Table 1.

Novel low frequency variants at fasting proinsulin loci previously identified by genome-wide association studies

SNP	Gene	Variant	Chr	Position	Minor/major allele	MAF	β̂ ± SE	Effect size in SD units ± SE	Proportion of trait variance explained	P value	Conditional P value
rs61741902	SGSM2	V996I	17	2,282,779	A/G	.014	.126 ± .021	.41 ± .07	.0047	8.7 × 10−10	4.8 × 10−10
rs35233100	MADD	R766X	11	47,306,630	T/C	.037	−.100 ± .013	−.32 ± .04	.0075	7.6 × 10−15	.0001

Chr, chromosome; MAF, minor allele frequency; SE, standard error; SD, standard deviation. Positions are from NCBI Build 37 with allele labels from the forward strand. Fasting proinsulin was log-transformed and adjusted for fasting insulin, BMI, age, and age². Effects are reported for the minor allele.β̂ coefficient units are ln(pmol/l). Conditional P values are reported after adjusting for the lead SNPs from GWAS signals (rs4790333 at SGSM2; rs7944584 and rs1051006 at MADD). Full results of conditional analysis are provided in Supplementary Table 4. For rs35233100, effect size in SD units (± SE) and proportion of trait variance explained after adjusting for rs7944584 and rs1051006, are −0.17 (± .05) and 0.0007, respectively. Based on analysis of 8,224 non-diabetic males.