SUPPLEMENTARY TABLE 1.Genotype and allele frequencies of candidate SNP loci in a Japanese population

SNP / risk allele % / 11*, n(%) / 12* n(%) / 22* n(%) / P for HWET#
rs4402960 (G>T) / Case / T / 33.8 / 717 (44.1) / 718 (44.2) / 190 (11.7) / 0.61
Ch3; IGF2BP2 / Control / 29.3 / 522 (49.9) / 437 (41.7) / 88 (8.4) / 0.80
rs10811661 (T>C) / Case / T / 60.7 / 603 (37.3) / 757 (46.8) / 256 (15.8) / 0.47
Ch9: CDKN2A/B / Control / 56.1 / 329 (31.4) / 520 (49.6) / 200 (19.1) / 0.83
rs1111875 (T>C) / Case / C / 32.5 / 739 (45.8) / 702 (43.5) / 174 (10.8) / 0.71
Ch10: HHEX / Control / 28.4 / 535 (51.2) / 425 (40.7) / 84 (8.0) / 0.97
rs7923837 (A>G) / Case / G / 22.2 / 976 (59.9) / 584 (35.9) / 69 (4.2) / 0.11
Ch10: HHEX / Control / 20.6 / 667 (63.2 / 341 (32.3) / 47 (4.5) / 0.68
rs5219 (C>T) / Case / T / 39.2 / 613 (37.5) / 763 (46.7) / 259 (15.8) / 0.40
Ch11: KCNJ11 / Control / 35.5 / 423 (40.2) / 512 (48.6) / 118 (11.2) / 0.05
rs7756992 (A>G) / Case / G / 51.0 / 398 (24.7) / 782 (48.6) / 430 (26.7) / 0.26
Ch6: CDKAL1 / Control / 47.4 / 293 (28.2) / 508 (48.9) / 238 (22.9) / 0.53
rs13266634 (C>T) / Case / C / 63.3 / 651 (40.3) / 740 (45.8) / 223 (13.8) / 0.58
Ch8: SLC30A8 / Control / 60.0 / 381 (36.5) / 491 (47.0) / 173 (16.6) / 0.49
rs1801282 (C>G) / Case / C / 96.8 / 1511 (93.7) / 98 (6.1) / 3 (0.2) / 0.33
Ch3: PPARG / Control / 97.3 / 1001 (94.8) / 53 (5.0) / 2 (0.2) / 0.15
rs7480010 (A>G) / Case / G / 20.1 / 1048(64.6) / 496(30.6) / 79(4.9) / 0.04
Ch11:LOC387761 / Control / 19.1 / 689(65.7) / 317(30.2) / 42(4.0) / 0.47
rs9300039 (C>A) / Case / C / 76.1 / 932 (57.8) / 590 (36.6) / 91 (5.6) / 0.85
Ch11: 41871942§ / Control / 75.3 / 592 (57.2) / 375 (36.2) / 68 (6.6) / 0.41
rs1113132 (G>C) / Case / G / 64.4 / 686 (42.5) / 711 (44.0) / 219 (13.6) / 0.11
Ch11: EXT2 / Control / 63.6 / 431 (41.1) / 472 (45.0) / 146 (13.9) / 0.36
rs11037909 (T>C) / Case / T / 64.5 / 685 (42.4) / 712 (44.1) / 218 (13.5) / 0.13
Ch11: EXT2 / Control / 63.7 / 431 (41.1) / 474 (45.2) / 144 (13.7) / 0.45
rs8050136 (C>A) / Case / A / 20.8 / 1027 (63.6) / 505 (31.3) / 84 (5.2) / 0.04
Ch16: FTO / Control / 19.4 / 685 (64.6) / 339 (32.0) / 36 (3.4) / 0.45
rs9939609 (T>A) / Case / A / 20.9 / 1026 (63.3) / 513 (31.6) / 82 (5.1) / 0.09
Ch16: FTO / Control / 19.5 / 681 (64.7) / 334 (31.7) / 38 (3.6) / 0.71

*11: homozygous of major allele, 12: heterozygous, 22: homozygous of minor allele, n: number of subjects. # Hardy-Weinberg equilibrium test, § position on the chromosome is indicated.

SUPPLEMENTARY TABLE 2.Association of candidate SNP loci with type 2 diabetes

SNP / gene / p value*
additive / dominant / recessive
rs4402960 / IGF2BP2 / 0.0005 / 0.0037 / 0.0341
rs10811661 / CDKN2A/B / 0.0009 / 0.0308 / 0.0142
rs1111875 / HHEX / 0.0017 / 0.0052 / 0.0795
rs7923837 / HHEX / 0.1892 / 0.1032 / 0.8873
rs5219 / KCNJ11 / 0.0067 / 0.1637 / 0.0084
rs7756992 / CDKAL1 / 0.0106 / 0.0464 / 0.0864
rs13266634 / SLC30A8 / 0.0161 / 0.0527 / 0.1187
rs8050136 / FTO / 0.1699 / 0.5176 / 0.0721
rs9939609 / FTO / 0.1800 / 0.4387 / 0.1337
rs1801282 / PPARG / 0.2298 / 0.9757 / 0.3253
rs9300039 / 41871942# / 0.5328 / 0.3265 / 0.8174
rs7480010 / LOC387761 / 0.3717 / 0.5350 / 0.4160
rs1113132 / EXT2 / 0.4917 / 0.6984 / 0.5903
rs11037909 / EXT2 / 0.5061 / 0.8766 / 0.5226

* P values for 2test by the method of Sladek et.al, #Position on the chromosome is indicated.

SUPPLEMENTARY TABLE 3. Association of candidate SNP loci with type 2 diabetes (Control subjects : over 50 years old)

SNP / gene / p value*
additive / dominant / recessive
rs4402960 / IGF2BP2 / 0.0033 / 0.0358 / 0.0081
rs13266634 / SLC30A8 / 0.0031 / 0.0052 / 0.0511
rs10811661 / CDKN2A/B / 0.0092 / 0.0343 / 0.0522
rs1111875 / HHEX / 0.0165 / 0.1076 / 0.0199
rs7923837 / HHEX / 0.6342 / 0.6768 / 0.7545
rs5219 / KCNJ11 / 0.0423 / 0.3003 / 0.0229
rs7756992 / CDKAL1 / 0.0080 / 0.0454 / 0.0338
rs8050136 / FTO / 0.2625 / 0.5868 / 0.0995
rs9939609 / FTO / 0.2147 / 0.4632 / 0.1180
rs1801282 / PPARG / 0.6197 / 0.2236 / 0.4831
rs9300039 / 41871942# / 0.6497 / 0.1519 / 0.9064
rs7480010 / LOC387761 / 0.5447 / 0.5275 / 0.8345
rs1113132 / EXT2 / 0.3105 / 0.6967 / 0.3008
rs11037909 / EXT2 / 0.3409 / 0.7786 / 0.3061

* P values for 2test by the method of Sladek et.al., #Position on the chromosome is indicated.

SUPPLEMENTARY TABLE 4. The minor allele frequencies of candidate SNPs for Type 2 diabetes in Japanese and white populations

gene / SNP / risk
allele / this study / HapMap-JPT / WTCCC/UKT2D / DGI / FUSION / French study / Icelandic study / HapMap-CEU
case / ctrl / case / ctrl / case / ctrl / case / ctrl / case / ctrl / case / ctrl
IGF2BP2 / rs4402960 / GT / T / 0.338 / 0.293 / 0.311 / 0.351 / 0.320 / 0.310 / 0.290 / 0.341 / 0.304 / ― / ― / ― / ― / 0.292
IGF2BP2 / rs1470579 / AC / C / ― / ― / 0.352 / ― / ― / 0.320 / 0.300 / ― / ― / ― / ― / ― / ― / 0.292
CDKN2A/B / rs10811661 / TC / T / 0.393 / 0.439 / 0.433 / 0.141 / 0.166 / 0.140 / 0.170 / 0.128 / 0.150 / ― / ― / ― / ― / 0.208
CDKN2A/B / rs564398 / TC / T / ― / ― / 0.102 / 0.405 / 0.442 / ― / ― / 0.407 / 0.418 / ― / ― / ― / ― / 0.375
HHEX / rs1111875 / TC* / C / 0.325 / 0.284 / 0.409 / 0.375 / 0.397 / - / 0.470 / 0.454 / 0.478 / 0.358 / 0.402 / 0.412 / 0.450 / 0.442
HHEX / rs7923837 / AG# / G / 0.222 / 0.206 / 0.193 / ― / ― / ― / ― / 0.378 / 0.403 / 0.335 / 0.377 / 0.376 / 0.417 / 0.375
HHEX / rs5015480 / CT / C / ― / ― / 0.189 / 0.379 / 0.425 / ― / ― / ― / ― / ― / ― / ― / ― / 0.448
KCNJ11 / rs5219 / CT / T / 0.392 / 0.355 / ― / ― / ― / - / 0.470 / 0.489 / 0.464 / ― / ― / ― / ― / ―
CDKAL1 / rs7756992 / AG / G / 0.510 / 0.474 / 0.466 / ― / ― / ― / ― / ― / ― / ― / ― / 0.270 / 0.232 / 0.250
CDKAL1 / rs7754840 / GC / C / ― / ― / 0.378 / ― / ― / 0.350 / 0.310 / 0.387 / 0.360 / ― / ― / ― / ― / 0.308
CDKAL1 / rs10946398 / AC / C / ― / ― / 0.378 / 0.361 / 0.319 / 0.350 / 0.310 / 0.384 / 0.357 / ― / ― / ― / ― / 0.308
SLC30A8 / rs13266634 / CT / C / 0.367 / 0.400 / 0.444 / 0.282 / 0.306 / - / 0.350 / 0.351 / 0.491 / 0.254 / 0.301 / 0.315 / 0.354 / 0.250
PPARG / rs1801282 / CG / C / 0.032 / 0.027 / 0.057 / ― / ― / ― / 0.140 / 0.152 / 0.177 / ― / ― / ― / ― / 0.075
LOC387761 / rs7480010 / AG / G / 0.201 / 0.191 / 0.227 / ― / ― / ― / ― / 0.172 / 0.168 / 0.336 / 0.301 / 0.271 / 0.273 / 0.246
41871942§ / rs9300039 / CA / C / 0.239 / 0.247 / 0.278 / ― / ― / ― / ― / 0.076 / 0.108 / ― / ― / ― / ― / 0.108
EXT2 / rs1113132 / GC / G / 0.356 / 0.364 / 0.344 / ― / ― / ― / ― / ― / ― / 0.237 / 0.267 / ― / ― / 0.300
EXT2 / rs11037909 / TC / T / 0.355 / 0.363 / 0.333 / ― / ― / ― / ― / ― / ― / 0.240 / 0.271 / ― / ― / 0.300
EXT2 / rs3740878 / AG / A / ― / ― / 0.341 / ― / ― / ― / ― / ― / ― / 0.240 / 0.272 / ― / ― / 0.302
EXT2 / rs729287 / CT / C / ― / ― / 0.420 / ― / ― / ― / ― / ― / ― / ― / ― / 0.241 / 0.252 / 0.300
FTO / rs8050136 / CA / A / 0.208 / 0.194 / 0.167 / 0.455 / 0.398 / ― / ― / 0.406 / 0.381 / ― / ― / ― / ― / 0.450
FTO / rs9939609 / TA / A / 0.209 / 0.195 / 0.167 / 0.453 / 0.398 / ― / ― / ― / ― / ― / ― / ― / ― / 0.450

Bold type: risk allele frequencies, *C > T in white populations.#G > A in white populations, §Position on the chromosome is indicated.