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. 2026 May 22;18:105. doi: 10.1186/s13073-026-01674-2

Table 2.

Genome-wide significant lead variants for the non-T2D-dependent component of GDM

SNP EA NEA Locus CHR POS MAFEUR BETAEUR——EUR SEEUR P EUR Function Nearest Gene P GDM P replication BETAEAS SEEAS P EAS
rs10154014 C T 50 20 48,356,146 0.139 2.143 0.168 4.03 × 10− 37 intergenic B4GALT5 0.089 - - - -
rs10830963 C G 36 11 92,708,710 0.288 -0.692 0.028 6.76 × 10− 133 intron MTNR1B 5.87 × 10− 216 1.11 × 10− 129 0.657 0.039 1.67 × 10− 63
rs10830964 C T 36 11 92,719,681 0.147 0.31 0.037 5.35 × 10− 17 downstream MTNR1B 5.38 × 10− 25 7.80 × 10− 12 -0.324 0.064 3.59 × 10− 7
rs10831057 A C 36 11 93,267,564 0.197 -0.264 0.038 6.53 × 10− 12 intron SMCO4 1.35 × 10− 18 - 0.006 0.051 9.09 × 10− 1
rs11020131 A G 36 11 92,713,376 0.02 -0.535 0.06 5.73 × 10− 19 intron MTNR1B 4.57 × 10− 28 1.58 × 10− 11 - - -
rs11190875 A G 32 10 102,999,459 0.157 1.807 0.189 1.05 × 10− 21 intron LBX1 0.034 - - - -
rs112432204 C T 36 11 92,708,092 0.027 -0.553 0.074 1.1 × 10− 13 intron MTNR1B 1.42 × 10− 21 1.64 × 10− 16 - - -
rs112569024 A T 25 7 157,944,883 0.153 1.487 0.233 1.84 × 10− 10 - PTPRN2 0.324 - - - -
rs113150876 A G 15 4 160,202,839 0.183 1.798 0.162 9.28 × 10− 29 intron RAPGEF2 0.061 - - - -
rs113777162 G T 20 6 38,690,353 0.28 1.997 0.11 5.1 × 10− 73 intron D-H8 0.148 - - - -
rs113977410 C T 5 1 226,826,772 0.08 2.875 0.172 8.47 × 10− 63 intron STUM 0.107 - - - -
rs114417557 A C 38 13 76,326,228 0.13 2.279 0.155 8.97 × 10− 49 intron LMO7 0.300 - - - -
rs11578147 A G 2 1 95,243,022 0.193 1.85 0.155 6.95 × 10− 33 intron SLC44A3 0.471 - -0.400 0.768 6.02 × 10− 1
rs12270363 G T 36 11 92,751,333 0.475 -0.174 0.028 8.51 × 10− 10 regulatory MTNR1B 1.58 × 10− 14 2.51 × 10− 9 -0.219 0.043 3.75 × 10− 7
rs12549902 A G 28 8 41,509,259 0.43 0.174 0.029 1.3 × 10− 9 upstream NKX6-3 0.002 1.92 × 10− 6 -0.054 0.030 7.04 × 10− 2
rs12625547 G T 51 20 50,154,647 0.186 -0.215 0.038 1.05 × 10− 8 intron NFATC2 3.19 × 10− 6 6.37 × 10− 4 0.060 0.056 2.84 × 10− 1
rs12795282 C T 33 11 25,443,086 0.219 1.64 0.161 2.72 × 10− 24 intergenic ANO3 0.262 - - - -
rs12804291 C T 36 11 92,705,307 0.091 0.325 0.059 3.83 × 10− 8 intron MTNR1B 2.73 × 10− 10 2.09 × 10− 8 - - -
rs13167145 G T 17 5 95,711,140 0.123 0.194 0.03 1.24 × 10− 10 intron PCSK1 7.15 × 10− 13 - - - -
rs142242199 A T 47 18 14,679,099 0.106 2.07 0.217 1.53 × 10− 21 intergenic ANKRD30B 0.033 - - - -
rs1447349 C G 36 11 92,676,440 0.065 -0.322 0.05 1.71 × 10− 10 intergenic MTNR1B 1.15 × 10− 18 1.19 × 10− 11 - - -
rs146228963 A G 36 11 92,737,847 0.077 0.317 0.053 2.51 × 10− 9 intergenic MTNR1B 8.56 × 10− 11 3.44 × 10− 7 - - -
rs147247861 C G 29 8 103,743,138 0.479 2.043 0.084 1.49 × 10− 131 - AP003356.1 0.407 - - - -
rs148124765 A T 40 15 84,657,647 0.101 1.701 0.279 1.08 × 10− 9 intron GOLGA6L4 0.331 - - - -
rs150205522 A G 36 11 93,064,637 0.052 -0.391 0.061 1.63 × 10− 10 intron DEUP1 4.38 × 10− 14 5.72 × 10− 7 - - -
rs150807747 A G 19 5 177,267,016 0.48 1.654 0.102 4.09 × 10− 59 intron FAM153A 0.624 - - - -
rs154453 C T 17 5 95,211,426 0.229 -0.193 0.034 1.29 × 10− 8 downstream GLRX 1.04 × 10− 11 1.32 × 10− 9 -0.150 0.079 5.84 × 10− 2
rs17400671 A G 46 18 8,659,445 0.072 1.912 0.349 4.46 × 10− 8 intergenic MTCL1 0.225 - - - -
rs183495841 A G 45 17 77,969,351 0.377 1.298 0.152 1.43 × 10− 17 intron TBC1D16 0.053 - - - -
rs199746255 A T 7 2 108,085,738 0.151 1.539 0.237 7.84 × 10− 11 intron RGPD4 0.108 - - - -
rs2089304 C T 43 16 32,457,793 0.395 2.43 0.068 6.3 × 10− 276 - PABPC1P13 0.023 - - - -
rs2405819 A T 26 8 2,747,064 0.323 1.478 0.14 5.9 × 10− 26 intergenic MYOM2 0.312 - - - -
rs2845871 C T 35 11 92,032,930 0.317 0.185 0.032 4.99 × 10− 9 intergenic FAT3 3.86 × 10− 9 4.46 × 10− 9 -0.017 0.033 6.12 × 10− 1
rs28691250 A C 13 4 128,947,455 0.096 2.284 0.193 3.51 × 10− 32 intron LARP1B 0.121 - - - -
rs35153269 A G 39 14 103,412,652 0.366 1.596 0.123 2.35 × 10− 38 intron AMN 0.059 - 0.035 0.581 9.52 × 10− 1
rs36049512 C T 49 20 11,602,755 0.185 2.954 0.082 2.94 × 10− 282 downstream BTBD3 0.030 - - - -
rs367810486 C T 11 4 35,607,479 0.125 2.122 0.184 1.23 × 1030 - RNU6-573P 0.323 - - - -
rs371504276 C T 10 3 129,184,764 0.052 2.114 0.384 3.57 × 1008 - IFT122 0.038 - - - -
rs375336641 A G 12 4 105,244,753 0.142 2.997 0.104 2.42 × 10181 intron CXXC4 0.086 - - - -
rs376750538 C G 42 16 29,284,832 0.355 1.005 0.179 2 × 10− 08 intron NPIPB11 0.266 - -0.278 0.425 5.13 × 10− 1
rs4285019 C T 9 3 110,166,875 0.115 2.353 0.174 1.22 × 10− 41 intergenic NECTIN3 0.181 - - - -
rs4526739 C T 36 11 92,665,020 0.358 -0.201 0.029 3.95 × 10− 12 intergenic MTNR1B 8.27 × 10− 20 1.47 × 10− 13 -0.386 0.058 3.94 × 10− 11
rs4639974 G T 37 12 48,851,067 0.215 1.345 0.201 2.41 × 10− 11 intergenic ANP32D 0.413 - - - -
rs4863928 A C 14 4 135,997,446 0.267 2.273 0.097 4.31 × 10− 121 intron PABPC4L 0.328 - - - -
rs5020059 A T 3 1 155,507,544 0.085 2.008 0.273 1.91 × 10− 13 intron ASH1L 0.260 - - - -
rs55726352 G T 24 7 148,740,846 0.294 1.334 0.165 7.52 × 10− 16 intergenic PDIA4 0.468 - - - -
rs56043976 C G 4 1 158,593,909 0.414 1.071 0.181 3.05 × 10− 09 intron OR10Z1 0.161 - - - -
rs58470262 C T 8 2 152,143,842 0.233 1.558 0.164 2.3 × 10− 21 - NMI 0.186 - - - -
rs61870173 A C 31 10 91,823,836 0.104 2.447 0.185 5.14 × 10− 40 intergenic KIF20B 0.005 - 0.002 0.074 9.82 × 10− 1
rs61919163 A G 36 11 93,071,705 0.067 -0.302 0.048 3.13 × 10− 10 intron DEUP1 5.07 × 10− 14 2.78 × 10− 8 0.011 0.032 7.22 × 10− 1
rs62381642 C G 18 5 170,799,941 0.133 2.21 0.168 1.11 × 10− 39 intergenic NPM1 0.464 - - - -
rs636696 G T 34 11 48,435,748 0.412 0.545 0.086 2.88 × 10− 10 intergenic OR4C5 0.404 - 0.226 0.089 1.13 × 10− 2
rs66619306 C G 41 15 97,521,162 0.3 1.607 0.13 5.92 × 10− 35 intergenic NR2F2 0.583 - - - -
rs66715133 C G 36 11 92,668,132 0.12 0.332 0.051 6.23 × 10− 11 upstream MTNR1B 8.21 × 10− 14 5.36 × 10− 8 -0.032 0.092 7.31 × 10− 1
rs6698457 A T 1 1 46,741,639 0.016 3.463 0.395 1.84 × 10− 18 intron LRRC41 0.418 - - - -
rs67907831 A C 27 8 3,471,259 0.205 1.76 0.156 1.69 × 10− 29 intron CSMD1 0.103 - - - -
rs7047201 C T 30 9 108,307,717 0.103 2.376 0.186 1.62 × 10− 37 - FSD1L 0.454 - - - -
rs71208329 C T 8 2 151,915,828 0.036 3.079 0.268 1.6 × 10− 30 intergenic RBM43 0.035 - 0.322 0.409 4.31 × 10− 1
rs72843707 A C 44 17 59,901,157 0.194 2.518 0.103 5.13 × 10− 131 intron BRIP1 0.115 - - - -
rs74584198 C T 22 6 57,309,137 0.179 2.016 0.143 2.12 × 10− 45 - PRIM2 0.643 - - - -
rs75211051 A T 23 6 127,668,660 0.187 1.891 0.155 4.08 × 10− 34 - ECHDC1 0.010 - - - -
rs77055503 A C 16 5 86,304,226 0.077 2.83 0.191 8.53 × 10− 50 intron RASA1 0.363 - - - -
rs77515437 A C 21 6 47,662,280 0.154 2.515 0.115 1.17 × 10− 105 intron ADGRF4 0.302 - - - -
rs77695435 C G 48 18 18,512,213 0.389 1.28 0.15 1.19 × 10− 17 - ROCK1 0.189 - - - -
rs780094 C T 6 2 27,741,237 0.411 -0.186 0.03 4.43 × 10− 10 intron C2orf16 8.26 × 10− 19 1.25 × 10− 9 -0.142 0.030 2.54 × 10− 6
rs78020513 C T 35 11 92,089,311 0.034 -0.462 0.084 4.07 × 10− 08 intron FAT3 4.54 × 10− 09 1.39 × 10− 7 - - -
rs78265553 A G 36 11 92,732,391 0.031 -0.464 0.068 1.01 × 10− 11 intergenic MTNR1B 1.10 × 10− 18 1.08 × 10− 12 - - -
rs80067804 C T 43 16 32,526,341 0.486 1.617 0.112 4.98 × 10− 47 - ABCD1P3 0.421 - - - -
rs9285019 C T 17 5 95,719,294 0.284 0.324 0.031 5.55 × 10− 26 intron PCSK1 4.46 × 10− 32 1.24 × 10− 16 -0.136 0.029 1.91 × 10− 6

EA Effect allele, NEA Non-effect allele, CHR Chromosome, POS Position, MAF Minor allele frequency, BETAEUR, the effect value for GWAS of T2D-independent GDM in European populations, SEEUR, the standard error value for GWAS of T2D-independent GDM in European populations, PEUR, the P value for GWAS of T2D-independent GDM in European populations, PGDM, the P value for GWAS of original GDM in European populations, Preplication, the P value for GWAS of T2D-independent GDM at replication stage in European populations, BETAEAS, the effect value for GWAS of T2D-independent GDM in East Asian populations, SEEUR, the standard error value for GWAS of T2D-independent GDM in East Asian populations, PEUR, the P value for GWAS of T2D-independent GDM in East Asian populations