Supplementary file 1
Participating centers.

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Supplementary file 2
Independent variants with p-value<1 × 10–05 in the SC-HGI_AMR GWAS meta-analysis (hg38).

EA: effect allele; NEA: non-effect allele; EAF: effect allele frequency; EAF_avg: averaged effect allele frequency; FreqSE: standard error of averaged effect allele frequency; SCOURGE_AMR: SCOURGE Latin-America; HGIB2_AMR: HGI meta-analysis of AMR studies.

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Supplementary file 3
Annotated SNPs in moderate-to-strong LD with lead SNPs of the genome-wide significant loci in the SC-HGI_AMR GWAS meta-analysis, with ANNOVAR.

NEA: non-effect allele; EA: effect allele; r2: maximum r2 of the SNP with one of the independent SNPs; IndSigSNP: the independent SNP which has the maximum r2 value with the SNP; dist: distance to the nearest gene; func: functional consequence of the SNP on the gene; CADD: CADD score; RDB: RegulomeDB score; minChrState: the minimum 15-core chromatin state across 127 tissues/cell types; commonChrState: the most common 15-core chromatin state across 127 tissues/cell types; posMapFilt: 1 if the SNP was used for positional mapping, 0 otherwise; eqtlMapFilt: 1 if the SNP was used for eQTL mapping, 0 otherwise.

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Supplementary file 4
Results from the MAGMA gene-based analysis in the SC-HGI_AMR GWAS meta-analysis (hg37).

NSNPS: number of SNPs in the gene; NPARAM: the number of relevant parameters used in the model; ZSTAT: z statistics.

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Supplementary file 5
Prioritized genes by eQTL and positional mapping by FUMA in the SC-HGI_AMR GWAS meta-analysis results (hg37).

HUGO: HGNC gene symbol; pLI: pLI score from ExAC database, probability of being intolerant to loss of function (higher the score, higher the intolerance); ncRVIS: non-coding residual variation intolerance score (higher the score, higher intolerance to non-coding variation); posMapSNPs: number of SNPs mapped by positional mapping; posMapMaxCADD: the maximum CADD score of mapped SNPs by positional mapping; eqtlMapSNPS: the number of SNPs mapped to the genes based on eQTL mapping; eqtlMapminP: the minimum eQTL p-value of mapped SNPs; eqtlMapminQ: the minimum eQTL FDR of mapped SNPs; eqtlMapts: tissue of mapped eQTLs; eqtlDirection: consequential direction of mapped eQTL SNPs after aligning the risk alleles; minGwasP: minimum GWAS p-value of mapped eQTLs; IndSigSNPs: independent SNPs that are in LD with the mapped SNPs.

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Supplementary file 6
Fine-mapped credible set derived with corrcoverage (95%) for the associated region in chromosome 2 (BAZ2B).

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Supplementary file 7
VEP annotations for the variants included in the fine-mapped credible sets for the novel associated loci in chromosome 2 (hg38).

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Supplementary file 8
V2G scores for the variants included in the fine-mapped credible sets in the novel risk loci from chromosomes 2 and 16 (hg38).

Shaded in green, the prioritized gene by the V2G score.

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Supplementary file 9
MultiXcan results for the SC-HGI_AMR GWAS meta-analysis.

N: number of tissues available for the gene; n_indep: number of independent components of variation kept among the tissues' predictions; p_i_best: best p-value of single tissue S-prediXcan association; t_i_best: name of best single tissue S-prediXcan association; p_i_worst: worst p-value of single tissue S-prediXcan association; t_i_worst: name of worst single tissue S-prediXcan association; eigen_max: eigenvalue of the top independent component in the SVD decomposition of predicted expression correlation; eigen_min: eigenvalue of the last independent component in the SVD decomposition of predicted expression correlation; eigen_min_kept: eigenvalue of the smallest independent component that was kept in the SVD decomposition of predicted expression correlation; z_min: minimum z-score among single-tissue S-prediXcan associations; z_max: maximum z-score among single-tissue S-prediXcan associations; z_mean: mean z-score among single tissue S-prediXcan associations; z_sd: standard deviation of the mean z-score among single-tissue S-prediXcan associations; tmi: trace of T*T', where T is the correlation of predicted expression levels for different tissues multiplied by its SVD pseudo-inverse and is an estimate for the number of independent components of variation in predicted expression across tissues.

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Supplementary file 10
Top 10 genes for the TWAS trained with the GALA II-SAGE models in admixed Americans.

Bonferroni correction thresholds: Pooled p<4.19E-06; PR p<4.99E-06; MX p<5.19E-06; AA p<4.67E-06. Var_g: variance of the gene expression; pred_perf_r2: cross-validated R2 of tissue model’s correlation to gene’s measured transcriptome; pref_perf_qval: qval of tissue model’s correlation to gene’s measured transcriptome; n_snps_used: number of snps from GWAS used in S-prediXcan analysis; n_snp_in_cov: number of snps in the covariance matrix; n_snps_in_model: number of snps in the model; best_gwas_p: the highest p-value from GWAS snps used in this model; largest_weight: the largest weight in this model.

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Supplementary file 11
Independent variants with p-value<1e-05 in the SC-HGI_ALL GWAS meta-analysis (hg38).

EA: effect allele; NEA: non-effect allele; EAF_avg: averaged effect allele frequency; FreqSE: standard error of averaged effect allele frequency.

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Supplementary file 12
Results of the 40 lead variants associated with COVID-19 hospitalization in the HGIv7 (hg38).

SC-HGI_ALL: meta-analysis SCOURGE-HGI_ALL; SC-HGI_AMR: meta-analysis SCOURGE-HGI_AMR; SC-HGI_3POP: meta-analysis SCOURGE-HGI_3POP.

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Supplementary file 13
Independent variants with p-value<1e-05 in the SC-HGI_3POP GWAS meta-analysis (hg38).

EA: effect allele; NEA: non-effect allele; EAF_avg: average effect allele frequency; FreqSE: standard error of averaged effect allele frequency.

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Supplementary file 14
Instruments used in the polygenic risk score model (hg38).

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Supplementary file 15
Multinomial regression results.

Reference class for the multinomial regression is ‘asymptomatic’.

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MDAR checklist
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