In the present study, HLA complex variations within populations have been established thoroughly based on allele frequency distributions. In addition, genetic diversity of populations has been subjected based on nucleotide diversity of HLA alleles on different loci by the present study and accordingly were tried to tracking our target population among Indian populations, neighbour Muslims countries and different geographical areas. Further analysis has been conducted to achieve a general outlook through HLA-A, -B, -C, -DQB1 genes based on phylogenetic and evolutionary point of view. The present study identified 42 HLA class II (DQB1) alleles in Muslim population of Srirangapatna area. Two alleles have been detected in the population with homologous equivalents without nucleotide substitutions (i.e. DQB1*03:01:02 and DQB1*03:23:01) and ten alleles (22.2%) comprised not only one or two nucleotide variations also lead to amino acid sequence alteration when compared to their most homologous neighbour alleles in IMGT Database.
