Table 5.

Main SNPs previously associated at GWAS-p value significant with natural HIV control, HIV disease progression, or viral load set point in Caucasian populations that has been analyzed in our study

CHR	Linked Gene	SNP	Allele	Reported effect	Reference	P	p (R)	OR	OR (R)	Q	I	ICSC p; OR (95%CI)	SHCS p; OR (95%CI)
6	HLA-C	rs9264942	C	Protective	Fellay et al., International HIV Controllers Study, et al.6,7,10	0.089	0.826	1.24	1.07	0.060	71.52	0.020; 1.38 (1.05–1.83)	0.317; 0.73(0.40–1.34)
6	HCP5	rs2395029	G	Protective	Dalmasso et al.; Fellay et al.; Le Clerc et al.; Limou et al.; International HIV Controllers Study et al.; Guergnon et al.5,6,7,8,9,10,11	0.005	0.005	1.70	1.70	0.561	0	0.006; 1.81 (1.18–2.77)	0.442; 1.37(0.60–3.22)
6	MICA	rs112243036	A	Protective	Le Clerc et al.23	0.011	0.011	1.45	1.45	0.582	0	0.012; 1.52 (1.09–2.11)	0.515; 1.24 (0.64–2.38)
6	TRIM10	rs9468692	T	Not Known	Fellay et al.6	0.883	0.883	0.96	0.96	0.427	0	0.584; 0.84 (0.47–1.52)	0.553; 1.32 (0.47–3.35)
6	HLA-B	rs9266409	C	Protective	Fellay et al.6	0.051	0.051	1.33	1.33	0.719	0	0.124; 1.29 (0.93–1.80)	0.211; 1.49 (0.80–2.69)
6	PSORS1C3	rs3131018	A	Protective	International HIV Controllers Study et al.10	0.898	0.898	0.98	0.98	0.693	0	0.763; 0.94 (0.67–1.34)	0.776; 1.09(0.58–2.05)
6	PSORS1C1	rs3815087	T	Protective	Limou et al.9	0.017	0.017	1.39	1.39	0.316	0,55	0.091; 1.29 (0.95–1.76)	0.051; 1.84 (0.99–3.40)
6	ZNRD1	rs9261174	C	Not Known	Fellay et al.6	0.761	0.761	1.06	1.06	0.960	0	0.796; 1.05 (0.71–1.54)	0.867; 1.08 (0.44–2.61)
6	RNF39	rs2074480	G	Not Known	Fellay et al.6	0.760	0.760	1.06	1.06	0.960	0	0.795; 1.05 (0.71–1.54)	0.867; 1.08 (0.44–2.61)
6	RNF39	rs2301753	T	Not Known	Fellay et al.6	0.760	0.760	1.06	1.06	0.960	0	0.795; 1.05 (0.71–1.54)	0.867; 1.08 (0.44–2.61)
6	ZNRD1	rs9261129	C	Not Known	Fellay et al.6	0.760	0.760	1.06	1.06	0.960	0	0.795; 1.05 (0.71–1.54)	0.867; 1.07 (0.45–2.61)
3	CXCR6	rs2234358	T	Non Protective	Limou et al.24	0.188	0.188	0.84	0.84	0.330	0	0.470; 0.89 (0.65–1.99)	0.142; 0.66 (0.38–1.15)
6	HLA-B	rs59440261	A	Protective	McLearn et al.25	0.003	0.003	1.78	1.78	0.657	0	0.005; 1.87 (1.21–2.90)	0.305; 1.52 (0.68–3.92)
3	CCRL2	rs1015164	A	Protective	McLearn et al.25	0.516	0.516	0.91	0.91	0.618	0	0.422; 0.89 (0.67–1.20)	0.866; 1.05 (0.55–2.00)

CHR. Chromosome; SNP. Single Nucleotide Polymorphism; A1. Reference allele (minor allele); P. Fixed-effects p value; P(R): Random-effects p value; OR. Fixed-effects Odds Ratio (for being LTNP-C); SHCS. Swiss HIV Cohort Study; ICSC. International HIV controllers Study Cohort; Q: p value for heterogeneity of OR; I. effect size for heterogeneity of OR; OR(R); Random-effects Odds ratio; CI, Confidence interval. Common SNPs found significant in our dataset are shown in bold. Gene names are shown in italics.