Table 2.
Details of 22 SNPs used in the replication phase including rank based on the most significant P-value from the discovery phase
| Rank | SNP | Chra | Bpb | Discovery—5 samples | Pd | Directione (A-K-F-OT-M) | Replication—10 samples |
Direction (B-CK-CS-CV-D-E-O-R1-R2-R3) | Meta-analysis |
||
|---|---|---|---|---|---|---|---|---|---|---|---|
| β (95% CI)c | β (95% CI) | P | β (95% CI) | P | |||||||
| 7 | rs1343654 | 2 | 11005484 | 0.22 (0.137, 0.303) | 1.81 × 10−7 | +++?+ | 0.028 (−0.015,0.07) | 2.04 × 10−1 | +−+++−++++ | 0.069 (0.0314, 0.107) | 5.68 × 10−5 |
| 20 | rs13094898 | 3 | 58290143 | −0.232 (−0.333, −0.131) | 6.78 × 10−6 | −−−−− | −0.063 (−0.132, 0.006) | 7.46 × 10−2 | −−−−+−−−−+ | −0.121 (−0.177,−0.065) | 6.63 × 10−5 |
| 14 | rs11715445 | 3 | 58343887 | 0.243 (0.14, 0.345) | 3.20 × 10−6 | +++++ | 0.066 (−0.003, 0.135) | 6.31 × 10−2 | ++++−+++++ | 0.125 (0.068, 0.181) | 5.95 × 10−5 |
| 21 | rs10018930 | 4 | 111029634 | −0.173 (−0.249, −0.097) | 7.50 × 10−6 | −−−−− | −0.035 (−0.084, 0.013) | 1.60 × 10−1 | +++−−+−−−+ | −0.075 (−0.115,−0.034) | 3.28 × 10−4 |
| 22 | rs10033229 | 4 | 111030074 | 0.172 (0.096, 0.247) | 8.31 × 10−6 | +++++ | 0.034 (−0.015, 0.083) | 1.68 × 10−1 | −−−++−+++− | 0.076 (0.035, 0.112) | 2.64 × 10−4 |
| 10 | rs13178105 | 5 | 78268128 | −0.247 (−0.347, −0.146) | 1.59 × 10−6 | −−−?− | −0.05 (−0.106,0.006) | 7.93 × 10−2 | +−−−+−−−−− | −0.097 (−0.146,−0.048) | 3.07 × 10−4 |
| 18 | rs583456 | 6 | 24948279 | 0.194 (0.111, 0.277) | 4.65 × 10−6 | +++++ | 0.036 (−0.012, 0.084) | 1.46 × 10−1 | −+++++++−0 | 0.077 (0.036, 0.118) | 7.48 × 10−4 |
| 13 | rs9490548 | 6 | 123090476 | −1.394 (−1.977, −0.811) | 2.75 × 10−6 | ??−?− | 0.011 (−0.33, 0.349) | 9.51 × 10−1 | ????−+?−+− | −0.355 (−0.645, −0.064) | 6.37 × 10−3 |
| 5 | rs7912000 | 10 | 45161041 | −0.289 (−0.396, −0.181) | 1.30 × 10−7 | −−−−− | 0.028 (−0.045, 0.1) | 4.51 × 10−1 | −−−+++−+−+ | −0.077 (−0.137,−0.018) | 2.13 × 10−3 |
| 3 | rs12266496 | 10 | 45169414 | 0.281 (0.180, 0.382) | 4.55 × 10−8 | +++++ | −0.031 (−0.093, 0.031) | 3.33 × 10−1 | −++−−−+−+− | 0.042 (−0.007,0.091) | 1.30 × 10−3 |
| 4 | rs7897547 | 10 | 45177653 | −0.288 (−0.392, −0.184) | 5.18 × 10−8 | −−−−− | 0.025 (−0.045, 0.094) | 4.87 × 10−1 | −−−+++−+−+ | −0.078 (−0.135, −0.021) | 1.30 × 10−3 |
| 2 | rs12771080 | 10 | 45181333 | −0.293 (−0.397, −0.189) | 3.33 × 10−8 | −−−−− | 0.028 (−0.042, 0.097) | 4.37 × 10−1 | −−−+++−+−+ | −0.077 (−0.134,−0.02) | 1.44 × 10−3 |
| 1 | rs12571148 | 10 | 45186816 | 0.298 (0.194, 0.402) | 2.01 × 10−8 | +++++ | −0.024 (−0.093, 0.046) | 5.02 × 10−1 | +++−−−+−+− | 0.081 (0.024, 0.138) | 8.98 × 10−4 |
| 19 | rs10771293 | 12 | 26843918 | −0.149 (−0.213, −0.085) | 5.61 × 10−6 | −−−−− | −0.012 (−0.052, 0.028) | 5.59 × 10−1 | −+−−+−++−− | −0.053 (−0.087,−0.019) | 1.02 × 10−3 |
| 12 | rs1570142 | 14 | 94856261 | −0.16 (−0.226, −0.093) | 2.51 × 10−6 | −−−−− | −0.006 (−0.048, 0.036) | 7.73 × 10−1 | −++−++−−−0 | −0.051 (−0.0866, −0.016) | 2.84 × 10−3 |
| 11 | rs7154685 | 14 | 94867604 | −0.16 (−0.225, −0.094) | 1.82 × 10−6 | −−−−− | −0.002 (−0.042, 0.038) | 9.14 × 10−1 | −++−−++−−+ | −0.047 (−0.08,−0.013) | 4.14 × 10−3 |
| 16 | rs1956704 | 14 | 94870584 | 0.154 (0.088, 0.219) | 3.97 × 10−6 | +++++ | 0 (−0.04, 0.04) | 9.85 × 10−1 | +−−++−−++− | 0.044 (0.01, 0.078) | 5.97 × 10−3 |
| 8 | rs4776318 | 15 | 67074656 | −0.169 (−0.238, −0.101) | 1.16 × 10−6 | −−−−− | −0.028 (−0.07, 0.014) | 1.95 × 10−1 | −−++−−+−−− | −0.069 (−0.104,−0.0334) | 1.75 × 10−4 |
| 15 | rs8025869 | 15 | 67084685 | 0.159 (0.092, 0.227) | 3.61 × 10−6 | +++++ | 0.024 (−0.016, 0.063) | 2.48 × 10−1 | ++−−++−−++ | 0.061 (0.027, 0.096) | 6.83 × 10−4 |
| 6 | rs4581716 | 16 | 7458135 | 0.185 (0.116, 0.255) | 1.79 × 10−7 | +++++ | 0.06 (0.015, 0.104) | 9.00 × 10−3 | −+++++++++ | 0.098 (0.061, 0.136) | 1.64 × 10−7 |
| 17 | rs10500355 | 16 | 7459347 | −0.162 (−0.23, −0.093) | 4.13 × 10−6 | −−−−− | −0.089 (−0.131,−0.044) | 7.34 × 10−5 | −−−+−−−−−− | −0.111 (−0.147,−0.074) | 3.92 × 10−9 |
| 9 | rs8109324 | 19 | 53238740 | 0.184 (0.109, 0.259) | 1.54 × 10−6 | +++++ | −0.01 (−0.056, 0.036) | 6.74 × 10−1 | −−+++−−++− | 0.045 (0.0066, 0.084) | 6.06 × 10−3 |
Studies are listed in order at the top of the Direction columns as AREDS (A), KORA (K), FES (F), OGP-Talana (OT), MESA (M) in the discovery set and BMES (B), Croatia-Korcula (CK), Croatia-Split (CS), Croatia-Vis (CV), DCCT (D), ERF (E), ORCADES(O), RS1 (R1), RS2 (R2), RS3 (R3) in the replication set.
aChr—chromosome location of SNP.
bBP—base pair position of SNP.
cβ (95% CI)—estimate of the effect size of the tested allele and its 95% confidence interval.
dP—significance level of the association test of MSE with this SNP.
dDirection—direction of effect of the tested allele (+ = protective, − = risk, 0 = no effect, ? = no data) in each sample.