Table 2.
Genome-wide significant associations with metabolic phenotypes for coding polymorphisms
| Trait | Basic information | Discovery (stage 2) | Replication (stage 3) | Combined | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| rs (dbSNP 129) | Chr-position (build 36) | Gene | Effect/other allele | EAF (%) | n | p value | n | Estimate | p value | n | p value | |
| Fasting serum HDL-cholesterol | None | 17-39281652 | CD300LG | T/C | 3.5 | 13,063 | 7.2 × 10−8 | 20,822 | −0.14 (0.027) | 1.5 × 10−7 | 33,885 | 8.5 × 10−14 |
| Type 2 diabetes | rs7607980 | 2-165259447 | COBLL1 | C/T | 12.5 | 12,177 | 3 × 10−7 | 36,407 | 0.88 (0.84–0.93) | 5.4 × 10−6 | 48,584 | 1.2 × 10−11 |
| Type 2 diabetes | rs2296172 | 1-39608404 | MACF1 | G/A | 23.4 | 12,175 | 0.00065 | 63,896 | 1.10 (1.06–1.14) | 5.8 × 10−7 | 76,071 | 8.2 × 10−10 |
Estimates are OR (95% CI) for binary variables (type 2 diabetes) or beta (SE) on a rank normalised scale for quantifiable traits (fasting serum HDL-cholesterol). Reported estimates are based on replication (stage 3) data. Estimates of effects and p values for binary traits in replication and combined meta-analyses were calculated based on effect size and SE where effect size was weighted according to the SEs by using the inverse corresponding SE. For quantifiable traits an overall z statistic was calculated relative to each reference allele estimated based on p value and direction of effect adjusted for the number of individuals in each sample. Alleles are given on the positive strand. Chromosome and position for SNPs are stated according to Build 36.3 (hg18). More details are given in ESM Table 9 and ESM Figs 14, 15
Chr, chromosome; EAF, effect allele frequency