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. 2017 Jul 24;26(R2):R172–R184. doi: 10.1093/hmg/ddx293

Table 1.

Loci influencing glycaemic traits

Locus Chr Index SNP Refs. Ancestry Alleles [E/O] Type of variant EAF Effect Size (SE) P-value Trait
ABO 9 rs505922 (38) EA C/T Intronic 0.47 −0.038 (0.006) 3.80 × 10−9 Disposition index
rs651007 (39) EA+AA A/G Upstream 0.20 0.020 (0.004) 1.30 × 10−8 FG
ADCY5b 3 rs11708067 (80) EA A/G Intronic 0.78 0.027 (0.003) 1.70 × 10−14 FG
rs2877716 (89) EA C/T Intronic 0.77 −0.023 (0.004) 3.6 × 10−8 HOMA-B
0.09 (0.01) 4.19 × 10−16 2hG_adjBMI
ADRA2A 10 rs10885122 (80) EA G/T Intergenic 0.87 0.022 (0.004) 9.70 × 10−8 FG
AKT2 rs184042322 (60) EA T/G P50T 0.012 10.400 (1.990) 9.98 × 10−10 FI
AMT (RBMA6b) 3 rs11715915 (6) EA C/T R318R 0.68 0.012 (0.002) 4.90 × 10−8 FG
ANK1 (WARSb, NKX6-3b) 8 rs6474359 (90) EA T/C Intronic 0.97 0.058 (0.011) 1.18 × 10−8 HbA1c
rs4737009 (49) EAA A/G Intronic 0.24 0.027 (0.004) 6.11 × 10−12 HbA1c
rs4737009 A/G Intronic 0.51 0.080 (0.010) 1.10 × 10−15 HbA1c
ANKRD55/MAP3K1 5 rs459193 (22) EA G/A Intergenic 0.73 0.015 (0.002) 1.12 × 10−10 FI_adjBMI
ARAP1 (STARD10b) 11 rs11603334 (22) EA G/A Intronic 0.83 0.019 (0.003) 1.10 × 10−11 FG
(24) 0.85 −0.093 (0.005) 3.20 × 10−102 Proinsulin
ARL15 5 rs4865796 (22) EA A/G Intronic 0.67 0.015 (0.003) 2.10 × 10−8 FI
0.015 (0.002) 2.20 × 10−12 FI_adjBMI
ATP11A 13 rs7998202 (90) EA G/A Upstream 0.14 0.031 (0.005) 5.24 × 10−9 HbA1c
BCL2 18 rs12454712 (26) EA T/C Intronic 0.58 0.050 (0.010) 1.9 × 10−8 ISI_adjBMI
C12orf51 (HECTD4) 12 rs2074356 (33) EAA T/NR Intronic NR −0.061 (0.008) 6.03 × 10−14 FG
−0.321 (0.039) 1.04 × 10−16 1hGlu
−0.165 (0.028) 5.91 × 10−09 2hG
CDKAL1 6 rs9368222 (22) EA A/C Intronic 0.28 0.014 (0.002) 1.00 × 10−9 FG
rs7747752 (91) EAA C/G Intronic 0.48 0.016 (0.002) 4.54 × 10−11 FG_adjBMI
rs7772603 (49) EAA C/T Intronic 0.42 −0.310 (NR) 1.50 × 10−8 HbA1c
rs9348440 (33) EAA A/NR Intronic NR 0.060 (0.010) 3.50 × 10−8 HbA1c
0.246 (0.028) 3.13 × 10−19 1hGlu
CDKN2B 9 rs10811661 (22) EA T/C Upstream 0.82 0.024 (0.003) 5.60 × 10−18 FG
0.023 (0.003) 5.12 × 10−15 FG_adjBMI
CRY2 11 rs11605924 (80) EA A/C Intronic 0.49 0.015 (0.003) 8.10 × 10−8 FG
CYBA 16 rs9933309 (49) EAA C/T Intronic 0.63 0.070 (0.010) 1.10 × 10−8 HbA1c
DGKBb/TMEM195 7 rs2191349 (80) EA T/G Intergenic 0.52 0.030 (0.003) 5.30 × 10−29 FG
DNLZ 9 rs3829109 (22) EA G/A Intronic 0.71 0.017 (0.003) 1.10 × 10−10 FG
DPYSL5 2 rs1371614 (92) EA T/C Intronic 0.25 0.020 (0.006) 1.33 × 10−12 FG_adjBMI
0.015 (0.006) 0.00021 FG_BMI30
EMID2 7 rs6947345 (93) EA C/T Intronic 0.98 0.162 (0.029) 3.80 × 10−8 FG
ERAP2 5 rs1019503 (22) EA A/G 3’UTR 0.48 0.063 (0.011) 8.90 × 10−9 2hG
FADS1b 11 rs174550 (80) EA T/C Intronic 0.64 0.017 (0.003) 8.30 × 10−9 FG
−0.020 (0.003) 5.30 × 10−10 HOMA-B
FAM133A X rs213676 (46) AA C/G Intergenic 0.98 0.147 (NR) 2.37 × 10−8 FI_adjBMI
FAM13A 4 rs3822072 (22) EA A/G Intronic 0.48 0.012 (0.002) 1.90 × 10−8 FI_adjBMI
FN3K 17 rs1046896 (90) EA T/C Upstream 0.31 0.035 (0.003) 1.57 × 10−26 HbA1c
FOXA2b 20 rs6048205 (92) EA A/G Downstream 0.95 0.023 (0.012) 0.0014 FG_BMI30
rs6113722 (22) EA G/A Downstream 0.96 0.035 (0.005 2.50 × 10−11 FG
FTO 16 rs1421085 (22) EA C/T Intronic 0.42 0.020 (0.003) 1.90 × 10−15 FI
G6PC2b/ABCB11 2 rs560887 (80) EA C/T Intronic 0.70 0.075 (0.003) 8.50 × 10−122 FG
rs552976 (90) EA G/A Intronic 0.62 −0.042 (0.004) 7.60 × 10−29 HOMA-B
rs138726309 (40) EA T/C H177Y 0.01 0.032 (0.004) 1.00 × 10−17 HbA1c
rs492594 (49) EAA C/G V219L 0.48 0.047 (0.003) 8.16 × 10−18 HbA1c
rs3755157 T/C Intronic 0.34 −0.102 (-0.02) 3.10 × 10−8 FG_adjBMI
0.02 (-0.004) 6.00 × 10−9 FG_adjBMI
0.07 (0.01) 2.80 × 10−11 HbA1c
G6PC3 17 rs12602486 (50) Malay G/T Downstream 0.03 −0.362 (0.035) 1.00 × 10−4 HbA1c
GCKb 7 rs4607517 (80) EA A/G Upstream 0.16 0.062 (0.004) 1.20 × 10−44 FG
rs6975024 (22) EA C/T Upstream 0.15 0.103 (0.016) 5.20 × 10−11 2hG
rs1799884 (90) EA C/T Upstream 0.18 0.038 (0.004) 1.45 × 10−20 HbA1c
rs1799884 (33) EAA A/NR Intronic NR 0.063 (0.007) 4.53 × 10−18 FG
0.208 (0.035) 2.82 × 10−9 1hGlu
0.162 (0.026) 2.59 × 10−10 2hG
GCKRb 2 rs780094 (80) EA C/T Intronic 0.62 0.029 (0.003) 1.70 × 10−24 FG
rs1260326 (89) T/C L446P 0.42 0.032 (0.004) 3.60 × 10−19 FI
0.035 (0.004) 5.0 × 10−20 HOMA-IR
0.100 (0.01) 7.05 × 10−11 2hG_adjBMI
GIPR 19 rs2302593 (22) EA C/G Intronic 0.50 0.014 (0.002) 9.30 × 10−10 FG
rs10423928 (89) EA A/T Downstream 0.18 0.09 (0.01) 1.98 × 10−15 2hG_adjBMI
GLIS3 9 rs7034200 (80) EA A/C Intronic 0.49 0.018 (0.003) 1.20 × 10−9 FG
−0.020 (0.004) 8.9 × 10−9 HOMA-B
GLP1R 6 rs10305492 (39) EA+AA A/G A316T 0.01 −0.09 (0.013) 3.40 × 10−12 FG
(40) EA 0.02 −0.073 (0.015) 4.60 × 10−7 FG_adjBMI
GLS2 12 rs2657879 (22) EA G/A L581P 0.18 0.016 (0.003) 3.90 × 10−8 FG_adjBMI
GPSM1 9 rs60980157 (38) EA T/C S391L 0.30 0.072 (0.013) 1.4 × 10−8 Insulinogenic index
GRB10 7 rs6943153 (22) EA T/C Intronic 0.34 0.015 (0.002) 1.60 × 10−12 FG
GRB14/COBL11 2 rs10195252 (22) EA T/C Upstream 0.59 0.016 (0.003) 4.90 × 10−7 FI
rs7607980 (92) EA T/C N939D 0.60 0.017 (0.002) 1.30 × 10−10 FI_adjBMI
rs7607980 (40) EA T/C N939D 0.86 0.039 (0.008)c 4.90 × 10−7 FI_BMI30
0.89 −0.071 (0.030) 3.00 × 10−13 HOMA-IR
0.030 (0.006) 6.70 × 10−8 FI_adjBMI
HBS1L/MYB 6 rs9399137 (49) EAA T/C Intronic 0.69 0.07 (0.01) 8.50 × 10−15 HbA1c
HFE 6 rs1800562 (90) EA G/A C282Y 0.94 0.063 (0.007) 2.59 × 10−20 HbA1c
HIP1 7 rs1167800 (22) A/G Intronic 0.54 0.016 (0.003) 2.60 × 10−9 FI
HK1 10 rs16926246 (90) EA C/T Intronic 0.90 0.089 (0.004) 3.11 × 10−54 HbA1c
HNF1A 12 rs2650000 (38) EA A/C Intergenic 0.46 −0.076 (0.012) 5.0 × 10−10 Insulinogenic index
IGF1 12 rs35767 (80) EA G/A Upstream 0.85 0.010 (0.006) 0.10 FI
rs35747 (92) EA A/G 0.82 0.013 (0.006) 0.04 HOMA-IR
0.021 (0.004) 8.85 × 10−10 FI_adjBMI
IGF1R 15 rs2018860 (48) EAA A/T Intronic 0.46 0.031 (0.006) 2.99 × 10−8 FG_adjBMI
IGF2BP2 3 rs7651090 (22) EA G/A Intronic 0.31 0.013 (0.002) 1.75 × 10−8 FG
0.30 0.064 (0.012) 4.50 × 10−8 2hG_adjBMI
IKBKAP 9 rs16913693 (22) EA T/G Intronic 0.97 0.043 (0.007) 3.50 × 10−11 FG
IRS1 2 rs2943634 (92) EA C/A Downstream 0.66 0.021 (0.010) 0.0036 FI_BMI30
rs2972143 (22) EA G/A Downstream 0.62 −0.015 (0.018) 2.00 × 10−10 HOMA-IR
rs2943645 (22) EA T/C Downstream 0.63 0.014 (0.003) 3.20 × 10−8 FI
0.019 (0.002) 2.30 × 10−19 FI_adjBMI
KANK1 9 rs3824420 (38) EA A/G R667H 0.03 0.107 (0.018) 1.6 × 10−9 Proinsulin AUC0-30
rs10815355 (48) EAA T/G Intronic 0.22 0.045 (0.007) 1.26 × 10−9 FG_adjBMI
KL 13 rs576674 (22) EA G/A Upstream 0.15 0.017 (0.003) 2.30 × 10−8 FG
LARP6 15 rs1549318 (24) EA T/C Downstream 0.61 0.019 (0.005) 2.4 × 10−10 Proinsulin
LYPLAL1 1 rs2820436 (22) EA C/A Downstream Downstream 0.67 0.015 (0.003) 4.40 × 10−9 FI
rs4846565 (22) EA G/A Downstream 0.67 0.013 (0.002) 1.80 × 10−9 FI_adjBMI
rs2785980 (92) EA T/C 0.67 0.018 (0.010) 0.097 FI_BMI30
MADDb (ACP2b) 11 rs7944584 (80) EA A/T Intronic 0.75 0.021 (0.003) 5.10 × 10−11 FG
rs10501320 (24) EA G/C Intronic 0.72 0.081 (0.006) 1.1 × 10−88 Proinsulin
rs10838687 (24) EA T/G Intronic 0.80 0.025 (0.005) 6.9 × 10−12 Proinsulin
rs35233100 (38) EA T/C R766X 0.04 −0.100 (0.013)a 7.6 × 10−15 Fasting proinsulin
MRPL33 2 rs3736594 (92) EA A/C Intronic 0.28 0.022 (0.003) 5.22 × 10−16 FG_adjBMI
MTNR1Bb 11 rs10830963 (80) EA G/C Intronic 0.30 0.067 (0.003) 1.10 × 10−102 FG
rs1387153 (90) EA T/C Upstream 0.27 −0.034 (0.004) 1.1 × 10−22 HOMA-B
rs10830962 (33) EAA C/NR Upstream NR 0.024 (0.004) 3.00 × 10−9 HbA1c
0.028 (0.004) 3.96 × 10−11 HbA1c
0.041 (0.006) 4.84 × 10−13 FG
0.191 (0.027) 3.24 × 10−12 1hGlu
MYL2 12 rs12229654 (33) EAA G/NR Intergenic NR −0.277 (0.039) 8.83 × 10−13 1hGlu
MYO9B 19 rs11667918 (49) EAA C/T Intronic 0.62 0.060 (0.010) 9.00 × 10−12 HbA1c
NAT2c 8 rs1208 (25) EA A/G K268R 0.57 −0.130 (0.03) 9.81 × 10−7 Insulin sensitivity
NYAP2 2 rs13422522 (26) EA C/G Intergenic 0.77 −0.060 (0.010) 1.2 × 10−11 ISI_adjBMI
OAS1 12 rs11066453 (33) EAA G/NR Intronic NR −0.242 (0.041) 4.54 × 10−09 1hGlu
OR4S1 11 rs1483121 (92) EA G/A Downstream 0.86 0.006 (0.008) 0.034 FG_BMI30
P2RX2 12 rs10747083 (22) EA A/G Upstream 0.66 0.013 (0.002) 7.60 × 10−9 FG
PAM 5 rs35658696 (38) EA G/A D563G 0.05 −0.152 (0.027) 1.9 × 10−8 Insulinogenic index
PCSK1b 5 rs13179048 (92) EA C/A Downstream 0.69 0.027 (0.013) 0.022 FG_BMI30
rs4869272 (22) EA T/C Downstream 0.69 0.018 (0.002) 1.00 × 10−15 FG
rs6234 (40) EA C/G Q665E 0.28 −0.022 (-0.004) 3.00 × 10−8 FG_adjBMI
rs6235 (40) EA G/C S690T 0.28 −0.022 (-0.004) 4.10 × 10−8 FG_adjBMI
rs6235 (24) EA G/C S690T 0.28 0.039 (0.005) 9.8 × 10−27 Proinsulin
PDGFC 4 rs4691380 (92) EA C/T Intronic 0.67 0.020 (0.010) 0.072 FI_BMI30
rs6822892 (22) EA A/G Intronic 0.68 −0.003 (0.019) 4.00 × 10−8 HOMA-IR
0.014 (0.002) 2.60 × 10−10 FI_adjBMI
PDK1/RAPGEF4 2 rs733331 (48) EAA A/G Intronic 0.56 0.036 (0.006) 6.98 × 10−11 FG_adjBMI
PDX1b 13 rs2293941 (92) EA A/G Upstream 0.22 0.016 (0.006) 0.0078 FG_BMI30
rs11619319 (22) EA G/A Upstream 0.23 0.019 (0.002) 1.30 × 10−15 FG
PELO 5 rs6450057 (46) EA T/C Intergenic 0.37 −0.011 (NR) 9.21 × 10−5 FI_adjBMI
AA T/C Intergenic 0.40 0.027 (NR) 3.11 × 10−6 FI_adjBMI
PEPD 19 rs731839 (22) EA G/A Intronic 0.34 0.015 (0.003) 1.70 × 10−8 FI
0.015 (0.002) 5.10 × 10−12 FI_adjBMI
PPARGb 3 rs17036328 (22) EA T/C Intronic 0.86 0.021 (0.003) 3.60 × 10−12 FI_adjBMI
PPIP5K2 5 rs36046591 (38) EA G/A S1228G 0.05 −0.152 (0.027) 2.3 × 10−8 Insulinogenic index
PPP1R3B 8 rs4841132 (92) EA A/G Upstream 0.10 0.054 (0.021) 0.0031 FG_BMI30
rs983309 (22) EA T/G Upstream 0.12 0.032 (0.016) 0.00073 FI_BMI30
rs2126259 (22) EA T/C Upstream 0.11 −0.055 (0.028) 2.00 × 10−8 HOMA-IR
rs11782386 (22) EA C/T Upstream 0.87 0.026 (0.003) 6.30 × 10−15 FG
0.029 (0.004) 3.80 × 10−14 FI
0.099 (0.017) 2.20 × 10−9 2hG
0.024 (0.003) 3.30 × 10−13 FI_adjBMI
PROX1 1 rs340874 (80) EA C/T Upstream 0.52 0.013 (0.003) 6.60 × 10−6 FG
RMST 12 rs17331697 (93) EA T/C Intronic 0.90 0.046 (0.007) 1.30 × 10−11 FG
RREB1b 6 rs17762454 (22) EA T/C Intronic 0.26 0.014 (0.002) 9.60 × 10−9 FG_adjBMI
RSPO3 6 rs2745353 (22) EA T/C Intronic 0.51 0.014 (0.002) 5.50 × 10−9 FI
SC4MOL 4 rs17046216 (45) AA + West African A/NR Intergenic NR 0.180 (0.030) 1.65 × 10−8 FI_adjBMI
0.190 (0.030) 2.88 × 10−8 HOMA-IR
SGSM2 17 rs4790333 (24) EA T/C Intronic 0.45 0.015 (0.004) 3.00 × 10−9 Proinsulin
rs61741902 (38) EA A/G V996I 0.01 0.126 (0.021)a 8.70 × 10−10 Fasting proinsulin
SIX2/SIX3 2 rs895636 (47) EAA T/C Intergenic 0.38 0.039 (0.006) 9.99 × 10−13 FG
SLC2A2b 3 rs11920090 (80) EA T/A Intronic 0.87 0.02 (0.004) 3.30 × 10−6 FG
SLC30A8b 8 rs13266634 (80) EA C/T R325W NR 0.027 (0.004) 5.50 × 10−10 FG
rs11558471 (94) EA C/T 3’UTR 0.70 0.02 (NR) 5.00 × 10−8 HbA1c
(22) EA A/G 0.68 0.029 (0.002) 7.80 × 10−37 FG
(24) EA A/G 0.69 0.028 (0.005) 3.1 × 10−18 Proinsulin
SNX7 1 rs9727115 (24) EA G/A Intronic 0.64 0.013 (0.005) 2.40 × 10−10 Proinsulind
SPTA1 1 rs2779116 (90) EA T/C Intronic 0.28 0.024 (0.004) 2.75 × 10−9 HbA1c
TBC1D30 12 rs150781447 (38) EA T/C R279C 0.02 0.204 (0.025) 1.3 × 10−16 Proinsulin AUC30-120
TCERG1L 10 rs7077836 (45) AA + West African T/NR Intergenic NR 0.280 (0.050) 7.50 × 10−9 FI_adjBMI
0.340 (0.050) 4.86 × 10−20 HOMA-IR
TCF7L2 10 rs7903146 (22) EA T/C Intronic 0.28 0.022 (0.002) 2.70 × 10−20 FG
rs12243326 (22) EA C/T Intronic 0.28 −0.018 (0.003) 6.10 × 10−11 FI
(24) EA 0.30 0.032 (0.007) 2.3 × 10−20 Proinsulin
(95) EA 0.28 0.05 (0.03) 1.48 × 10−7 HbA1c
(89) EA 0.21 0.07 (0.01) 4.23 × 10−10 2hG_adjBMI
TET2 4 rs9884482 (22) EA C/T Intronic 0.35 0.017 (0.002) 1.40 × 10−11 FI
rs974801 (22) EA G/A Intronic 0.39 0.014 (0.002) 3.30 × 10−11 FI_adjBMI
TMEM79 1 rs6684514 (49) EAA G/A V147M 0.76 0.09 (0.01) 1.30 × 10−23 HbA1c
TMPRSS6 22 rs855791 (90) EA A/G V736A 0.42 0.027 (0.004) 2.74 × 10−14 HbA1c
TOP1/ZHX3b 20 rs6072275 (22) EA A/G Intronic 0.16 0.016 (0.003) 1.70 × 10−8 FG
UHRF1BP1 6 rs4646949 (92) EA T/G Intronic 0.75 0.009 (0.010) 0.16 FI_BMI30
rs6912327 (22) EA T/C Intronic 0.80 0.017 (0.003) 2.30 × 10−8 FI_adjBMI
URB2 1 rs141203811 (40) EA T/A E594V 0.001 0.282 (-0.066) 3.10 × 10−7 FI_adjBMI
VPS13C/C2CD4A/B 15 rs17271305 (89) EA G/A Intronic 0.42 0.060 (0.010) 4.11 × 10−8 2hG_adjBMI
rs11071657 (80) EA A/G Downstream 0.63 0.008 (0.003) 0.01 FG
rs4502156 (24) EA T/C Downstream 0.58 0.029 (0.004) 3.5 × 10−20 Proinsulin
WARS 14 rs3783347 (22) EA G/T Intronic 0.79 0.017 (0.003) 1.30 × 10−10 FG
YSK4 2 rs1530559 (22) EA A/G Intronic 0.52 0.015 (0.003) 3.40 × 10−8 FI
ZBED3 5 rs7708285 (22) EA G/A Intronic 0.27 0.015 (0.003) 1.20 × 10−8 FG_adjBMI

Chr, Chromosome; EA, European ancestry; EAA, East Asian ancestry; AA, African American ancestry; Allele, [E, Effect allele/O, Other allele]; EAF, Effect allele frequency; NR, Not reported/available; FG, fasting glucose (mmol/L); FG_adjBMI, fasting glucose BMI adjusted; FG_BMI30, Fasting glucose in individuals with BMI = 30 kg/m2; FI, fasting insulin (pmol/L); FI_adjBMI, fasting insulin BMI adjusted; 2hG, 2 h glucose (mmol/L); HbA1c, glycated haemoglobin (%); HOMA-B, β-cell function by homeostasis model assessment; HOMA-IR, insulin resistance by homeostasis model assessment; Proinsulin (pmol/L); ISI_adjBMI, Modified Stumvoll Insulin Sensitivity Index, adjusted for BMI. Effect estimates are taken from original references are all rounded to three decimal points.

Effect sizes for ISI are presented as the SD per effect allele.

a

Coefficient units are ln(pmol/l).

b

Likely effector transcript at the locus.

c

Signal at NAT2 did not reach genome-wide significance.

d

Signal at SNX7 reached genome-wide significance after adjusting for fasting glucose (P = 5.4 × 10−9).