Two-SNP results for KA population on chromosome 9 (top) and DA population on chromosome 1 (bottom). HST p-values are below the diagonal; TRANSMIT p-values are above; estimated minor allele frequencies are on the left margin. The square identified by "i" represents the ith most significant (by both HST and TRANSMIT) SNP pair ranked by the sum of the TRANSMIT and HST p-values. For example, in the top panel, "3" (in the first row) means that HST and TRANSMIT p-values for pair B8321–B8341 are both significant and the sum of their p-values is the third most significant. Hj and Tj represent the jth significant SNP pair by HST and TRANSMIT, respectively. Note, on the top panel, "2"-H2, "3"-H3 coincide; only "2" and "3" are identified. Similarly for the bottom panel, "4"-T5, "6"-H4 coincide and only "4" and "6" are identified.