Supplementary Figure 4 : Relationship between association at classical HLA alleles and the frequency with which these alleles occur in non-ancestral MHC 8.1 haplotypes.

From: Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn's disease

Supplementary Figure 4

Linear regression demonstrating the relationship between the classical HLA alleles that were associated with prognosis and the frequency with which they occur in haplotypes other than the ancestral MHC 8.1 haplotype in Caucasians. Allele frequency and haplotype data were obtained from the National Bone Marrow Donor Program (Six-Locus High Resolution HLA ACBDRB3/4/5DRB1DQB1 Haplotype Frequencies). Data were not available for HLA-DQA1. In our data, the frequency with which the lead SNP (rs9279411) was associated with non-AH8.1 haplotypes was 0.0149, suggesting that rs9279411 is a better tag for AH8.1 than any of its constituent HLA alleles (and explaining the difference in P values between the HLA alleles and the SNP association).