Table 2.

Classical HLA alleles

SNP	Allele frequency	Beta	SE	p-value
B_801	0.143	4.3 × 10 –4	9.4 × 10 –5	3.9 × 10 –6
DRB1_301	0.147	3.7 × 10 –4	9.2 × 10 –5	5.6 × 10 –5
DRB3_9901	0.655	−2.6 × 10–4	6.9 × 10–5	1.5 × 10–4
DRB3_101	0.166	3.3 × 10 –4	8.8 × 10 –5	2.0 × 10 –4
DQA1_501	0.230	2.9 × 10 –4	7.8 × 10 –5	2.1 × 10 –4
C_701	0.175	3.2 × 10 –4	8.6 × 10 –5	2.4 × 10 –4
DQB1_201	0.148	3.4 × 10 –4	9.2 × 10 –5	2.7 × 10 –4

The table shows the allele frequencies, beta, standard error and p values of all classical HLA alleles with a p value below 5 × 10^–4 [computed through Bolt-LMM] and MAF > 0.01. SNPs in bold are part of the HLA A1-B8-DR3-DQ2 [ancestral MHC 8.1] haplotype.