Table 4.
Top SNPs from Ordinal Analysis
| SNP | Chr | Genea | Alleles | Discovery (n=855) |
European Replication (n=154)d |
African American Replication (n=117)d |
||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MAFb | OR (95% CI) |
Pc | MAF | OR (95% CI) |
P | MAF | OR (95% CI) |
P | ||||
| rs7001034e | 8 | FZD3 | G/T | 0.40 | 0.57 (0.48–0.69) |
3.1 ×10−9 | ||||||
| rs7833751f | 8 | FZD3 | G/T | 0.40 | 0.58 (0.49–0.70) |
7.5 × 10−9 | 0.41 | 1.67f (0.88–3.19) |
0.058 | |||
| rs5934683 | X | /SHROOM2 | C/T | 0.36 | 1.61 (1.33–1.93) |
6.0 × 10−7 | 0.33 | 0.99g (0.54–1.82) |
0.49 | 0.30 | 1.96g (0.49–7.89) |
0.17 |
| rs2941627 | 8 | /ZFPM2 | A/G | 0.13 | 1.91 (1.40–2.51) |
3.5 × 10−6 | 0.15 | 1.37g (0.68–2.73) |
0.19 | 0.25 | 0.49g (0.24–0.97) |
0.021 |
| rs7973533 | 12 | /BCAT1 | T/G | 0.46 | 0.66 (0.55–0.79) |
8.4 × 10−6 | 0.44 | 0.75 (0.47–1.19) |
0.11 | 0.27 | 1.13 (0.65–1.94) |
0.33 |
a
Intergenic SNPs are denoted by the closest flanking annotated gene.
b
Minor allele frequency (MAF) was calculated within the indicated cohort.
c
P-values are two-sided for discovery analysis and one-sided for replication.
d
As stated in the replication plan, all analyses were exploratory except for the FZD3 SNP.
e
There was no available TaqMan assay for rs7001034 to use in replication studies.
f
This SNP tags rs7001034 in the European population but not in the African American population.
g
Analysis assumed a dominant model.