Table 1.

Independently associated amino acid positions in HLA proteins identified by stepwise forward conditional analysis

Step	Position	Alleles*	Position P†	Model P‡	Cumulative variance explained§
1	HLA-B 97	V/N/W/T/R/S	4.6 x 10−143	na	0.102
2	HLA-B 67	Y/F/S/C/M	3.7 x 10−112	3.2 x 10−15	0.112
3	HLA-B 45	E/T/K/M	8.2 x 10−49	1.8 x 10−4	0.114
4	HLA-A 77	N/S/D	1.8 x 10−12	9.4 x 10−12	0.122
5	HLA-A 95	L/I/V	3.6 x 10−5	3.2 x 10−7	0.123

na, not applicable.

^*Per allele association statistics and frequencies are listed in SI Appendix, Table S4.

^†Position P values were calculated by a multi–degree-of-freedom omnibus test, including covariates and all alleles at that position.

^‡Model P values were calculated by the likelihood ratio test comparing the model from the previous step to a model including the next position.

^§Cumulative variance explained was calculated by linear regression and represents the variance explained by including the positions identified at each step to the model from the previous step.