Table 2. Detailed results for the most interesting signals on 19q13.2.
FinnTwin | Young Finns Study | FINRISK2007 | MAF | GWAS meta-analysis | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Location with respect to CYP2A6 | MAF | GWAS beta 1 (SD), p-value | % of variance explained | MAF | GWAS beta 1 (SD), p-value | % of variance explained | MAF | GWAS beta 1 (SD), p-value | % of variance explained | FINRISK 2 | EUR 3 | p-value | beta (coded allele) | beta (minor allele) | Estimated change in NMR 4 | |
rs56113850 | C>T in intron 4 | 0.46 | -0.61 (0.07), p = 2.78E-17 | 14.4% | 0.45 | -0.70 (0.05), p = 4.56E-45 | 22.8% | 0.45 | -0.60 (0.07), p = 8.76E-19 | 17.0% | 0.44 | 0.41 | 5.77E-86 | -0.65 | -0.65 | -0.15 |
rs113288603 5 | C>T in intron 1 | 0.15 | -0.01 (0.10), p = 0.89 | <0.01% | 0.15 | 0.07 (0.08), p = 0.34 | 0.14% | 0.15 | -0.03 (0.10), p = 0.78 | 0.04% | 0.15 | 0.09 | 0.663 | 0.02 | -0.02 | -0.005 |
esv2663194 | del of exons 1–2 | 0.03 | 0.78 (0.23), p = 8.71E-04 | 3.12% | 0.04 | 1.18 (0.14), p = 4.14E-16 | 7.95% | 0.03 | 1.12 (0.24), p = 5.16E-06 | 4.72% | 0.03 | 0.02 | 3.34E-23 | 1.08 | -1.08 | -0.25 |
rs12461964 6 | G>A in intron 1 | 0.48 | -0.53 (0.07), p = 9.35E-15 | N/A 7 | 0.44 | -0.63 (0.05), p = 2.25E-36 | N/A 7 | 0.45 | -0.63 (0.06), p = 4.79E-22 | 19.7% | 0.45 | 0.51 | 3.66E-76 | -0.61 | -0.61 | -0.14 |
CYP2A6*2 8 | L160H | <0.01 | N/A 9 | 0.30% | 0.02 | 1.45 (0.21), p = 7.62E-12 | 6.12% | 0.02 | 0.81 (0.33), p = 0.01 | 1.46% | 0.01 | 0.03 | 8.64E-13 | 1.27 | -1.27 | -0.29 |
CYP2A6*9 10 | promoter (-48T>G) | 0.14 | 0.45 (0.10), p = 1.06E-05 | 4.05% | 0.12 | 0.64 (0.08), p = 1.74E-14 | 6.98% | 0.13 | 0.81 (0.11), p = 1.72E-13 | 12.22% | 0.11 | 0.07 | 1.54E-30 | 0.63 | -0.63 | -0.14 |
CYP2A6*14 11 | S29N | 0.02 | 0.21 (0.24), p = 0.39 | 0.28% | 0.02 | 0.33 (0.22), p = 0.14 | 0.19% | 0.01 | -0.11 (0.31), p = 0.73 | 0.02% | 0.01 | 0.04 | 0.191 | 0.19 | -0.19 | -0.04 |
CYP2A6*18 12 | Y392F | 0.02 | -1.22 (0.30), p = 4.71E-05 | 2.93% | 0.02 | -0.84 (0.19), p = 1.39E-05 | 2.70% | <0.01 | N/A 9 | <0.01% | 0.02 | 0.02 | 5.24E-09 | -0.95 | -0.95 | -0.22 |
CYP2A6*21 13 | K476R | 0.02 | 0.92 (0.23), p = 7.83E-05 | 2.63% | 0.03 | 0.66 (0.15), p = 1.39E-05 | 2.65% | 0.02 | 0.79 (0.28), p = 5.25E-03 | 1.90% | 0.02 | 0.01 | 1.39E-10 | 0.75 | -0.75 | -0.17 |
MAF, minor allele frequency; GWAS, genome-wide association study; SD, standard deviation; EUR, 1000Genomes reference panel of individuals of European descent; N/A, not available;
1 beta reported for the coded allele;
2 MAF calculated among 19857 FINRISK individuals;
3 MAF reported for the EUR population at the Ensembl database;
4 change in NMR is estimated by multiplying SD of NMR (SD = 0.23 in the combined meta-analysis sample) by the effect size of the minor allele;
5 rs113288603 showed no association in the GWAS but was identified as an independent signal in analyses conditioned on the top-SNP (rs56113850);
6 identified as an independent SNP only in the FINRISK2007 GWAS sample;
7 rs12461964 was not an independent signal in FinnTwin or YFS, thus variance explained was not estimated;
8 rs1801272;
9 not included in the GWAS due to MAF<0.01;
10 rs28399433;
11 rs28399435;
12 rs1809810;
13 rs6413474.