Associations between 4-digit HLA Class I alleles and HIV-1 set point in a subset of 1,204 subjects with full results.

P-values are shown for all Class I alleles that have a nominally significant association with HIV-1 viral load at set point (with the exception of B*5701, discussed in the text). All linear regression models include gender, age and the 12 Eigenstrat axes as covariates. Most of the association signals disappear once the top associated SNPs are added. However, A*3201, B*1302, B*2705 and B*3502 still have an independent effect. See Table S4 for a complete list of all HLA Class I allele results. In addition, Table S5 lists all pairs of HLA-B and HLA-C alleles that are in LD (with an r2>0.1) and therefore can represent the same association signal (as for example in the case of HLA-C*0602, which is often on the same haplotype as HLA-B*5701).