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

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

ISSN: 1756-994X