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Table 2 Fasting glucose top hits

From: Exploration of haplotype research consortium imputation for genome-wide association studies in 20,032 Generation Scotland participants

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
  1. 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