Genetic variations, including single nucleotide polymorphisms (SNP), variable numbers of repetitive sequences such as microsatellite polymorphisms, and small insertion-deletion polymorphisms (INDELs), have been reportedly associated with various diseases. SNP is just a single base change in a DNA sequence, with the usual alternative of two possible nucleotides at a given position. Microsatellite polymorphisms are variations in the number of short nucleotide repeats observed at microsatellite loci. INDELs are small insertions and deletions ranging from 1 to 10,000 bp in length. Another variation in the human genome is that of genomic structural variants, including copy number variations (CNVs). The CNVs involve gains or losses of several to hundreds of kilobases of genomic DNA among phenotypically normal individuals and at least 291,801 CNV regions have been identified. Recent studies have described the associations of CNVs with various common disorders, especially with mental illness. In order to make an extensive public catalog of human genetic variations, including SNPs and structural variants, and their haplotype contexts, the 1,000 Genomes Project has been performed with international collaboration using the genomes of about 2,500 unidentified people from about 25 populations around the world with next-generation sequencing technologies. This resource will support genome-wide association studies and other medical research studies. In this review, we focus on HapMap and the association between the various genetic variations and diseases.