Table 3.

Lead variants associated with COVID-19 phenotypes and replication in COVID-19hgi

Analysis:Ancestry:controls(:sex)a	CHR:POS:NEA:EA	rsid	EAF	OR	±95 CI	P value	Replication analysis	OR (P value)	Locus
Susceptibility:ALL:Population	3:45835417:G:A	rs73062389	0.058	1.2070	[1.15; 1.27]	4.26 × 10−15	C2	1.17 (1.08 × 10−54)	SLC6A20
Hospitalization:ALL:Population	3:45850783:T:A	rs72893671	0.081	1.4043	[1.28; 1.54]	5.12 × 10−13	B2	1.35 (6.95 × 10−51)	SLC6A20;LZTFL1
Severe:ALL:Population	3:45862952:T:C	rs71325088	0.073	1.6206	[1.38; 1.90]	2.25 × 10−9	A2	1.88 (9.89 × 10−46)	SLC6A20;LZTFL1
Susceptibility:ALL:Population	9:136145425:C:A	rs9411378	0.219	1.1013	[1.07; 1.13]	3.30 × 10−12	C2b	1.07 (1.08 × 10−38)	ABO
Death:ALL:Population	19:45411941:T:C	rs429358	0.154	1.3983	[1.24; 1.57]	3.06 × 10−8	A2	0.96 (0.27)	APOE
Ancestry-specific results
Susceptibility:nEUR:Population	10:78250184:T:C	rs114026383	0.016	2.3943	[1.79; 3.20]	4.10 × 10−9	C2c	1.05 (0.27)	LRMDA
Sex-specific results
Susceptibility:ALL:Population:F	2:192774154:G:A	rs147509469	0.037	1.2589	[1.16; 1.37]	2.64 × 10−8	C2	1.007 (0.58)	CAVIN2;TMEFF2

CHR, chromosome; POS, position (hg19 genome build); NEA, non effect allele; EA, effect allele; EAF, effect allele frequency; 95 CI, 95% confidence interval [lower bound; upper bound]; P: p value (from the last data release, analyzed on 06.18.21 for susceptibility and hospitalization, and 05.09.21 for severe and death phenotypes).

^aIndicate the ancestry by label, the control set, and, when it is the case, the corresponding sex-stratified analyses (F, females; M, males).

^bFor the replication of the ABO variant, rs9411378 was not available and the best proxy available rs635634 (LD r² = 0.53) was used instead.

^cFor the replication of the LRMDA variant, the C2 analysis restricted to AFR participants was used.