Table 3.
Haplotype analysis.
| Haplotype | Non-Hispanic whites (n = 2,883) | African-Americans (n = 254) | ||||
|---|---|---|---|---|---|---|
| Haplotype frequency | βa (95% CI), pooled samplee | P-value, pooled samplee | Haplotype frequency | βa (95% CI), pooled samplee | P-value, pooled samplee | |
| CHROMOSOME 4 (GC): rs1526692, rs6837549, rs2201124, rs705120, rs4588, rs1155563 | ||||||
| AAGCCAa | 0.43 | 0.0 | 0.17 | 0.0 | ||
| GCAAAGb | 0.21 | −3.9 (−4.6, −3.2) | 9.8 × 10−30 | 0.05 | 2.7 (−1.8, 7.1) | 0.24 |
| ACGACAc | 0.07 | −1.0 (−2.0, 0.0) | 0.05 | 0.10 | 1.1 (−2.5, 4.7) | 0.54 |
| GCACCAa | 0.07 | −0.7 (−1.7, 0.3) | 0.17 | 0.09 | 4.6 (1.2, 8.0) | 8.5 × 10−3 |
| GCGACAc | 0.07 | −1.3 (−2.4, −0.3) | 0.01 | 0.12 | 2.1 (−1.2, 5.5) | 0.21 |
| AAGAAGb | 0.03 | −4.6 (−6.2, −3.1) | 3.2 × 10−9 | – | – | – |
| ACGCCAa | 0.03 | −0.7 (−2.4, 0.9) | 0.40 | 0.16 | −1.0 (−5.2, 2.1) | 0.52 |
| GAGCCAa | – | – | – | 0.10 | −1.4 (−5.1, 2.3) | 0.47 |
| GAGACAc | – | – | – | 0.06 | −1.9 (−6.5, 2.7) | 0.43 |
| AAGACAc | – | – | – | 0.04 | 1.0 (−4.9, 6.9) | 0.74 |
| Rare pooledd | 0.08 | −2.3 (−3.3, −1.3) | 5.4 × 10−6 | 0.11 | −1.9 (−5.2, 1.4) | 0.26 |
| CHROMOSOME 11 (CYP2R1): rs11023203, rs11023227, rs10766188, rs1993116, rs12794714 | ||||||
| GAAAG | 0.34 | 0.0 | 0.26 | 0.0 | ||
| AGGGA | 0.26 | −2.1 (−2.8, −1.5) | 6.1 × 10−10 | 0.09 | −2.4 (−5.8, 1.0) | 0.17 |
| GAAGG | 0.15 | −0.7 (−1.5, 0.1) | 0.07 | 0.53 | −1.8 (−7.2, 3.7) | 0.53 |
| GAAGA | 0.06 | −1.4 (−2.5, −0.2) | 0.02 | 0.03 | −1.6 (−3.9, 0.6) | 0.15 |
| GGGGA | 0.05 | −2.0 (−3.2, −0.8) | 1.5 × 10−3 | – | – | – |
| GAGGA | 0.03 | −1.8 (−3.3, −0.3) | 0.02 | – | – | – |
| AGAGA | 0.03 | −2.9 (−4.6, −1.3) | 4.0 × 10−4 | – | – | – |
| Rare pooledd | 0.08 | −1.0 (−2.1, 0.0) | 0.05 | 0.11 | −0.8 (−3.9, 2.2) | 0.59 |
All models adjusted for age at blood draw, estimated ancestry proportions, and breast cancer case status.
Corresponds to the “Gc1s” vitamin D binding protein variant in Non-Hispanic whites (based on genotypes for rs705120 and rs4588).
Corresponds to the “Gc2” vitamin D binding protein variant in Non-Hispanic whites (based on genotypes for rs705120 and rs4588).
Corresponds to the “Gc1f” vitamin D binding protein variant in Non-Hispanic whites (based on genotypes for rs705120 and rs4588).
Rare haplotypes (frequency < 2%) pooled together.
Change in 25(OH)D (in ng/mL) per copy of the index haplotype relative to the most common haplotype (“AAGCCA” for chromosome 4, “GAAAG” for chromosome 11), controlling for all other haplotypes.
Bold values indicate SNP with lowest independently measured p-value (based on pooled sample).