Allele C of rs3817198 in the 11p15 region (Figure 2) was reported8 to be associated with breast cancer with an allelic OR of 1.07 (P = 3 × 10−9 ). This study included about 21,860 cases and 22,578 controls allowing for such a modest effect to achieve genome-wide significance. A study9 of CGEMS (The Cancer Genetic Markers of Susceptibility Project) with 9,770 cases and 10,799 controls reported ORs of 1.02 and 1.12 for heterozygous and homozygous carriers of the same variant respectively. Using information in their supplementary material, we deduced a P of 0.06. Rs3817198 is not on the Illumina chips used to type the majority of the Icelandic samples, but is included on the 1M Illumina chips for which we have data on 124 trios. Single track assay was used to type another 90 trios, giving a total of 214 trios with genotypes for rs3817198 that translates to a training set of 856 haplotypes. Adapting the statistical model employed by IMPUTE10, allele probabilities of rs3817198 were calculated for individuals with phased and parental origin determined haplotypes for this region
