We also compared the minor allele frequencies (MAFs) of these variants in our cases, as well as their controls from the HapMap-CEU population (http://www.ncbi.nlm.nih.gov/SNP/) (Supplementary Table 4). The MAFs for all these eight SNPs were relatively consistent between the population controls of GWAS and of replication samples. When looking the genetic variation at these chromosomal regions more widely, the MAFs for the variants on 6p21.2 were well in line with the HapMap-CEU. The MAFs of the variants near the HLA-DRA gene, on 6p21.32, were considerably lower in both of the GWAS and replication population controls as compared with the HapMap-CEU. This is likely to reflect the genetically complicated nature of that particular chromosomal region with widely extending structures of LD and with high variation in different populations.
