SNPs with a broad range of phenotypes. Due to the large number of possible SNP variants (more than 149 million as of June 2015 ) it is still very expensive to sequence all SNPs. That is why GWAS use customizable arrays (SNP chips) to genotype only a subset of the variants identified as tag snps. Most GWAS use products from the two primary genotyping platforms. The Affymetrix platform prints DNA probes on a glass or silicone chip that hybridize to specific alleles in the sample DNA. The Illumina platform uses bead-based technology, with longer DNA sequences and produces better specificity. Both platforms are able to genotype more than a million tag SNPs using either pre-made or custom DNA oligos. Genome-wide studies are predicated on the common disease-common variant (CD/CV) hypothesis which states that common disorders are influenced by common genetic variation. Effect size (penetrance) of the common variants needs to be smaller relative to those found in rare disorders. That means that the common SNP can explain only a small portion of the variance due to genetic factors and that common diseases are influenced by multiple common alleles of small effect size. Another hypothesis is that common diseases are caused by rare variants that are synthetically linked to common variants. In that case the signal produced from GWAS is an indirect (synthetic) association between one or more rare causal variants in linkage disequilibrium. It is important to recognize that this phenomenon is possible when selecting a group for tag SNPs. When a disease is found to be associated with a haplotype, some SNPs in that haplotype will have synthetic association with the disease. To pinpoint the causal SNPs we need a greater resolution in the selection of haplotype blocks. Since whole genome sequencing technologies are rapidly changing and becoming less expensive it is likely that they will replace the current genotyping technologies providing the resolution needed to pinpoint causal variants. HapMap Because whole genome sequencing of individuals is still cost prohibitive, the international HapMap Project was constructed with a goal to map the human genome to haplotype groupings (haplotype blocks) that can describe common patterns of human genetic variation. By mapping the entire genome to haplotypes, tag SNPs can be identified to represent the haplotype blocks examined by genetic studies. An important factor to consider when planning a genetic study is the frequency and risk incurred by specific alleles. These