Supplementary Table 1: Details of genes and SNPs selected from 1q21-23 and 20q13 regions, their allelic and genotyping distributions, and their association with type 2 diabetes

Gene / SNP / Chromosome position / Position in gene / Allele 1/2 / Genotype Cases / Genotype Controls / MAF Cases / MAF Controls / OR (95%CI) / P
1q21-23 (Chr 1: 158Mb-160Mb)
DUSP23 / rs3806185 / 158015510 / 5' Flank / C/T / 474 /444 /101 / 466 /443 /97 / 0.317 / 0.317 / 1.00 (0.87 -1.15) / 0.992
rs3820099 / 158015812 / 5' Flank / A/C / 302 /507 /210 / 307 /508 /191 / 0.455 / 0.442 / 1.04 (0.92 -1.18) / 0.542
SLAMF8 / rs2501343 / 158061200 / 5' Flank / C/A / 835 /179 /5 / 814 /181 /11 / 0.093 / 0.101 / 1.11 (0.89 -1.37) / 0.356
rs12046006 / 158062102 / 5' Flank / T/C / 707 /289 /23 / 702 /282 /22 / 0.164 / 0.162 / 1.00 (0.84 -1.19) / 0.979
rs7418910 / 158072355 / 3' UTR / C/T / 912 /104 /3 / 894 /107 /5 / 0.054 / 0.058 / 1.13 (0.86 -1.49) / 0.366
VSIG8 / rs2501334 / 158099539 / 5' Flank / T/C / 378 /486 /153 / 377 /479 /150 / 0.389 / 0.387 / 1.02 (0.90 -1.17) / 0.738
rs2501338 / 158089294 / 3' Flank / A/T / 517 /423 /79 / 526 /414 /66 / 0.285 / 0.271 / 1.05 (0.91 -1.21) / 0.495
TAGLN2 / rs7513326 / 158162160 / 5' Flank / G/A / 365 /506 /147 / 375 /474 /157 / 0.394 / 0.392 / 1.01 (0.89 -1.15) / 0.884
rs1934075 / 158162603 / 5' Flank / C/T / 413 /471 /133 / 428 /463 /115 / 0.362 / 0.344 / 1.08 (0.95 -1.24) / 0.255
rs12122337 / 158153046 / 3' Flank / MAF <0.05
IGSF9 / rs1316275 / 158180012 / 5' UTR / A/G / 394 /487 /136 / 408 /459 /132 / 0.373 / 0.362 / 1.04 (0.91 -1.19) / 0.552
rs13052 / 158163750 / 3' UTR / A/G / 407 /404 /158 / 348 /453 /155 / 0.371 / 0.399 / 1.10 (0.97 -1.26) / 0.134
SLAMF9 / rs3806199 / 158190881 / 5' Flank / Assay failed
rs2840584 / 158192055 / 5' Flank / T/C / 526 /421 /72 / 526 /390 /90 / 0.277 / 0.283 / 1.04 (0.91 -1.2) / 0.541
rs2789419 / 158187450 / 3' Flank / T/A / 542 /401 /72 / 549 /374 /82 / 0.268 / 0.268 / 1.00 (0.87 -1.15) / 0.968
PIGM / rs2275404 / 158265064 / 3' Flank / G/A / 793 /216 /9 / 781 /206 /17 / 0.115 / 0.119 / 1.04 (0.85 -1.27) / 0.691
KCNJ10 / rs2486253 / 158276043 / 3' UTR / G/T / 665 /309 /45 / 664 /314 /28 / 0.196 / 0.184 / 1.10 (0.93 -1.29) / 0.267
KCNJ9 / rs4656876 / 158317016 / 5' Flank / C/G / 503 /418 /97 / 457 /449 /100 / 0.301 / 0.323 / 1.14 (0.99 -1.30) / 0.068
rs2753268 / 158324876 / 3' UTR / C/T / 662 /314 /42 / 610 /339 /57 / 0.195 / 0.225 / 1.20 (1.03 -1.40) / 0.022
IGSF8 / rs1131891 / 158328008 / 3' UTR / G/A / 842 /164 /13 / 845 /149 /12 / 0.093 / 0.086 / 1.07 (0.86 -1.33) / 0.543
rs3747619 / 158326384 / 3' Flank / Assay failed
ATP1A2 / rs3761685 / 158351267 / 5' Flank / T/C / 834 /171 /12 / 819 /177 /10 / 0.096 / 0.098 / 1.00 (0.81 -1.24) / 0.987
rs2070703 / 158378484 / 3' UTR / Assay failed
rs1046995 / 158379365 / 3' UTR / T/C / 556 /400 /63 / 533 /386 /87 / 0.258 / 0.278 / 1.06 (0.92 -1.22) / 0.426
rs3747625 / 158379995 / 3' UTR / T/A / 556 /400 /62 / 532 /387 /85 / 0.257 / 0.277 / 1.06 (0.92 -1.22) / 0.448
ATP1A4 / rs881291 / 158412797 / 5' Flank / A/G / 527 /413 /77 / 561 /372 /73 / 0.279 / 0.258 / 1.12 (0.97 -1.29) / 0.112
rs1408664 / 158413772 / 5' Flank / T/C / 450 /457 /112 / 443 /441 /122 / 0.334 / 0.34 / 1.03 (0.90 -1.18) / 0.679
rs860294 / 158423866 / 3' Flank / Assay failed
CASQ1 / rs659235 / 158425780 / 5' Flank / G/A / 727 /270 /22 / 704 /273 /29 / 0.154 / 0.165 / 1.06 (0.89 -1.25) / 0.544
PEA15 / rs1803942 / 158450564 / 3' UTR / Non-polymorphic
WDR42A / rs1132881 / 158452919 / 3' UTR / Non-polymorphic
PEX19 / rs2820421 / 158522628 / 5' Flank / T/G / 489 /434 /96 / 511 /422 /73 / 0.307 / 0.283 / 1.13 (0.98 -1.30) / 0.086
rs2301297 / 158521552 / 5' UTR / MAF <0.05
rs10594 / 158513809 / 3' UTR / G/C / 385 /476 /158 / 401 /476 /129 / 0.389 / 0.365 / 1.11 (0.97 -1.26) / 0.123
COPA / rs1886417 / 158580357 / 5' Flank / T/G / 381 /478 /158 / 402 /475 /128 / 0.39 / 0.364 / 1.12 (0.98 -1.28) / 0.085
rs3737794 / 158579954 / 5' UTR / C/G / 817 /157 /2 / 836 /144 /7 / 0.082 / 0.08 / 1.02 (0.81 -1.30) / 0.850
rs16831746 / 158525859 / 3' UTR / Non-polymorphic
NCSTN / rs2147471 / 158578469 / 5' Flank / T/G / 387 /475 /157 / 403 /475 /128 / 0.387 / 0.363 / 1.11 (0.97 -1.27) / 0.120
rs1324738 / 158579249 / 5' Flank / G/A / 858 /158 /2 / 848 /141 /9 / 0.08 / 0.08 / 1.00 (0.79 -1.26) / 0.982
rs12724113 / 158595428 / 3' Flank / G/A / 533 /394 /79 / 529 /398 /71 / 0.274 / 0.27 / 1.01 (0.87 -1.16) / 0.930
NHLH1 / rs10908776 / 158600986 / 5' Flank / C/T / 840 /176 /3 / 842 /156 /8 / 0.089 / 0.085 / 1.05 (0.84 -1.32) / 0.648
rs10908778 / 158607766 / 3' UTR / T/C / 478 /425 /109 / 431 /456 /114 / 0.318 / 0.342 / 1.10 (0.96 -1.26) / 0.154
rs7521304 / 158608639 / 3' UTR / G/T / 477 /445 /97 / 488 /438 /80 / 0.313 / 0.297 / 1.08 (0.94 -1.25) / 0.256
VANGL2 / rs11582932 / 158635996 / 5' Flank / T/G / 260 /519 /239 / 249 /521 /235 / 0.49 / 0.493 / 1.03 (0.91 -1.17) / 0.651
rs11265391 / 158664643 / 3' UTR / MAF <0.05
SLAMF6 / rs11265412 / 158719933 / 3' Flank / HWE deviated
CD84 / rs977020 / 158816203 / 5' Flank / T/C / 545 /367 /82 / 547 /368 /60 / 0.267 / 0.25 / 1.08 (0.93 -1.25) / 0.309
rs1055880 / 158784316 / 3' UTR / G/A / 668 /314 /37 / 660 /31036 / 0.19 / 0.19 / 1.03 (0.87 -1.21) / 0.758
rs11585738 / 158782886 / 3' UTR / A/G / 660 /317 /42 / 644 /319/43 / 0.197 / 0.201 / 1.05 (0.90 -1.23) / 0.553
SLAMF1 / rs11265455 / 158886775 / 5' Flank / A/G / 654 /324 /41 / 711 /272 /23 / 0.199 / 0.158 / 1.32 (1.12 -1.56) / 0.001
rs2295613 / 158883681 / 5' UTR / C/T / 855 /155 /8 / 811 /183 /4 / 0.084 / 0.096 / 1.19 (0.95 -1.50) / 0.124
rs1061217 / 158846639 / 3' UTR / C/T / 291 /495 /233 / 308 /487 /211 / 0.471 / 0.452 / 1.05 (0.93 -1.19) / 0.447
CD48 / rs352684 / 158948399 / 5' Flank / G/A / 448 /468 /103 / 464 /419 /123 / 0.331 / 0.33 / 1.01 (0.88 -1.16) / 0.872
rs1126644 / 158915173 / 3' UTR / A/G / 531 /384 /82 / 526 /398 /71 / 0.275 / 0.271 / 1.02 (0.89 -1.18) / 0.778
SLAMF7 / rs495706 / 158989880 / 3' UTR / G/A / 571 /386 /62 / 543 /386 /76 / 0.25 / 0.268 / 1.11 (0.96 -1.28) / 0.170
LY9 / rs540224 / 159029994 / 5' Flank / C/T / 293 /490 /235 / 268 /515 /223 / 0.472 / 0.478 / 1.01 (0.89 -1.15) / 0.854
rs1556517 / 159038385 / 3' UTR / G/T / 613 /342 /55 / 631 /324 /47 / 0.224 / 0.209 / 1.09 (0.94 -1.27) / 0.255
CD244 / rs12036670 / 159099485 / 5' Flank / Assay failed
rs16832486 / 159099152 / 5' UTR / MAF <0.05
rs480104 / 159067670 / 3' UTR / G/C / 490 /425 /104 / 472 /435 /98 / 0.311 / 0.314 / 1.00 (0.87 -1.14) / 0.976
rs485618 / 159067104 / 3' UTR / G/A / 365 /496 /158 / 370 /486 /147 / 0.398 / 0.389 / 1.05 (0.92 -1.20) / 0.467
ITLN1 / rs17551654 / 159121848 / 5' Flank / Assay failed
rs1333062 / 159112908 / 3' Flank / G/T / 370 /478 /171 / 384 /493 /128 / 0.402 / 0.373 / 1.15 (1.01 -1.32) / 0.032
ITLN2 / rs12730072 / 159191443 / 5' Flank / C/T / 825 /176 /18 / 806 /190 /10 / 0.104 / 0.104 / 1.01 (0.82 -1.24) / 0.947
rs6701920 / 159181541 / 3' UTR / Non-polymorphic
F11R / rs1062827 / 159233468 / 3' UTR / G/A / 797 /207 /11 / 734 /248 /22 / 0.113 / 0.145 / 1.36 (1.13 -1.65) / 0.001
rs12565932 / 159234079 / 3' UTR / T/C / 800 /207 /12 / 736 /248 /22 / 0.113 / 0.145 / 1.35 (1.12 -1.64) / 0.002
ARHGAP30 / rs3820098 / 159307242 / 5' Flank / T/G / 850 /154 /8 / 820 /159 /4 / 0.084 / 0.085 / 1.00 (0.79 -1.26) / 0.978
rs12070248 / 159282335 / 3' Flank / MAF <0.05
PVRL4 / rs11265550 / 159327014 / 5' Flank / T/A / 232 /535 /252 / 260 /498 /247 / 0.49 / 0.501 / 1.06 (0.93 -1.20) / 0.378
rs12116949 / 159308687 / 3' UTR / C/A / 513 /414 /91 / 502 /416 /88 / 0.293 / 0.294 / 1.01 (0.88 -1.16) / 0.855
PFDN2 / rs11576830 / 159335460 / 3' Flank / A/C / 650 /326 /35 / 637 /317 /51 / 0.196 / 0.209 / 1.07 (0.91 -1.25) / 0.425
NIT1 / rs4523530 / 159351397 / 5' Flank / G/T / 400 /491 /128 / 398 /454 /154 / 0.367 / 0.379 / 1.05 (0.92 -1.20) / 0.434
rs17389237 / 159359385 / 3' Flank / A/G / 745 /253 /21 / 737 /243 /26 / 0.145 / 0.147 / 1.00 (0.84 -1.20) / 0.991
DEDD / rs10797093 / 159370069 / 5' Flank / T/G / 657 /322 /40 / 647 /311 /47 / 0.197 / 0.202 / 1.03 (0.88 -1.20) / 0.754
rs34359959 / 159357091 / 3' Flank / Non-polymorphic
UFC1 / rs4656988 / 159389527 / 5' Flank / G/A / 417 /480 /122 / 411 /453 /142 / 0.355 / 0.366 / 1.04 (0.92 -1.19) / 0.516
rs3813614 / 159395783 / 3' Flank / Assay failed
USP21 / rs3813615 / 159395864 / 5' Flank / Assay failed
rs3402 / 159402045 / 3' UTR / MAF <0.05
PPOX / rs35194262 / 159401832 / 5' Flank / Non-polymorphic
rs2301286 / 159402848 / 5' UTR / C/A / 419 /478 /122 / 414 /452 /140 / 0.354 / 0.364 / 1.04 (0.91 -1.19) / 0.569
B4GALT3 / rs17392570 / 159414395 / 5' Flank / A/G / 742 /256 /20 / 729 /250 /26 / 0.145 / 0.15 / 1.02 (0.85 -1.22) / 0.835
rs36013429 / 159406362 / 3' Flank / Assay failed
ADAMTS4 / rs3813623 / 159435789 / 5' Flank / G/T / 841 /165 /12 / 804 /193 /9 / 0.093 / 0.105 / 1.13 (0.92 -1.39) / 0.246
rs4233366 / 159425771 / 3' Flank / HWE deviated
NDUFS2 / rs33941127 / 159434628 / 5' Flank / HWE deviated
FCER1G / rs11587213 / 159451499 / 5' Flank / A/G / 564 /386 /69 / 558 /369 /79 / 0.257 / 0.262 / 1.02 (0.88 -1.18) / 0.782
rs2070901 / 159451682 / 5' Flank / HWE deviated
rs11421 / 159455560 / 3' UTR / T/C / 752 /242 /25 / 735 /256 /15 / 0.143 / 0.142 / 1.01 (0.84 -1.21) / 0.953
APOA2 / rs5082 / 159460307 / 5' Flank / T/C / 592 /364 /63 / 569 /378 /59 / 0.24 / 0.247 / 1.05 (0.90 -1.21) / 0.550
rs6413454 / 159458834 / 3' Flank / Non-polymorphic
TOMM40L / rs3813627 / 159461772 / 5' Flank / G/T / 458 /455 /106 / 459 /440 /107 / 0.327 / 0.325 / 1.01 (0.88 -1.16) / 0.894
rs3813628 / 159462790 / 5' UTR / A/C / 448 /445 /96 / 456 /438 /98 / 0.322 / 0.32 / 1.01 (0.88 -1.17) / 0.844
rs2307421 / 159466404 / 3' UTR / NP
NR1I3 / rs2502805 / 159476465 / 5' Flank / C/T / 462 /453 /103 / 478 /424 /102 / 0.324 / 0.313 / 1.07 (0.93 -1.22) / 0.344
rs2307415 / 159472982 / 5' UTR / MAF <0.05
PCP4L1 / rs4656998 / 159493365 / 5' Flank / G/A / 700 /292 /26 / 712 /267 /26 / 0.169 / 0.159 / 1.10 (0.93 -1.31) / 0.277
rs4477295 / 159520904 / 3' UTR / G/C / 652 /325 /42 / 627 /341 /38 / 0.201 / 0.207 / 1.00 (0.85 -1.17) / 0.998
rs12091289 / 159521258 / 3' UTR / G/C / 651 /326 /42 / 627 /341 /38 / 0.201 / 0.207 / 1.00 (0.85 -1.17) / 0.998
MPZ / rs3813630 / 159546873 / 5' Flank / A/G / 418 /470 /130 / 447 /437 /122 / 0.359 / 0.339 / 1.10 (0.97 -1.26) / 0.147
rs16832786 / 159541529 / 3' UTR / T/C / 768 /228 /22 / 731 /255 /20 / 0.134 / 0.147 / 1.07 (0.89 -1.28) / 0.467
SDHC / rs12239492 / 159600899 / 3' UTR / G/C / 658 /316 /45 / 680 /298 /28 / 0.199 / 0.176 / 1.19 (1.01 -1.40) / 0.036
rs4600063 / 159599815 / 3' UTR / A/G / 658 /316 /45 / 680 /298 /28 / 0.199 / 0.176 / 1.19 (1.01 -1.40) / 0.036
C1ORF192 / rs16832884 / 159605084 / 5' Flank / A/G / 658 /316 /45 / 680 /298 /28 / 0.199 / 0.176 / 1.19 (1.01 -1.40) / 0.036
rs16832869 / 159601359 / 3' UTR / G/A / 658 /316 /43 / 680 /298 /28 / 0.198 / 0.176 / 1.18 (1.00 -1.39) / 0.051
HSPA6 / rs4657053 / 159759831 / 5' Flank / C/T / 271 /475 /193 / 327 /452 /181 / 0.459 / 0.424 / 1.14 (1.00 -1.30) / 0.051
rs12125379 / 159760670 / 5' UTR / Assay failed
rs9427403 / 159760946 / 5' UTR / HWE deviated
rs1042881 / 159763154 / 3' UTR / Assay failed
FCGR3A / rs485337 / 159786615 / 5' Flank / Non-polymorphic
rs448312 / 159779089 / 3' UTR / Assay failed
rs15811 / 159778309 / 3' UTR / Assay failed
FCGR2C / rs41299290 / 159764377 / 3' Flank / Assay failed
FCGR3B / rs435985 / 159860441 / 3' UTR / Assay failed
rs431875 / 159859510 / 3' Flank / Assay failed
FCGR2B / rs3820451 / 159898094 / 5' Flank / Non-polymorphic
rs844 / 159914157 / 3' UTR / Assay failed
FCRLA / rs17413333 / 159942204 / 5' Flank / G/A / 445 /447 /125 / 472 /439 /95 / 0.343 / 0.312 / 1.13 (0.99 -1.29) / 0.081
rs1538972 / 159943181 / 5' Flank / A/G / 710 /269 /40 / 683 /295 /27 / 0.171 / 0.174 / 1.01 (0.86 -1.19) / 0.886
rs1340977 / 159943528 / 5' UTR / C/T / 305 /503 /208 / 305 /497 /203 / 0.453 / 0.449 / 1.01 (0.89 -1.14) / 0.918
rs6683580 / 159951193 / 3' Flank / A/G / 449 /456 /114 / 469 /430 /106 / 0.336 / 0.319 / 1.06 (0.93 -1.22) / 0.376
FCRLB / rs1891019 / 159958057 / 5' Flank / T/C / 360 /487 /172 / 337 /497 /171 / 0.408 / 0.417 / 1.04 (0.92 -1.18) / 0.538
rs11590932 / 159958778 / 5' Flank / T/C / 553 /404 /62 / 558 /377 /71 / 0.259 / 0.258 / 1.02 (0.89 -1.18) / 0.756
rs16858733 / 159964601 / 3' Flank / G/C / 675 /306 /37 / 682 /292 /31 / 0.187 / 0.176 / 1.07 (0.90 -1.26) / 0.451
DUSP12 / rs905593 / 159984363 / 5' Flank / C/T / 757 /238 /24 / 752 /237 /17 / 0.14 / 0.135 / 1.03 (0.86 -1.24) / 0.749
rs12121310 / 159985839 / 5' Flank / A/C / 412 /482 /125 / 428 /450 /127 / 0.359 / 0.35 / 1.01 (0.89 -1.16) / 0.859
rs3820449 / 159993796 / 3' Flank / C/T / 687 /303 /29 / 687 /295 /24 / 0.177 / 0.171 / 1.02 (0.86 -1.21) / 0.813
ATF6 / rs16863838 / 160001742 / 5' Flank / G/C / 815/ 93/ 11 / 837/ 160/ 8 / 0.106 / 0.088 / 1.26 (1.02 -1.56) / 0.035
rs1136046 / 160195395 / 3' UTR / G/A / 584/ 370/ 65 / 620/ 345/ 41 / 0.245 / 0.212 / 1.22 (1.05 -1.42) / 0.011
20q13 (Chr 20: 46Mb-52Mb)
SULF2 / rs6018901 / 46125843 / 5' Flank / G/A / 887 /129 /2 / 849 /150 /6 / 0.065 / 0.081 / 1.26 (0.99 -1.62) / 0.062
rs11086240 / 46132081 / 3' Flank / G/T / 837 /173 /8 / 816 /181 /9 / 0.093 / 0.099 / 1.09 (0.88 -1.35) / 0.439
PREX1 / rs1885290 / 46878986 / 5' Flank / G/A / 548 /382 /87 / 507 /408 /91 / 0.273 / 0.293 / 1.13 (0.98 -1.30) / 0.083
rs2598 / 46675025 / 3' UTR / C/T / 395 /433 /100 / 375 /429 /107 / 0.341 / 0.353 / 1.06 (0.92 -1.22) / 0.435
ENSG00000166646 / rs6019380 / 46752252 / 5' Flank / C/T / 437 /454 /127 / 411 /454 /140 / 0.348 / 0.365 / 1.09 (0.95 -1.24) / 0.216
rs6095246 / 46754236 / 3' UTR / A/G / 395 /457 /166 / 411 /447 /148 / 0.388 / 0.369 / 1.07 (0.94 -1.22) / 0.285
ARFGEF2 / rs6066912 / 46970831 / 5' Flank / T/G / 443 /442 /134 / 422 /462 /120 / 0.348 / 0.35 / 1.02 (0.90 -1.17) / 0.749
rs707533 / 47085661 / 3' UTR / T/C / 544 /400 /73 / 511 /418 /76 / 0.268 / 0.284 / 1.12 (0.97 -1.29) / 0.128
CSE1L / rs17632 / 47146470 / 3' UTR / G/A / 413 /432 /170 / 393 /462 /144 / 0.38 / 0.375 / 1.02 (0.90 -1.16) / 0.756
STAU1 / rs348292 / 47239222 / 5' Flank / T/C / 340 /484 /195 / 332 /486 /187 / 0.429 / 0.428 / 1.03 (0.91 -1.17) / 0.674
rs1043361 / 47164565 / 3' UTR / T/C / 355 /401 /171 / 360 /463 /141 / 0.401 / 0.386 / 1.06 (0.93 -1.21) / 0.352
DDX27 / rs13038202 / 47269025 / 5' Flank / G/A / 863 /144 /12 / 856 /138 /11 / 0.082 / 0.08 / 1.02 (0.82 -1.28) / 0.842
ZNFX1 / rs6648 / 47328649 / 5' Flank / T/C / 848 /142 /11 / 838 /142 /12 / 0.082 / 0.084 / 1.08 (0.86-1.35) / 0.506
rs6122779 / 47326421 / 5' Flank / A/G / 299 /468 /250 / 279 /507 /219 / 0.476 / 0.47 / 1.03 (0.90 -1.16) / 0.702
rs7689 / 47295857 / 3' UTR / C/T / 547 /396 /75 / 538 /394 /74 / 0.268 / 0.269 / 1.01 (1.15 -0.88) / 0.942
C20ORF199 / rs6067025 / 47287427 / 3' Flank / A/G / 298 /468 /253 / 275/511 /220 / 0.478 / 0.473 / 1.02 (0.90 -1.16) / 0.720
KCNB1 / rs1502245 / 47534755 / 5' Flank / A/G / 296 /513 /205 / 312 /475 /209 / 0.455 / 0.448 / 1.04 (0.91 -1.18) / 0.588
rs1051295 / 47422312 / 3' UTR / A/G / 592 /365 /61 / 583 /354 /68 / 0.239 / 0.244 / 1.00 (0.86 -1.15) / 0.964
PTGIS / rs5602 / 47555385 / 3' UTR / G/A / 357 /496 /165 / 330 /474 /202 / 0.406 / 0.436 / 1.16 (1.02 -1.31) / 0.026
B4GALT5 / rs951497 / 47764927 / 5' Flank / G/A / 771 /225 /23 / 761 /228 /16 / 0.133 / 0.129 / 1.04 (0.86 -1.25) / 0.709
rs235032 / 47684154 / 3' UTR / HWE deviated
SLC9A8 / rs6020063 / 47862270 / 5' Flank / G/C / 504 /408 /105 / 525 /388 /92 / 0.304 / 0.285 / 1.08 (0.94 -1.23) / 0.287
rs1062840 / 47938873 / 3' UTR / C/T / 818 /181 /20 / 819 /177 /10 / 0.108 / 0.098 / 1.17 (0.95 -1.43) / 0.143
rs3210880 / 47939745 / 3' UTR / MAF <0.05
SPATA2 / rs1008687 / 47965499 / 5' Flank / C/A / 612 /299 /60 / 539 /299 /44 / 0.216 / 0.219 / 1.01 (0.87 -1.19) / 0.867
rs632376 / 47954017 / 3' UTR / C/T / 368 /448 /201 / 361 /484 /161 / 0.418 / 0.401 / 1.08 (0.95 -1.22) / 0.242
ZNF313 / rs16994995 / 47985663 / 5' Flank / Non-polymorphic
rs6125829 / 48002336 / 3' UTR / A/C / 366 /453 /200 / 359 /486 /161 / 0.419 / 0.402 / 1.08 (0.95 -1.22) / 0.252
SNAI1 / rs6020170 / 48031066 / 5' Flank / T/C / 692 /285 /39 / 669 /302 /34 / 0.179 / 0.184 / 1.01 (0.86 -1.19) / 0.920
rs1543442 / 48038206 / 3' UTR / C/T / 585 /362 /65 / 575 /364 /62 / 0.243 / 0.244 / 1.01 (0.88 -1.18) / 0.849
UBE2V1 / rs170825 / 48204298 / 5' Flank / G/T / 244 /521 /251 / 284 /486 /235 / 0.503 / 0.476 / 1.12 (0.99 -1.27) / 0.079
rs8585 / 48132330 / 3' UTR / Assay failed
rs1049871 / 48131198 / 3' UTR / Assay failed
CEBP / rs1888086 / 48239722 / 5' Flank / A/G / 919 /92 /9 / 898 /105 /3 / 0.053 / 0.055 / 1.02 (0.78 -1.34) / 0.882
rs4253449 / 48243032 / 3' Flank / MAF <0.05
LOC284751 / rs4811022 / 48341398 / 5' Flank / Assay failed
rs6125971 / 48349173 / 3' Flank / T/C / 571 /381 /62 / 546 /385 /75 / 0.249 / 0.266 / 1.10 (0.95 -1.27) / 0.199
PTPN1 / rs6096014 / 48633765 / 3' UTR / Non-polymorphic
rs16995311 / 48634509 / 3' Flank / Assay failed
ENSG00000182066 / rs914458 / 48644360 / 5' Flank / C/G / 664 /317 /38 / 677 /301 /28 / 0.193 / 0.177 / 1.12 (0.95 -1.32) / 0.182
rs6020622 / 48641049 / 3' Flank / MAF <0.05
C20orf175 / rs2426186 / 48687517 / 5' Flank / C/T / 464 /429 /125 / 459 /432 /101 / 0.334 / 0.32 / 1.04 (0.91 -1.19) / 0.527
rs6096019 / 48647352 / 3' UTR / Assay failed
PARD6B / rs231582 / 48780691 / 5' Flank / G/C / 487 /403 /99 / 510 /386 /87 / 0.304 / 0.285 / 1.09 (0.95 -1.26) / 0.209
rs6020721 / 48800483 / 3' UTR / T/G / 311 /494 /209 / 284 /519 /201 / 0.45 / 0.459 / 1.04 (0.91 -1.18) / 0.594
rs1054185 / 48802413 / 3' UTR / C/T / 512 /406 /99 / 524 /394 /88 / 0.297 / 0.283 / 1.07 (0.93 -1.22) / 0.357
BCAS4 / rs6020752 / 48844676 / 5' Flank / A/G / 377 /477 /143 / 384 /453 /155 / 0.383 / 0.384 / 1.02 (0.89 -1.16) / 0.804
rs6702 / 48927016 / 3' UTR / C/T / 546 /410 /63 / 545 /391 /70 / 0.263 / 0.264 / 1.00 (0.86 -1.15) / 0.990
ADNP / rs761240 / 48941299 / 3' UTR / C/A / 901 /113 /5 / 906 /95 /5 / 0.06 / 0.052 / 1.12 (0.86 -1.47) / 0.402
rs875068 / 48939602 / 3' UTR / G/C / 476 /440 /103 / 503 /403 /100 / 0.317 / 0.3 / 1.09 (0.95 -1.24) / 0.235
DPM1 / rs2281282 / 49008741 / 5' Flank / Assay failed
MOCS3 / rs2426214 / 49007217 / 5' Flank / Assay failed
rs6013047 / 49011502 / 3' Flank / MAF <0.05
KCNG1 / rs6020919 / 49073584 / 5' Flank / Assay failed
rs1850 / 49053678 / 3' UTR / A/G / 524 /401 /92 / 511 /412 /83 / 0.288 / 0.288 / 1.02 (0.89 -1.17) / 0.806
NFATC2 / rs4811191 / 49593442 / 5' Flank / C/T / 591 /347 /79 / 582 /354 /64 / 0.248 / 0.241 / 1.06 (0.92 -1.22) / 0.431
rs763944 / 49440622 / 3' Flank / C/T / 288 /494 /237 / 262 /506 /238 / 0.475 / 0.488 / 1.07 (0.94 -1.21) / 0.306
ATP9A / rs6021427 / 49819497 / 5' Flank / T/A / 686 /272 /38 / 660 /300 /34 / 0.175 / 0.185 / 1.05 (0.89 -1.24) / 0.543
rs1048712 / 49651027 / 3' UTR / G/A / 416 /487 /96 / 427 /428 /112 / 0.34 / 0.337 / 1.01 (0.88 -1.16) / 0.846
rs3827044 / 49649693 / 3' UTR / A/C / 268 /517 /233 / 261 /515 /230 / 0.483 / 0.485 / 1.03 (0.90 -1.17) / 0.706
rs1048807 / 49646956 / 3' UTR / T/C / 709 /290 /20 / 699 /274 /33 / 0.162 / 0.169 / 1.07 (0.90 -1.27) / 0.425
SALL4 / rs6021451 / 49852802 / 5' Flank / T/G / 742 /251 /25 / 755 /238 /12 / 0.148 / 0.13 / 1.19 (0.99 -1.43) / 0.066
rs6021435 / 49833487 / 3' Flank / T/G / 582 /365 /72 / 555 /379 /72 / 0.25 / 0.26 / 1.05 (0.91 -1.22) / 0.475
ZFP64 / rs3761137 / 50242571 / 5' Flank / C/T / 319 /484 /215 / 293 /496 /216 / 0.449 / 0.462 / 1.06 (0.94 -1.20) / 0.361
rs16996504 / 50200713 / 3' Flank / MAF <0.05
rs7268277 / 50132712 / 3' Flank / A/G / 453 /451 /115 / 448 /444 /113 / 0.334 / 0.333 / 1.01 (0.88 -1.15) / 0.913
TSHZ2 / rs2741373 / 51539379 / 3' UTR / T/C / 637 /334 /47 / 607 /349 /49 / 0.21 / 0.222 / 1.08 (0.93 -1.26) / 0.335
ENSG00000197670 / rs1555925 / 51602996 / 5' UTR / G/C / 385 /479 /155 / 374 /480 /152 / 0.387 / 0.39 / 1.05 (0.92 -1.19) / 0.495
rs6063966 / 51626495 / 3' Flank / G/A / 751 /251 /17 / 754 /231 /21 / 0.14 / 0.136 / 1.02 (0.85 -1.23) / 0.814
ENSG00000197349 / rs2766671 / 51617909 / 5' Flank / Assay failed
ZNF217 / rs3748501 / 51632902 / 5' UTR / T/C / 858 /148 /13 / 863 /139 /4 / 0.085 / 0.073 / 1.23 (0.97 -1.54) / 0.083
rs16998248 / 51631747 / 5' UTR / T/A / 686 /297 /36 / 649 /319 /38 / 0.181 / 0.196 / 1.02 (0.87 -1.20) / 0.814
rs1555926 / 51618351 / 3' UTR / T/C / 849 /163 /5 / 851 /148 /7 / 0.085 / 0.081 / 1.02 (0.81 -1.28) / 0.884
rs1056949 / 51617096 / 3' UTR / MAF <0.05
ENSG00000149617 / rs13039214 / 51926806 / 5' Flank / A/G / 428 /456 /134 / 424 /464 /118 / 0.356 / 0.348 / 1.02 (0.89 -1.16) / 0.775
rs1859902 / 51922612 / 3' Flank / T/C / 682 /296 /41 / 631 /323 /52 / 0.186 / 0.212 / 1.14 (0.97 -1.33) / 0.101

MAF: minor allele frequency, OR: odds ratio, CI: confidence interval. OR (95%CI) and P values presented were calculated using logistic regression assuming additive model adjusted for age, sex and BMI. OR (95%CI) are presented with respect to the risk alleles that are underlined. Chromosome positions are relative to NCBI Build 36.3 assembly, dbSNP b126. SNPs showing association at P<0.05 are highlighted in bold text.

Supplementary Table 2: SNPs showing association with type 2 diabetes in BMI stratified analysis

SNP / Gene / Position in gene / Alleles / RAF / OR (95%CI) / P
Type 2 diabetes patients / Controls
Subjects
Normal-weight subjects (284 patients; 446 controls)
rs2753268 / IGSF8 / 3' UTR / C/T / 0.836 / 0.773 / 1.45 (1.10 -1.89) / 7.510-3
rs881291 / ATP1A4 / 5' Flank / A/G / 0.308 / 0.240 / 1.42 (1.12 -1.80) / 3.810-3
rs10908778 / NHLH1 / 3' UTR / T/C / 0.692 / 0.640 / 1.30 (1.03 -1.64) / 0.0264
rs2598 / PREX1 / 3' UTR / C/T / 0.722 / 0.642 / 1.43 (1.11 -1.82) / 4.910-3
rs6019380 / ENSG00000166646 / 5' Flank / C/T / 0.714 / 0.635 / 1.37 (1.10 -1.72) / 6.210-3
rs6095246 / ENSG00000166646 / 3' UTR / A/G / 0.423 / 0.366 / 1.25 (1.01 -1.55) / 0.042
rs1008687 / SPATA2 / 5' Flank / C/A / 0.796 / 0.744 / 1.37 (1.05 -1.79) / 0.021
rs6125971 / LOC284751 / 3' Flank / T/C / 0.785 / 0.734 / 1.33 (1.03 -1.72) / 0.026
rs6021451 / SALL4 / 5' Flank / T/G / 0.182 / 0.141 / 1.36 (1.02 -1.81) / 0.035
rs3748501 / ZNF217 / 5' UTR / T/C / 0.116 / 0.079 / 1.46 (1.03 -2.09) / 0.034
Overweight/obese subjects (665 patients; 588 controls)
rs11265455 / SLAMF1 / 5' Flank / A/G / 0.201 / 0.162 / 1.31 (1.06-1.62) / 0.012
rs1333062 / ITLN1 / 3' Flank / G/T / 0.400 / 0.344 / 1.28 (1.09-1.52) / 3.410-3
rs1062827 / F11R / 3' UTR / G/A / 0.884 / 0.851 / 1.35 (1.08 -1.69) / 0.011
rs12565932 / F11R / 3' UTR / T/C / 0.883 / 0.851 / 1.33 (1.06 -1.69) / 0.013
rs2070901 / FCER1G / 5' Flank / G/T / 0.417 / 0.368 / 1.22 (1.04-1.43) / 0.014
rs2502805 / NR1I3 / 5' Flank / C/T / 0.336 / 0.297 / 1.20 (1.01-1.43) / 0.033
rs4657053 / HSPA6 / 5' Flank / C/T / 0.467 / 0.411 / 1.25 (1.06-1.48) / 7.310-3
rs5602 / PTGIS / 3' UTR / G/A / 0.596 / 0.556 / 1.18 (1.39 -1.01) / 0.042

RAF: risk allele frequency, OR: odds ratio, CI: confidence interval. OR (95%CI) and P values presented were adjusted for age and sex. OR (95%CI) are presented with respect to the risk alleles that are underlined.

Supplementary Table 3: Association of SNPs with quantitative traits related to type 2 diabetes in North Indians

SNP / Gene / Minor Allele / Trait / Mean 11 / Mean 12 / Mean 22 / BETA / L95 / U95 / P
1q21-23
rs3806185 / DUSP23 / T / WHR / 0.91 ± 0.08 / 0.93 ± 0.08 / 0.92 ± 0.08 / 0.01 / 0.00 / 0.01 / 0.043
TG / 1.45 ± 0.86 / 1.65 ± 0.88 / 1.57 ± 0.83 / 0.11 / 0.03 / 0.18 / 9.910-3
Creatinine / 67.18 ± 18.56 / 70.72 ± 18.56 / 68.95 ± 18.56 / 1.77 / 0.00 / 3.54 / 0.041
rs3820099 / DUSP23 / C / CRP / 1.72 ± 2.02 / 2.06 ± 2.06 / 2.06 ± 1.88 / 0.21 / 0.03 / 0.40 / 0.026
rs12046006 / SLAMF8 / G / FPG / 4.81 ± 0.62 / 4.93 ± 0.66 / 4.85 ± 0.66 / 0.08 / 0.01 / 0.16 / 0.028
rs2501334 / SLAMF8 / C / CRP / 2.10 ± 2.00 / 1.93 ± 2.04 / 1.68 ± 1.97 / -0.21 / -0.39 / -0.02 / 0.028
rs1316275 / IGSF9 / C / WC / 87.1 ± 11.3 / 87.5 ± 11.7 / 85.1 ± 11.6 / -0.7 / -1.32 / -0.08 / 0.027
WHR / 0.92 ± 0.07 / 0.92 ± 0.08 / 0.91 ± 0.08 / -0.01 / -0.01 / 0.00 / 0.042
HDL-C / 1.10 ± 0.34 / 1.12 ± 0.36 / 1.17 ± 0.36 / 0.03 / 0.00 / 0.07 / 0.044
rs2789419 / SLAMF9 / T / Creatinine / 69.84 ± 19.45 / 68.07 ± 17.68 / 67.18 ± 15.91 / -1.77 / -3.54 / 0.00 / 0.029
rs881291 / ATP1A4 / C / HbA1c / 5.19 ± 0.49 / 5.23 ± 0.47 / 5.31 ± 0.44 / 0.05 / 0.00 / 0.09 / 0.032
TG / 1.46 ± 0.87 / 1.66 ± 0.87 / 1.69 ± 0.76 / 0.14 / 0.06 / 0.23 / 6.610-4
rs1408664 / ATP1A4 / G / TG / 1.64 ± 0.87 / 1.46 ± 0.86 / 1.55 ± 0.85 / -0.09 / -0.17 / -0.01 / 0.020
rs659235 / CASQ1 / A / HC / 0.94 ± 0.11 / 0.95 ± 0.10 / 0.94 ± 0.10 / 1.02 / 0.25 / 1.79 / 9.510-3
WC / 87.0 ± 12.0 / 87.7 ± 11.2 / 88.2 ± 12.5 / 1.07 / 0.27 / 1.87 / 9.210-3
Urea / 9.00 ± 3.11 / 8.60 ± 2.72 / 8.03 ± 3.14 / -0.36 / -0.72 / -0.01 / 0.044
UA / 292.25 ± 223.34 / 313.04 ± 223.34 / 402.14 ± 283.34 / 29.11 / 4.16 / 54.05 / 0.023
rs10594 / PEX19 / C / HbA1c / 5.18 ± 0.47 / 5.22 ± 0.49 / 5.26 ± 0.47 / 0.04 / 0.00 / 0.09 / 0.040
rs1324738 / NCSTN / A / Creatinine / 68.95 ± 18.56 / 67.18 ± 18.56 / 64.53 ± 15.91 / -2.65 / -6.19 / 0.00 / 0.027
rs3737794 / COPA / C / Creatinine / 69.84 ± 18.56 / 67.18 ± 19.45 / 60.11 ± 10.61 / -2.65 / -5.3 / 0.00 / 0.033
rs1886417 / COPA / C / HbA1c / 5.18 ± 0.47 / 5.22 ± 0.49 / 5.26 ± 0.47 / 0.04 / 0.00 / 0.09 / 0.043
CRP / 1.84 ± 2.04 / 1.98 ± 2.00 / 2.27 ± 2.01 / 0.20 / 0.01 / 0.39 / 0.042
rs10908776 / NHLH1 / A / LDL-C / 2.89 ± 0.87 / 3.05 ± 0.82 / 2.79 ± 1.02 / 0.14 / 0.01 / 0.28 / 0.039
rs7521304 / NHLH1 / T / BMI / 23.70 ± 4.80 / 24.30 ± 4.90 / 24.70 ± 5.20 / 0.50 / 0.02 / 0.97 / 0.040
rs1061217 / SLAMF1 / T / HDL-C / 1.10 ± 0.35 / 1.11 ± 0.34 / 1.17 ± 0.37 / 0.03 / 0.00 / 0.06 / 0.041
rs11265455 / SLAMF1 / C / FPI / 47.7 ± 50.94 / 43.38 ± 46.50 / 18.24 ± 37.20 / -8.10 / -14.10 / -2.10 / 8.410-3
C-peptide / 0.62 ± 0.34 / 0.57 ± 0.33 / 0.51 ± 0.29 / -0.05 / -0.09 / -0.01 / 0.019
HOMA-IR / 1.74 ± 1.92 / 1.59 ± 1.78 / 0.72 ± 1.54 / -0.29 / -0.52 / -0.06 / 0.012
rs540224 / LY9 / A / Creatinine / 68.07 ± 18.56 / 68.95 ± 18.56 / 70.72 ± 18.56 / 1.77 / 0.00 / 3.54 / 0.034
rs1556517 / LY9 / A / HDL-C / 1.10 ± 0.35 / 1.16 ± 0.36 / 1.18 ± 0.360 / 0.05 / 0.01 / 0.09 / 0.012
rs485618 / CD244 / A / WC / 88.3 ± 11.7 / 86.1 ± 11.0 / 86.83± 12.2 / -1.02 / -1.64 / -0.41 / 1.210-3
HbA1c / 5.24 ± 0.48 / 5.20 ± 0.48 / 5.15 ± 0.48 / -0.05 / -0.09 / -0.01 / 0.027
C-peptide / 0.63 ± 0.34 / 0.58 ± 0.32 / 0.59 ± 0.38 / -0.04 / -0.07 / 0.00 / 0.030
HDL-C / 1.15 ± 0.35 / 1.11 ± 0.36 / 1.07 ± 0.33 / -0.04 / -0.07 / -0.01 / 0.013
rs1333062 / ITLN1 / A / BMI / 24.4 ± 4.80 / 24.10 ± 4.90 / 22.9 ± 4.80 / -0.62 / -1.07 / -0.17 / 6.810-3
rs12730072 / ITLN2 / A / TC / 4.48 ± 1.08 / 4.63 ± 0.99 / 5.14 ± 0.74 / 0.19 / 0.04 / 0.35 / 0.011
LDL-C / 2.88 ± 0.88 / 3.02 ± 0.80 / 3.35 ± 0.76 / 0.17 / 0.05 / 0.29 / 6.910-3
rs1062827 / F11R / T / CRP / 1.89 ± 2.03 / 2.11 ± 1.93 / 3.00 ± 2.44 / 0.29 / 0.04 / 0.55 / 0.025
rs12565932 / F11R / C / CRP / 1.88 ± 2.03 / 2.11 ± 1.93 / 3.00 ± 2.44 / 0.30 / 0.04 / 0.56 / 0.022
rs3820098 / ARHGAP30 / C / LDL-C / 2.94 ± 0.85 / 2.81 ± 0.91 / 1.87 ± 1.04 / -0.17 / -0.31 / -0.03 / 0.016
rs17389237 / NIT1 / G / WC / 86.8 ± 11.5 / 87.7 ± 11.3 / 85.1 ± 13.7 / 1.10 / 0.28 / 1.93 / 9.110-3
WHR / 0.92 ± 0.08 / 0.92 ± 0.08 / 0.94 ± 0.07 / 0.01 / 0.00 / 0.02 / 0.010
HbA1c / 5.19 ± 0.47 / 5.26 ± 0.50 / 5.30 ± 0.47 / 0.06 / 0.00 / 0.12 / 0.036
C-peptide / 0.59 ± 0.34 / 0.64 ± 0.33 / 0.65 ± 0.40 / 0.05 / 0.01 / 0.10 / 0.012
rs17392570 / B4GALT3 / G / WC / 86.8 ± 11.5 / 87.6 ± 11.3 / 86.9 ± 13.4 / 1.20 / 0.38 / 2.03 / 4.210-3
WHR / 0.92 ± 0.08 / 0.92 ± 0.08 / 0.94 ± 0.07 / 0.01 / 0.00 / 0.02 / 0.014
HbA1c / 5.19 ± 0.47 / 5.25 ± 0.49 / 5.32 ± 0.48 / 0.06 / 0.00 / 0.12 / 0.036
C-peptide / 0.59 ± 0.34 / 0.63 ± 0.32 / 0.66 ± 0.41 / 0.05 / 0.01 / 0.09 / 0.021
rs11587213 / FCER1G / G / WC / 86.6 ± 11.7 / 87.5 ± 11.4 / 87.3 ± 11.2 / 0.72 / 0.06 / 1.38 / 0.032
WHR / 0.92 ± 0.08 / 0.92 ± 0.08 / 0.93 ± 0.07 / 0.01 / 0.00 / 0.01 / 0.042
Urea / 9.07 ± 3.03 / 8.93 ± 3.11 / 8.21 ± 2.75 / -0.33 / -0.60 / -0.07 / 0.014
rs3813627 / TOMM40L / A / WC / 87.6 ± 11.8 / 86.2 ± 11.0 / 87.5 ± 12.1 / -0.67 / -1.30 / -0.03 / 0.040
rs3813628 / TOMM40L / C / WC / 87.6 ± 11.8 / 86.2 ± 11.1 / 87.3 ± 12.4 / -0.67 / -1.31 / -0.02 / 0.042
rs4656998 / PCP4L1 / T / TG / 1.58 ± 0.86 / 1.51 ± 0.90 / 1.18 ± 0.73 / -0.11 / -0.21 / -0.01 / 0.029
rs4477295 / PCP4L1 / C / TC / 4.56 ± 1.05 / 4.45 ± 1.08 / 4.22 ± 0.90 / -0.13 / -0.25 / -0.02 / 0.024
LDL-C / 2.97 ± 0.86 / 2.84 ± 0.87 / 2.56 ± 0.74 / -0.15 / -0.25 / -0.06 / 1.310-3
Uric Acid / 289.28 ± 223.94 / 320.76 ± 225.72 / 326.7 ± 253.64 / 29.70 / 5.94 / 53.46 / 0.014
rs12091289 / PCP4L1 / C / TC / 4.56 ± 1.05 / 4.45 ± 1.08 / 4.22 ± 0.90 / -0.13 / -0.25 / -0.02 / 0.024
LDL-C / 2.97 ± 0.86 / 2.84 ± 0.87 / 2.56 ± 0.74 / -0.15 / -0.25 / -0.06 / 1.310-3
UA / 289.28 ± 223.94 / 320.76 ± 225.72 / 330.86 ± 253.64 / 29.70 / 5.94 / 53.46 / 0.014
rs4657053 / HSPA6 / A / LDL-C / 2.97 ± 0.86 / 2.92 ± 0.86 / 2.77 ± 0.81 / -0.09 / -0.16 / -0.01 / 0.021
rs6683580 / FCRLA / C / FPI / 41.34 ± 47.28 / 49.2 ± 51.36 / 53.10 ± 52.14 / 6.90 / 2.34 / 11.46 / 3.010-3
HOMA-IR / 1.51 ± 1.80 / 1.79 ± 1.94 / 1.99 ± 1.96 / 0.27 / 0.10 / 0.45 / 2.310-3
TG / 1.61 ± 0.80 / 1.51 ± 0.93 / 1.42 ± 0.87 / -0.08 / -0.16 / -0.01 / 0.035
rs1891019 / FCRLB / C / FPG / 4.77 ± 0.60 / 4.88 ± 0.64 / 4.89 ± 0.67 / 0.06 / 0.01 / 0.12 / 0.023
FPI / 41.28 ± 47.04 / 47.22 ± 50.22 / 51.30 ± 52.86 / 4.56 / 0.18 / 8.94 / 0.042
HOMA-IR / 1.48 ± 1.77 / 1.74 ± 1.92 / 1.89 ± 1.97 / 0.19 / 0.03 / 0.36 / 0.024
rs11590932 / FCRLB / C / Creatinine / 69.84 ± 18.56 / 68.07 ± 18.56 / 66.30 ± 16.80 / -1.77 / -3.54 / 0.00 / 0.039
rs16858733 / FCRLB / C / BMI / 24.20 ± 4.90 / 23.70 ± 4.90 / 23.00 ± 4.80 / -0.59 / -1.14 / -0.04 / 0.035
FPG / 4.80 ± 0.62 / 4.91 ± 0.64 / 5.11 ± 0.64 / 0.13 / 0.06 / 0.20 / 3.310-4
FPI / 43.38 ± 48.00 / 50.4 ± 52.86 / 60.18 ± 53.82 / 8.82 / 3.12 / 14.58 / 2.510-3
HOMA-IR / 1.57 ± 1.81 / 1.87 ± 2.00 / 2.44 ± 1.97 / 0.40 / 0.19 / 0.62 / 3.210-4
rs905593 / DUSP12 / T / FPG / 4.81 ± 0.62 / 4.93 ± 0.66 / 5.08 ± 0.60 / 0.14 / 0.05 / 0.22 / 1.110-3
rs12121310 / DUSP12 / C / FPG / 4.8 ± 0.64 / 4.85 ± 0.62 / 4.97 ± 0.65 / 0.08 / 0.02 / 0.13 / 9.410-3
rs3820449 / DUSP12 / T / HC / 94.4 ± 10.3 / 93.6 ± 10.7 / 94.2 ± 10.7 / -0.79 / -1.57 / -0.02 / 0.045
rs16863838 / ATF6 / G / UA / 292.84 ± 224.53 / 340.96 ± 226.31 / 396.79 ± 318.98 / 52.27 / 19.01 / 84.94 / 1.910-3
rs1136046 / ATF6 / A / BMI / 24.30 ± 4.80 / 23.60 ± 4.90 / 23.30 ± 5.20 / -0.65 / -1.17 / -0.13 / 0.015
C-peptide / 0.59 ± 0.32 / 0.61 ± 0.36 / 0.66 ± 0.39 / 0.04 / 0.00 / 0.08 / 0.045
20q13
rs2598 / PREX1 / T / HbA1c / 5.25 ± 0.48 / 5.19 ± 0.49 / 5.17 ± 0.50 / -0.05 / -0.09 / 0.00 / 0.040
rs13038202 / DDX27 / A / WC / 86.7 ± 11.3 / 88.4 ± 12.6 / 93.0 ± 12.0 / 1.37 / 0.29 / 2.45 / 0.013
FPI / 44.46 ± 49.8 / 52.80 ± 49.44 / 70.14 ± 25.56 / 9.12 / 1.44 / 16.8 / 0.020
HOMA-IR / 1.63 ± 1.89 / 1.90 ± 1.86 / 2.54 ± 1.20 / 0.31 / 0.02 / 0.6 / 0.036
rs6067025 / C20ORF199 / G / WC / 87.8 ± 12.2 / 87.0 ± 11.2 / 85.9 ± 11.2 / -0.73 / -1.33 / -0.12 / 0.018
rs7689 / ZNFX1 / T / FPG / 4.82 ± 0.63 / 4.85 ± 0.64 / 5.00 ± 0.58 / 0.06 / 0.00 / 0.13 / 0.044
rs6122779 / ZNFX1 / G / WC / 87.7 ± 12.2 / 87.0 ± 11.2 / 85.9 ± 11.2 / -0.70 / -1.30 / -0.10 / 0.023
rs6648 / ZNFX1 / C / WC / 86.6 ± 11.2 / 88.3 ± 12.8 / 92.9 ± 11.4 / 1.26 / 0.20 / 2.32 / 0.020
FPI / 44.52 ± 49.80 / 51.6 ± 50.94 / 68.76 ± 24.48 / 7.74 / 0.18 / 15.3 / 0.045
rs1051295 / KCNB1 / G / FPG / 4.82 ± 0.63 / 4.85 ± 0.64 / 5.00 ± 0.62 / 0.06 / 0.00 / 0.13 / 0.043
rs1062840 / SLC9A8 / T / BMI / 24.30 ± 4.80 / 23.00 ± 5.30 / 23.10 ± 4.90 / -1.19 / -1.89 / -0.48 / 1.010-3
rs632376 / SPATA2 / T / BMI / 24.30 ± 4.80 / 24.20 ± 4.80 / 23.00 ± 5.50 / -0.53 / -0.96 / -0.10 / 0.016
rs1008687 / SPATA2 / A / BMI / 24.40 ± 4.70 / 23.40 ± 4.90 / 22.10 ± 5.70 / -1.13 / -1.66 / -0.60 / 3.410-5
HC / 95.6 ± 10.1 / 93.1 ± 10.5 / 91.6 ± 10.8 / -0.79 / -1.52 / -0.06 / 0.035
FPI / 52.56 ± 48.54 / 39.42 ± 51.36 / 33.06 ± 55.56 / -9.00 / -14.64 / -3.36 / 1.810-3
HOMA-IR / 1.94 ± 1.83 / 1.40 ± 1.95 / 1.26 ± 2.06 / -0.35 / -0.57 / -0.14 / 1.210-3
rs6125829 / ZNF313 / C / BMI / 24.30 ± 4.80 / 24.20 ± 4.80 / 23.00 ± 5.40 / -0.51 / -0.94 / -0.08 / 0.021
rs6020170 / SNAI1 / C / BMI / 24.30 ± 4.80 / 23.50 ± 5.10 / 24.00 ± 4.70 / -0.65 / -1.20 / -0.11 / 0.019
FPI / 48.66 ± 49.38 / 41.58 ± 50.22 / 30.84 ± 47.28 / -6.30 / -11.88 / -0.78 / 0.02
HOMA-IR / 1.79 ± 1.86 / 1.5 ± 1.91 / 1.10 ± 1.77 / -0.26 / -0.47 / -0.05 / 0.017
rs170825 / UBE2V1 / T / FPG / 4.8 ± 0.65 / 4.84 ± 0.63 / 4.91 ± 0.61 / 0.06 / 0.01 / 0.11 / 0.031
FPI / 39.54 ± 48.78 / 45.96 ± 49.5 / 53.34 ± 50.34 / 6.54 / 2.28 / 10.74 / 2.610-3
HOMA-IR / 1.4 ± 1.88 / 1.69 ± 1.86 / 1.98 ± 1.88 / 0.27 / 0.10 / 0.43 / 1.310-3
rs914458 / ENSG00000182066 / G / HDL-C / 1.14 ± 0.35 / 1.09 ± 0.34 / 1.09 ± 0.51 / -0.04 / -0.08 / 0.00 / 0.044
rs231582 / PARD6B / C / CRP / 2.12 ± 2.05 / 1.84 ± 1.97 / 1.70 ± 2.03 / -0.22 / -0.41 / -0.02 / 0.034
rs1054185 / PARD6B / T / CRP / 2.11 ± 2.04 / 1.81 ± 1.97 / 1.73 ± 2.00 / -0.22 / -0.41 / -0.02 / 0.032
rs761240 / ADNP / A / CRP / 1.90 ± 1.99 / 2.44 ± 2.23 / 2.94 ± 1.97 / 0.47 / 0.08 / 0.86 / 0.019
rs6013047 / MOCS3 / G / HC / 93.9 ± 10.4 / 97.4 ± 10.1 / 85.4 ± 11.6 / 1.48 / 0.14 / 2.81 / 0.031
rs1850 / KCNG1 / G / FPI / 41.1 ± 50.28 / 50.34 ± 48.24 / 52.86 ± 50.94 / 5.34 / 0.60 / 10.08 / 0.028
HOMA-IR / 1.50 ± 1.91 / 1.84 ± 1.82 / 1.92 ± 1.92 / 0.19 / 0.01 / 0.37 / 0.043
TC / 4.57 ± 1.04 / 4.47 ± 1.08 / 4.36 ± 1.06 / -0.13 / -0.23 / -0.03 / 0.011
HDL-C / 1.15 ± 0.36 / 1.10 ± 0.34 / 1.11 ± 0.33 / -0.04 / -0.08 / -0.01 / 0.017
rs7268277 / ZFP64 / G / HC / 94.8 ± 10.5 / 93.3 ± 10.3 / 95.0 ± 10.9 / -0.69 / -1.29 / -0.09 / 0.025
rs2741373 / TSHZ2 / C / FPI / 42.48 ± 48.12 / 51.0 ± 52.02 / 50.40 ± 49.20 / 6.18 / 1.02 / 11.34 / 0.019
C-peptide / 0.58 ± 0.33 / 0.63 ± 0.36 / 0.65 ± 0.35 / 0.04 / 0.00 / 0.08 / 0.032
HOMA-IR / 1.54 ± 1.81 / 1.86 ± 1.99 / 2.00 ± 1.83 / 0.27 / 0.07 / 0.47 / 7.910-3
LDL-C / 2.86 ± 0.87 / 2.97 ± 0.84 / 3.07 ± 0.91 / 0.11 / 0.02 / 0.20 / 0.021
UA / 284.53 ± 228.1 / 329.67 ± 220.97 / 301.16 ± 223.94 / 32.08 / 9.50 / 54.65 / 5.510-3
rs1555925 / ENSG00000197670 / C / Creatinine / 70.72 ± 18.56 / 67.18 ± 18.56 / 69.84 ± 18.56 / -1.77 / -3.54 / 0.00 / 0.044
rs1056949 / ZNF217 / G / WC / 86.8 ± 11.5 / 89.0 ± 10.9 / 105.1 ± 13.8 / 1.52 / 0.04 / 3.00 / 0.044
Urea / 8.93 ± 3.03 / 8.03 ± 2.82 / 5.18 ± 7.03 / -0.84 / -1.50 / -0.19 / 0.012
rs1555926 / ZNF217 / C / BMI / 23.90 ± 4.90 / 25.10 ± 5.00 / 23.20 ± 4.90 / 0.85 / 0.08 / 1.62 / 0.031
UA / 305.32 ± 226.91 / 279.77 ± 216.81 / 267.30 ± 308.88 / -36.23 / -71.87 / -0.59 / 0.046
rs1859902 / ENSG00000149617 / C / LDL-C / 2.85 ± 0.88 / 3.03 ± 0.83 / 2.94 ± 0.80 / 0.14 / 0.05 / 0.23 / 2.510-3
rs13039214 / ENSG00000149617 / G / TG / 1.60 ± 0.89 / 1.55 ± 0.88 / 1.37 ± 0.72 / -0.10 / -0.18 / -0.02 / 0.014

Data are presented as mean values ± standard deviations. , L95 and U95 represent unit change in the parameter per minor allele with 95% confidence interval.  values are presented in inverse normal units of the parameters. 11: homozygote for minor allele; 12: heterozygote; 22: homozygote for major allele. HC: Hip circumference (cm); WC: waist circumference (cm); FPG: fasting plasma glucose (mmol/L); FPI: fasting plasma insulin (pmol/L); HOMA-IR: homeostasis model assessment of insulin resistance; TC: total cholesterol (mmol/L); TG: triglyceride (mmol/L); UA: uric acid (μmol/L). Analysis for obesity related traits is adjusted for age and sex whereas analysis for other traits is adjusted for age, sex and BMI.

Supplementary Figure 1: Plot describing the position of genes and SNPs on chromosomal regions 1q21 and their respective P values for association with type 2 diabetes

Legend: The plot was generated using LocusZoom ( Gene annotations were taken from the University of California Santa Cruz genome browser. LD block was drawn using the genotype data from the present study using Haploview 4.2.

Supplementary Figure 2: Plot describing the position of genes and SNPs on chromosomal regions 20q13 and their respective P values for association with type 2 diabetes

Legend: The plot was generated using LocusZoom ( Gene annotations were taken from the University of California Santa Cruz genome browser. LD block was drawn using the genotype data from the present study using Haploview 4.2.

Supplementary Figure 3: Multidimensional scaling based on markers genotyped in stage 1 samples

Legend:The multidimensional scaling analysis was performed based on 608 unlinked markers (r2<0.20) genotyped in stage 1 samples that were used to obtain the positions on the first and second dimensions using PLINK.

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