As stated earlier, the HLA region at 6p21.32 is known for its complexity and extended LD ranging across multiple HLA and non-HLA genes in the region, and the HLA alleles may be captured by tag SNPs even outside the region.23 As the two most significant sets of variants with leading SNPs (rs4714329 at 6p21.2 and rs9268528 at 6p21.32) resided only approximately 8 Mb distance from each other, we investigated whether there would be LD between them. We also analyzed their haploblock structures, and which other SNPs would tag them in the data. Although the variants were strongly linked within the set, especially on the 6p21.32 loci, there was no LD between the two sets. Furthermore, they did not share same haploblocks, and no tagging was evident across the two sets (data not shown).
