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Joint distribution of allele frequencies as a function of the LD
| Alleles | aj | Aj | Allele frequency |
| ak | pjpk + Djk | (1 − pj) pk − Djk | pk |
| Ak | (1 − pk) pj − Djk | (1 − pj) (1 − pk) + Djk | 1 − pk |
| pj | 1 − pj | 1 |
aj and ak are the minor alleles of SNP j and SNP k, and Aj and Ak are their major alleles, respectively The MAFs of SNP j and SNP k are pj and pk, respectively. Djk is the LD parameter.
