Table 1.

Genetic loci significantly associated at genome-wide level (P<5×10⁻⁸) with fasting insulin or fasting glucose from the JMA in the combined discovery and follow-up analysis

FASTING INSULIN
		alleles		Stage 1: Discovery (26 cohorts) N=51,750			Stage 2: Follow-up (22 cohorts) N=31,450			Combined (48 cohorts) N=83,116
Nearest Gene	Index SNP	R Freq	O Freq	BMI=25 Effect (SE)	BMI=30 Effect (SE)	JMA P (Het P)	BMI=25 Effect (SE)	BMI=30 Effect (SE)	JMA P (Het P)	BMI=25 Effect (SE)	BMI=30 Effect (SE)	JMA P (Het P)
COBLL1-GRB14	rs7607980	T 0.88	C 0.12	0.021 (0.004)	0.04 (0.005)	6.1×10−14 (0.25)	0.026 (0.006)	0.039 (0.008)	4.9×10−7 (0.04)	0.023 (0.003)	0.039 (0.004)	4.3×10−20 (0.06)
IRS1	rs2943634	C 0.66	A 0.34	0.018 (0.003)	0.026 (0.004)	1.7×10−12 (0.62)	0.018 (0.008)	0.021 (0.010)	3.6×10−3 (0.53)	0.018 (0.003)	0.025 (0.004)	2.5×10−14 (0.70)
PPP1R3B	rs4841132	A 0.10	G 0.90	0.02 (0.004)	0.031 (0.006)	1.4×10−7 (0.50)	0.034 (0.013)	0.032 (0.016)	7.3×10−4 (0.45)	0.021 (0.004)	0.031 (0.006)	1.7×10−10 (0.52)
PDGFC	rs4691380	C 0.67	T 0.33	0.016 (0.003)	0.021 (0.004)	1.5×10−8 (0.36)	0.017 (0.008)	0.020 (0.010)	7.2×10−2 (0.31)	0.016 (0.003)	0.021 (0.004)	5.3×10−9 (0.37)
UHRF1BP1	rs4646949	T 0.75	G 0.25	0.016 (0.003)	0.021 (0.004)	5.9×10−8 (0.08)	0.0009 (0.008)	0.009 (0.010)	1.6×10−1 (0.24)	0.014 (0.003)	0.020 (0.004)	3.7×10−8 (0.05)
LYPLAL1	rs2785980	T 0.67	C 0.33	0.016 (0.003)	0.017 (0.004)	7.7×10−8 (0.03)	0.011 (0.009)	0.018 (0.010)	9.7×10−2 (0.20)	0.016 (0.003)	0.017 (0.004)	2.0×10−8 (0.03)

FASTING GLUCOSE
		alleles		Stage 1: Discovery (29 cohorts) N=58,074			Stage 2: Follow-up (23 cohorts) N=38,422			Combined (52 cohorts) N=96,496
Nearest Gene	Index SNP	R Freq	O Freq	BMI=25 Effect (SE)	BMI=30 Effect (SE)	JMA P (Het P)	BMI=25 Effect (SE)	BMI=30 Effect (SE)	JMA P (Het P)	BMI=25 Effect (SE)	BMI=30 Effect (SE)	JMA P (Het P)
ARAP1	rs11603334	G 0.83	A 0.17	0.025 (0.004)	0.033 (0.005)	4.4×10−11 (0.25)	0.016 (0.005)	0.026 (0.007)	2.2×10−4 (0.004)	0.022 (0.003)	0.030 (0.004)	2.4×10−14 (0.01)
FOXA2	rs6048205	A 0.95	G 0.05	0.044 (0.007)	0.033 (0.009)	7.1×10−10 (0.14)	0.033 (0.009)	0.023 (0.012)	1.4×10−3 (0.03)	0.040 (0.005)	0.029 (0.007)	1.6×10−12 (0.03)
DPYSL5	rs1371614	T 0.25	C 0.75	0.020 (0.004)	0.026 (0.005)	2.9×10−9 (0.19)	0.019 (0.005)	0.015 (0.006)	2.1×10−4 (0.47)	0.020 (0.003)	0.022 (0.004)	2.3×10−12 (0.23)
PCSK1	rs13179048	C 0.69	A 0.31	0.021 (0.003)	0.016 (0.004)	1.6×10−9 (0.24)	0.028 (0.010)	0.027 (0.013)	2.2×10−2 (0.16)	0.022 (0.003)	0.018 (0.004)	1.6×10−10 (0.18)
PDX1	rs2293941	A 0.22	G 0.78	0.022 (0.004)	0.015 (0.005)	1.3×10−8 (0.47)	0.013 (0.005)	0.016 (0.006)	7.8×10−3 (0.04)	0.019 (0.003)	0.016 (0.004)	5.3×10−10 (0.10)
PPP1R3B	rs4841132	A 0.10	G 0.90	0.026 (0.005)	0.028 (0.007)	7.9×10−7 (0.94)	0.033 (0.015)	0.054 (0.021)	3.1×10−3 (0.02)	0.027 (0.005)	0.030 (0.007)	7.6×10−9 (0.55)
OR4S1	rs1483121	G 0.86	A 0.14	0.027 (0.005)	0.022 (0.006)	6.5×10−8 (0.70)	0.014 (0.006)	0.006 (0.008)	3.4 ×10−2 (0.42)	0.021 (0.004)	0.015 (0.005)	1.6×10−8 (0.56)

Directly genotyped and imputed SNPs were tested for association with fasting glucose or fasting insulin by Joint Meta-Analysis (JMA) of the SNP and SNP×BMI effects. The effect estimates presented are derived from the JMA for the specified BMI in kg/m². A test of heterogeneity (Het P) was performed for each locus. From the discovery analysis, 50 loci were promoted to the follow-up analysis (31 for fasting insulin and 20 for fasting glucose; PPP1R3B was followed-up in both traits). R/O Freq = Trait raising allele/other allele and frequency of trait raising allele; SNP = single nucleotide polymorphism; JMA = joint meta-analysis; het = heterogeneity. N = Sample size presented is the maximum observed among the SNPs in the table.