Haplotype analyses methods: SNPs genotyped in Stage I in a region of ∼100kb containing rs2046210 were used to reconstruct haplotypes. LD between SNPs was assessed by Haploview26. Haplotype blocks were defined using the methods of Gabriel et al16 and 9 blocks were observed (Supplementary Figure S3). Block 5 includes rs2046210 and seven other SNPs, rs7740686, rs7763637, rs9397436, rs9397437, rs6908732, rs852004, and rs865898 (Supplementary Table S4). Associations of haplotypes with breast cancer risk were analyzed with HAPSTAT software27 based on additive models. Additional analyses were performed for haplotypes defined using SNPs included in blocks 4 and 5 with a total of 15 SNPs (Supplementary Figure S3, Supplementary Table S4).
