Table 3.

Gene variants associated with HIV-1C infection

Cohort	CHR	SNP	Coordinates	Allele (minor)	Test	NMISS	OR	STAT	P value	Gene	Distance	RR	AR	EF
WGS	5	rs572880838	77590422	G	ALLELIC	333	6.711	5.78	7.62E-09	AP3B1	0	1.210	0.074	0.029
	5	rs572880838	77590422	G	DOM	333	6.711	5.78	7.62E-09	AP3B1	0	NaN	NaN	NaN
	20	rs6076463	3012815	T	ALLELIC	336	0.172	−4.93	8.33E-07	PTPRA	0	0.564	−0.029	0.030
	20	rs6076463	3012815	T	DOM	336	0.172	−4.93	8.33E-07	PTPRA	0	NaN	NaN	NaN
	20	rs3787480	3016895	A	ALLELIC	336	0.179	−4.59	4.46E-06	PTPRA	0	0.573	−0.025	0.025
	20	rs3787480	3016895	A	DOM	336	0.179	−4.59	4.46E-06	PTPRA	0	NaN	NaN	NaN
MA	15	rs9920504	73284181	C	ALLELIC	422	0.465	−4.41	1.03E-05	NEO1	59870	0.648	−0.102	0.018
	15	rs7172316	73287152	G	ALLELIC	430	0.470	−4.39	1.14E-05	NEO1	56899	0.654	−0.100	0.017
	15	rs9920504	73284181	C	DOM	422	0.437	−4.06	4.94E-05	NEO1	59870	0.398	−0.040	0.015
	15	rs7172316	73287152	G	DOM	430	0.445	−4.01	6.05E-05	NEO1	56899	0.395	−0.039	0.015

AR, attributable risk; EF, explained fraction; Distance, distance to the closest gene (see column Gene); NaN, not a valid number; NMISS, number of nonmissing individuals included; RR, relative risk; STAT, coefficient t-statistic.