.26(0.12-0.53)	0.0002*	0.94(0.14-6.05)	0.95
rs1893217	PTPN2	chr18:12809341	A/G	2.79(1.36-5.73)	0.005	1.56(0.76-3.16)	0.21	6.95(1.06-45.26)	0.04
rs2111485	FAP, IFIH1	chr2:162254026	G/A	0.62(0.32-1.19)	0.15	0.96(0.49-1.87)	0.91	0.21(0.04-0.98)	0.04
rs2187668	HLA-DQA1	chr6:32638107	C/T	1.36(0.66-2.78)	0.39	2.14(1.06-4.31)	0.03	1.15(0.15-8.48)	0.88
rs2476601	PHTF1, PTPN22	chr1:113834946	G/A	3.17(1.02-9.85)	0.04	0.36(0.09-1.48)	0.16	1.52(0.11-21.01)	0.75
rs6679677	PHTF1, PTPN22	chr1:11376n86	C/A	2.95(1.14-7.60)	0.02	0.59(0.21-1.61)	0.30	1.52(0.11-21.01)	0.75

^aModels adjusted for age, sex and treatment drug (ipilimumab or tremelimumab; nivolumab or pembrolizumab)

Controls: ICI responders; Cases: ICI non-responders

NA refers to SNPs removed in QC step; the top three SNPs in each treatment cohort are bolded.

^*Asterisk indicates p-value surpassing the Bonferroni multiple testing adjustment (p<0.002).