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The first model in simulations based on empirical data: 2 tagSNPs display strong LD with the unscored causal locus. TagSNPs 3 and 5 are genotyped and SNP 12 is the unscored functional locus. Haplotype 11 by SNPs 3 and 5 perfectly tagsSNP 12. The haplotype frequencies are estimated from 23 Americans of European descend in the PGA database
| Haplotype/SNP | 3 | 5 | 12 | Haplotype frequency |
| 1 | 0 | 0 | 0 | 0.847 |
| 2 | 0 | 1 | 0 | 0.087 |
| 3 | 1 | 0 | 0 | 0.022 |
| 4 | 1 | 1 | 1 | 0.044 |
