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The criteria for searching for tSNPs were as follows: MAF (minor allele frequency) of CHB > 0.10, and a linkage disequilibrium value of r >0.8.
The linkage disequilibrium D' value suggests only a negligible level of recombination in the population studied.
Furthermore, positions 106 and 237 were in linkage disequilibrium (D' value of 0.766) [ 26, 27]).
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Figure 1a shows the pairwise linkage disequilibrium values observed in the control sample.
Figure 2 shows the positions of the 47 SNPs in the ESR1 gene that were genotyped in the ULSAM cohort and the linkage disequilibrium values between the SNPs.
Thus, relatively high linkage disequilibrium values (low K, H) reflect balanced trees (and scenarios) whereas low values reflect star scenarios (see [46], [51] for details and a graphical description).
Because approximately 2.8 Mb separates these markers, a distance far in excess of typical linkage disequilibrium values in the Indian population [23], we conclude that these two SNPs are not independently linked to a separate single causative mutation.
We also estimated linkage disequilibrium values D' and r2 [ 14, 15].
Average linkage disequilibrium values may further tell if the population is more rural or more metropolitan.
Linkage disequilibrium values (D′) and Hardy Weinberg equilibrium were tested with Haploview 4.0 software.
Incomplete linkage was found: the linkage disequilibrium values were 0.78 in D′ and 0.52 in r.
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