Table 2.
Fasting glucose top hits
| Gene | SNP | Chr | Position | Effect allele | GS minor allele frequency | HRC MAF | GS p value | GS effect size | Meta top SNP | Meta p value | GS and meta SNP R2 | GS and meta SNP D’ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PROX1-AS1 | rs79687284 | 1 | 214150821 | C | 0.036 | 0.0306 | 1.87E-08 | 0.20 | rs340874 | 6.80E-08 | 0.02 | 0.99 |
| GCKR | rs780095 | 2 | 27741105 | G | 0.427 | 0.4516 | 8.20E-09 | 0.07 | rs1260326 | 1.26E-24 | 0.72 | 0.93 |
| G6PC2 | rs560887* | 2 | 169763148 | C | 0.291 | 0.2861 | 2.09E-75 | 0.24 | rs560887 | 4.68E-100 | 1 | 1 |
| SLC2A2 | rs8192675 | 3 | 170724883 | C | 0.284 | 0.3067 | 8.41E-11 | –0.09 | rs11920090 | 1.90E-11 | 0.32 | 0.99 |
| YKT6 | rs917793 | 7 | 44245853 | T | 0.183 | 0.1766 | 1.46E-28 | 0.17 | rs4607517 | 1.39E-51 | 1 | 1 |
| SLC30A8 | rs11558471* | 8 | 118185733 | G | 0.323 | 0.3129 | 4.63E-13 | –0.09 | rs11558471 | 3.96E-21 | 1 | 1 |
| Y_RNA | rs143399767 | 9 | 96182703 | C | 0.011 | 0.0160 | 1.42E-08 | 0.36 | NA | NA | NA | NA |
| PDX1 | rs7981781 | 13 | 28499962 | A | 0.234 | 0.2296 | 5.01E-10 | 0.09 | rs2293941 | 2.93E-08 | 0.99 | 0.99 |
| WDR4 | rs370189685 | 21 | 44276432 | C | 0.001 | 0.0009 | 2.75E-08 | –1.15 | NA | NA | NA | NA |
Summary of top hits of the imputed GWAS analysis of fasting plasma glucose (15,226 people after those with diabetes were removed) in Generation Scotland, compared with top hits in a meta-analysis reported in [50]. Starred (*) SNPs indicate the same SNP in the GS and meta-analysis datasets. Entries in bold are within 500,000 bases of a SNP that reached genome-wide significance in the genotyped GWAS analysis. Entries with missing meta-analysis top SNPs (indicated by NA) are novel associations that did not reach significance in the meta-analysis