In this study, we report a novel SNP, rs2046211, that is associated with breast cancer risk in African–American women. The signal tagged by rs2046211 seems to be a different one from the signal tagged by rs2046210, which was initially identified in Chinese women (1
). In our analyses, the association with rs2046210 was statistically significant only after adjusting for rs2046211, which may explain the previously failed efforts to replicate rs2046210 association with breast cancer in African ancestry populations (2
). The present results also help to narrow the position of the causal variants tagged by rs2046210 and rs2046211 because both SNPs are located in a smaller LD block of about 15kb in HapMap YRI samples.
Interestingly, in genome-wide association study, data from the Women’s Health Initiative African American SHARe Study, the OR for the G-allele of rs2046211 was 0.91 (95% CI = 0.71–1.18) (supplementary data in (6
)). Meta-analysis of our estimates (BWHS + WCHS) with the Women’s Health Initiative estimates resulted in an overall breast cancer risk of 0.86 (95% CI = 0.75–0.97), P
= 0.02 for the G-allele of rs2046211.
The high-risk rs2046210 A-allele is more frequent in African ancestry populations (e.g. 69% in HapMap YRI, 61% in the BWHS) as compared with east Asian ancestry populations (e.g. 38% in HapMap CHB) or European ancestry populations (e.g. 29% in HapMap CEU). This difference in allele frequencies suggests that in African ancestry populations, the rs2046210-A allele may consist of different haplotypes, with different risk associations. Our results show that in African Americans, the rs2046210-A allele was present in both a high-risk haplotype (i.e. the CA haplotype) and a low-risk haplotype (i.e. the GA haplotype) composed of a second SNP rs2046211 newly found in our analyses. Previous replication efforts may have failed because they were only measuring the marginal effect of the rs2046210-A allele, which would be attenuated in an African ancestry population without considering the neighboring rs2046211. It is noteworthy that the frequency of the G-allele of rs2046211 is as low as 2% in HapMap CHB population as compared with 15% in HapMap YRI population and 10% in this study, suggesting that in east Asian populations the low-risk haplotype is either absent or in low frequency. The rs2046210-A allele in east Asian populations would consist, mostly, of the high-risk haplotype.
Our present results shed light on the findings of previous genotyping efforts in the 6q25.1 region. Stacey et al
). conducted extensive genotyping in the 6q25.1 region and identified several SNPs associated with breast cancer in east Asian, European, Nigerian and African–American women. In particular, they reported a significant association between rs9397435 (minor allele frequency = 32.6% in east Asian women, 6.3% in European women and 6.3% in Nigerian and African–American women) and breast cancer risk in the three different ancestries. Rs9397435 is highly correlated (r
= 0.72, D′ = 1.00) with rs2046210 in the HapMap CHB population. The fact that Stacey et al.
). reported similar ORs for both SNPs in east Asian women (OR = 1.23 for rs9397435 and OR = 1.24 for rs2046210) suggests that both SNPs are tagging the same causal variant in east Asian populations. Although not significant, we found rs9397435 to have an OR in the same direction as that reported by Stacey et al.
in African ancestry women (OR = 1.17 in the BWHS and OR = 1.35 in Stacey et al.
)). It is noteworthy that the G-allele of rs9397435 (i.e. the high-risk allele reported by Stacey et al.
) is in complete LD with the high-risk CA haplotype we report in this study. The fact that the association between the high-risk CA haplotype and breast cancer risk was not modified by the presence of the rs9397435-G allele suggests that the association reported by Stacey et al.
in African ancestry women is probably due to the complete LD with the high-risk CA haplotype. Insufficient power may explain the failure to find a significant association of rs9397435 by itself in the BWHS. The G-allele of rs9397435 has a frequency of 7.6% in the BWHS, and the high-risk CA haplotype has frequency of 50% in the BWHS. This means that rs9397435 G-allele is just a subhaplotype of the high-risk CA haplotype. The power to detect an OR of 1.14 (i.e. the OR of the high-risk CA haplotype) in a subhaplotype of 7.6% frequency (i.e. the GCA subhaplotype) is only 31%.
In functional studies of the region between the C6orf97
genes, Cai et al.
) identified two candidate functional SNPs. Rs6913578 and rs7763637 are in high LD with rs2046210 in Chinese and European ancestry populations but not in African ancestry populations. These two SNPs were associated with breast cancer risk in both Chinese women and European ancestry Americans, and the associations were stronger than with rs2046210 in European ancestry Americans. The SNPs were not associated with breast cancer risk in African Americans; however, the per-allele ORs approached statistical significance after control for rs2046210. Although we did not genotype either of these two SNPs, which are in perfect LD (r
= 1.00) in HapMap YRI population, we genotyped the proxy rs3757322 (r
= 0.96). Although rs3757322 was not significantly associated with breast cancer risk by itself, we found that in the presence of the high-risk CA haplotype, the G-allele of rs3757322 is indeed associated with higher risk of breast cancer. Our results show that the associations reported by Cai et al.
) in African–American women are most probably due to the high-risk CA haplotype, as shown by the high LD between rs3757322 and the high-risk CA haplotype and the absence of independent effect of rs3757322 after conditioning for the high-risk CA haplotype.
In summary, the results provide evidence of a second signal, tagged by rs2046211, in the 6q25.1 region that is independent of rs2046210 previously reported in east Asian women. Haplotype analysis of rs2046211 and rs2046210 showed that the latter is indeed associated with breast cancer risk in African–American women after adjusting for the haplotype background that included rs2046211.