Table 2.
The most significantly associated SNPs (P<1×10−4 in the discovery phase) between CDH10 and CDH9 on 5p14.1
| SNP | Position* | Minor/ major allele* |
Discovery cohorts |
Replication cohorts |
P value (combined) |
||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| MAF† (AGRE) |
P value (AGRE) |
Z score‡ (AGRE) |
Case MAF (ACC) |
Control MAF (ACC) |
P value (ACC) |
Odds ratio§ (ACC) |
P value (discovery cohorts) |
P value (CAP) | P value (CART) | ||||
| rs4307059 | 26003460 | C/T | 0.38 | 1.1×10−5 | 4.40 | 0.35 | 0.39 | 2.2×10−4 | 1.19 | 3.4×10−8 | 1.2×10−2 | 1.6×10−2 | 2.1×10−10 |
| rs7704909 | 25934678 | C/T | 0.39 | 1.6×10−5 | 4.31 | 0.36 | 0.40 | 6.2×10−4 | 1.17 | 1.4×10−7 | 9.1×10−3 | 4.0×10−2 | 9.9×10−10 |
| rs12518194 | 25987318 | G/A | 0.39 | 1.3×10−5 | 4.36 | 0.36 | 0.39 | 1.0×10−3 | 1.16 | 2.0×10−7 | 9.3×10−3 | 1.8×10−2 | 1.1×10−9 |
| rs4327572 | 26008578 | T/C | 0.39 | 2.2×10−5 | 4.24 | 0.36 | 0.39 | 2.0×10−3 | 1.15 | 6.2×10−7 | 7.3×10−3 | 1.5×10−2 | 2.7×10−9 |
| rs1896731 | 25934777 | C/T | 0.34 | 1.7×10−3 | −3.14 | 0.38 | 0.34 | 1.7×10−3 | 0.87 | 1.7×10−5 | 7.7×10−5 | 9.9×10−1 | 4.8×10−8 |
| rs10038113 | 25938099 | C/T | 0.40 | 1.4×10−3 | −3.19 | 0.43 | 0.39 | 2.4×10−3 | 0.87 | 2.1×10−5 | 2.8×10−5 | 4.5×10−1 | 7.4×10−8 |
*
The chromosome coordinates and allele designation are on the basis of the forward strand of the NCBI 36 genome assembly.
†
The minor allele frequencies (MAF) are calculated on the basis of AGRE parents of European ancestry.
‡
Positive Z score indicates overtransmission of the major allele.
§
The odds ratio is calculated with respect to the major allele.