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(1) Background: The heritability of breast cancer is partly explained but much of the genetic contribution remains to be identified. Haplotypes are often used as markers of ethnicity as they are preserved through generations. We have previously demonstrated that haplotype analysis, in addition to standard SNP association studies, could give novel and more detailed information on genetic cancer susceptibility. (2) Methods: In order to examine the association of a SNP or a haplotype to breast cancer risk, we performed a genome wide haplotype association study, using sliding window analysis of window sizes 1-25 and 50 SNPs, in 3200 Swedish breast cancer cases and 5021 controls. (3) Results: We identified a novel breast cancer susceptibility locus in 8p21.1 (OR 2.08; p 3.92 × 10-8), confirmed three known loci in 10q26.13, 11q13.3, 16q12.1-2 and further identified novel subloci within these three loci. Altogether 76 risk SNPs, 3302 risk haplotypes of window size 2-25 and 113 risk haplotypes of window size 50 at p < 5 × 10-8 on chromosomes 8, 10, 11 and 16 were identified. In the known loci haplotype analysis reached an OR of 1.48 in overall breast cancer and in familial cases OR 1.68. (4) Conclusions: Analyzing haplotypes, rather than single variants, could detect novel susceptibility loci even in small study populations but the method requires a fairly homogenous study population.

Table S1: Association familial BC window size 1-25 Chr 1 Table S2: Association familial BC window size 1-25 Chr 2 Table S3: Association familial BC window size 1-25 Chr 3 Table S4: Association familial BC window size 1-25 Chr 4 Table S5: Association familial BC window size 1-25 Chr 5 Table S6: Association familial BC window size 1-25 Chr 6 Table S7: Association familial BC window size 1-25 Chr 7 Table S8: Association familial BC window size 1-25 Chr 8 Table S9: Association familial BC window size 1-25 Chr 9 Table S10: Association familial BC window size 1-25 Chr 10 Table S11: Association familial BC window size 1-25 Chr 11 Table S12: Association familial BC window size 1-25 Chr 12 Table S13: Association familial BC window size 1-25 Chr 13 Table S14: Association familial BC window size 1-25 Chr 14 Table S15: Association familial BC window size 1-25 Chr 15 Table S16: Association familial BC window size 1-25 Chr 16 Table S17: Association familial BC window size 1-25 Chr 17 Table S18: Association familial BC window size 1-25 Chr 18 Table S19: Association familial BC window size 1-25 Chr 19 Table S20: Association familial BC window size 1-25 Chr 20 Table S21: Association familial BC window size 1-25 Chr 21 Table S22: Association familial BC window size 1-25 Chr 22 Table S23: Association familial BC window size 1-25 Chr 23

Table S1: Association EC window size 1-25 Chr 1 Table S2: Association EC window size 1-25 Chr 2 Table S3: Association EC window size 1-25 Chr 3 Table S4: Association EC window size 1-25 Chr 4 Table S5: Association EC window size 1-25 Chr 5 Table S6: Association EC window size 1-25 Chr 6 Table S7: Association EC window size 1-25 Chr 7 Table S8: Association EC window size 1-25 Chr 8 Table S9: Association EC window size 1-25 Chr 9 Table S10: Association EC window size 1-25 Chr 10 Table S11: Association EC window size 1-25 Chr 11 Table S12: Association EC window size 1-25 Chr 12 Table S13: Association EC window size 1-25 Chr 13 Table S14: Association EC window size 1-25 Chr 14 Table S15: Association EC window size 1-25 Chr 15 Table S16: Association EC window size 1-25 Chr 16 Table S17: Association EC window size 1-25 Chr 17 Table S18: Association EC window size 1-25 Chr 18 Table S19: Association EC window size 1-25 Chr 19 Table S20: Association EC window size 1-25 Chr 20 Table S21: Association EC window size 1-25 Chr 21 Table S22: Association EC window size 1-25 Chr 22 Table S23: Association EC window size 1-25 Chr 23

Supplementary information (overview supplementary materials) Figure S1: MDS plot Figure S2: QQ plot Figure S3: Manhattan plot Table S1: Association BC all window size 1-25 Chr 8 Table S2: Association familial BC Chr 8 Table S3: Association BC all window size 1-25 Chr 10 Table S4: Association window size 50 Chr 10 Table S5: Association familial BC Chr 10 Table S6: Association BC all window size 1-25 Chr 11 Table S7: Association window size 50 Chr 11 Table S8: Association familial BC Chr 11 Table S9: Association BC all window size 1-25 Chr 16 Table S10: Association window size 50 Chr 16 Table S11: Association familial BC Chr 16 Table S12: Significant SNPs this study compare BCAC SNPs Table S13: Published BCAC SNPs compare SNPs this study