Spreadsheet: cde3326e-271c-4dff-8a7a-bbdd95fc6008
Sheet: Sheet1

Table S2. The loci that were followed up in GIANT Stage 2. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8 | Unnamed: 9 | Unnamed: 10
Locus (Chromosomal Region) | SNP                     (Effect/Non-Effect allele) | Phenotype | MAF | Stage | N | ß (SE) | Z-score | Weighted-Z P-value | I2 | Heterogeneity P-value
BARHL2 (1p22.2) | rs6699397 (G/A) | WHR | 0.398 | Stage 1 | 37663 | 0.036 (0.008) | 4.617 | 3.90E-06 | 0.00% | 0.779
 |  |  |  | Stage 2 | 56244 | 0.001 (0.006) | 0.129 | 8.97E-01 | 10.51% | 0.286
 |  |  |  | Stage 1+2 Combined | 93907 | 0.015 (0.005) | 3.137 | 1.70E-03 | 13.34% | 0.184
LYPLAL1 (1q41) | rs2605100 (G/A) | WHR | 0.308 | Stage 1 | 37698 | 0.038 (0.008) | 4.631 | 3.64E-06 | 25.36% | 0.108
 |  |  |  | Stage 2 | 55323 | 0.014 (0.006) | 2.169 | 3.01E-02 | 3.13% | 0.416
 |  |  |  | Stage 1+2 Combined | 93022 | 0.023 (0.005) | 4.720 | 2.36e-06 | 18.66% | 0.106
TBCE (1q42.3) | rs6429082 (C/T) | WC | 0.458 | Stage 1 | 38511 | 0.036 (0.008) | 4.74 | 2.14e-06 | 0 | 0.713
 |  |  |  | Stage 2 | 51135 | 0.018 (0.006) | 3.077 | 0.00209 | 0 | 0.936
 |  |  |  | Stage 1+2 Combined | 89647 | 0.026 (0.005) | 5.567 | 2.59e-08 | 0 | 0.911
PSME4 (2p16.1) | rs805412 (G/A) | WHR | 0.457 | Stage 1 | 37703 | 0.033 (0.007) | 4.363 | 1.29E-05 | 0.00% | 0.906
 |  |  |  | Stage 2 | 46000 | 0.004 (0.006) | 0.626 | 5.31E-01 | 0.00% | 0.615
 |  |  |  | Stage 1+2 Combined | 83704 | 0.017 (0.005) | 3.498 | 4.69E-04 | 0.00% | 0.641
ATP6V1C2 (2p25.1) | rs12993133 (C/T) | WHR | 0.25 | Stage 1 | 24513 | 0.046 (0.011) | 4.030 | 5.59E-05 | 0.00% | 0.853
 |  |  |  | Stage 2 | 37820 | 0.001 (0.009) | 0.115 | 9.08E-01 | 0.00% | 0.516
 |  |  |  | Stage 1+2 Combined | 62333 | 0.018 (0.007) | 2.702 | 6.90E-03 | 4.34% | 0.388
ATP6V1C2 (2p25.1) | rs12993133 (C/T) | WC | 0.25 | Stage 1 | 25432 | 0.045 (0.011) | 3.922 | 8.80E-05 | 0.00% | 0.507
 |  |  |  | Stage 2 | 37634 | 0.004 (0.009) | 0.471 | 6.37E-01 | 0.00% | 0.596
 |  |  |  | Stage 1+2 Combined | 63067 | 0.019 (0.007) | 2.968 | 2.99E-03 | 8.06% | 0.316
DCTD (4q35.1) | rs13116494 (A/C) | WC | 0.368 | Stage 1 | 34451 | 0.040 (0.009) | 4.43 | 9.42e-06 | 0.0408 | 0.404
 |  |  |  | Stage 2 | 36169 | 0.016 (0.008) | 2.057 | 0.0397 | 0.0159 | 0.441
 |  |  |  | Stage 1+2 Combined | 70620 | 0.027 (0.006) | 4.716 | 2.4e-06 | 0.0715 | 0.323
[NAME] (5q33.3) | rs6892723 (G/C) | WC | 0.383 | Stage 1 | 36911 | 0.034 (0.008) | 4.302 | 1.69e-05 | 0.0024 | 0.46
 |  |  |  | Stage 2 | 51656 | 0.005 (0.006) | 0.75 | 0.453 | 0.0602 | 0.365
 |  |  |  | Stage 1+2 Combined | 88568 | 0.017 (0.005) | 3.476 | 0.00051 | 0.1266 | 0.202
HCRTR2 (6p11-q11)* | rs11970116 (A/T) | WC | 0.38 | Stage 1 | 38475 | 0.040 (0.008) | 4.914 | 8.91e-07 | 0.2974 | 0.0681
 |  |  |  | Stage 2 | 51523 | 0.003 (0.007) | 0.349 | 0.727 | 0.2214 | 0.13
 |  |  |  | Stage 1+2 Combined | 89999 | 0.019 (0.005) | 3.632 | 0.000282 | 0.3586 | 0.0034
IL17A (6p12) | rs10085177 (C/T) | WC | 0.017 | Stage 1 | 34292 | 0.101 (0.023) | 4.540 | 5.63E-06 | 1.73% | 0.438
 |  |  |  | Stage 2 | 45805 | -0.004 (0.017) | -0.256 | 7.98E-01 | 11.11% | 0.28
 |  |  |  | Stage 1+2 Combined | 80098 | 0.034 (0.013) | 2.911 | 3.61E-03 | 21.55% | 0.0697
TFAP2B (6p12) | rs987237 (G/A) | WHR | 0.098 | Stage 1 | 37725 | 0.043 (0.010) | 4.194 | 2.74e-05 | 0.00% | 0.771
 |  |  |  | Stage 2 | 55575 | 0.012 (0.008) | 1.498 | 0.134 | 0.00% | 0.693
 |  |  |  | Stage 1+2 Combined | 93300 | 0.024 (0.006) | 3.926 | 8.62e-05 | 0.00% | 0.673
TFAP2B (6p12) | rs987237 (G/A) | WC | 0.098 | Stage 1 | 38635 | 0.038 (0.010) | 3.867 | 1.10E-04 | 35.57% | 0.0314
 |  |  |  | Stage 2 | 55385 | 0.033 (0.008) | 4.273 | 1.92E-05 | 0.00% | 0.556
 |  |  |  | Stage 1+2 Combined | 94021 | 0.035 (0.006) | 5.863 | 4.54E-09 | 15.35% | 0.149
TFAP2B (6p12.3)* | rs4715215 (C/T) | WHR | 0.333 | Stage 1 | 37729 | 0.033 (0.008) | 4.201 | 2.66E-05 | 0.00% | 0.657
 |  |  |  | Stage 2 | 37095 | 0.012 (0.008) | 1.776 | 7.58E-02 | 0.00% | 0.972
 |  |  |  | Stage 1+2 Combined | 74824 | 0.023 (0.005) | 4.337 | 1.44E-05 | 0.00% | 0.91
[NAME] (6p25.3) | rs1328884 (C/A) | WHR | 0.098 | Stage 1 | 37553 | 0.051 (0.012) | 4.415 | 1.01E-05 | 0.00% | 0.671
 |  |  |  | Stage 2 | 43704 | -0.005 (0.010) | -0.431 | 6.67E-01 | 0.00% | 0.997
 |  |  |  | Stage 1+2 Combined | 81258 | 0.020 (0.007) | 2.794 | 5.21E-03 | 0.00% | 0.847
[NAME] (6p25.3) | rs3761987 (A/T) | WC | 0.5 | Stage 1 | 38626 | 0.031 (0.008) | 4.086 | 4.4e-05 | 0 | 0.576
 |  |  |  | Stage 2 | 63849 | -0.002 (0.006) | -0.288 | 0.773 | 0 | 0.611
 |  |  |  | Stage 1+2 Combined | 102475 | 0.010 (0.004) | 2.387 | 0.017 | 0.0645 | 0.321
PDGFRL (8p22-p21.3) | rs2245667 (C/G) | WC | 0.4 | Stage 1 | 38364 | 0.038 (0.008) | 4.583 | 4.59e-06 | 0 | 0.484
 |  |  |  | Stage 2 | 45789 | 0.018 (0.007) | 2.568 | 0.0102 | 0 | 0.544
 |  |  |  | Stage 1+2 Combined | 84154 | 0.026 (0.005) | 5.117 | 3.11e-07 | 0.0046 | 0.466
MSRA (8p23.1) | rs7826222 (G/C) | WC | 0.183 | Stage 1 | 36865 | 0.045 (0.011) | 4.356 | 1.32e-05 | 0.0155 | 0.441
 |  |  |  | Stage 2 | 35247 | 0.034 (0.010) | 3.521 | 0.00043 | 0 | 0.952
 |  |  |  | Stage 1+2 Combined | 72113 | 0.040 (0.007) | 5.699 | 1.2e-08 | 0 | 0.845
[NAME] (8p23.3) | rs4737325 (T/C) | WC | 0.2 | Stage 1 | 38628 | 0.043 (0.010) | 4.475 | 7.63e-06 | 0.0228 | 0.43
 |  |  |  | Stage 2 | 39293 | -0.015 (0.009) | -1.557 | 0.119 | 0.1935 | 0.185
 |  |  |  | Stage 1+2 Combined | 77922 | 0.014 (0.007) | 2.185 | 0.0289 | 0.3132 | 0.0153
ECHDC3 (10p14) | rs12414558 (A/G) | WHR | 0.067 | Stage 1 | 37547 | 0.063 (0.015) | 4.191 | 2.78E-05 | 26.92% | 0.0926
 |  |  |  | Stage 2 | 35678 | -0.026 (0.012) | -1.941 | 5.22E-02 | 29.96% | 0.088
 |  |  |  | Stage 1+2 Combined | 73225 | 0.010 (0.009) | 1.754 | 7.94E-02 | 44.40% | 0.000408
ECHDC3 (10p14) | rs12414558 (A/G) | WC | 0.067 | Stage 1 | 38457 | 0.066 (0.015) | 4.394 | 1.11E-05 | 2.79% | 0.423
 |  |  |  | Stage 2 | 35491 | -0.022 (0.012) | -1.924 | 5.44E-02 | 11.62% | 0.302
 |  |  |  | Stage 1+2 Combined | 73948 | 0.014 (0.009) | 1.968 | 4.90E-02 | 31.69% | 0.017
[NAME] (10p15.3) | rs17321467 (T/C) | WHR | 0.076 | Stage 1 | 37506 | 0.054 (0.011) | 4.700 | 2.61E-06 | 0.00% | 0.858
 |  |  |  | Stage 2 | 51857 | -0.006 (0.009) | -0.839 | 4.01E-01 | 33.65% | 0.0309
 |  |  |  | Stage 1+2 Combined | 89364 | 0.018 (0.007) | 2.517 | 1.18E-02 | 28.81% | 0.0195
PKNOX2 (11q24.2) | rs608501 (G/A) | WHR | 0.433 | Stage 1 | 37654 | 0.033 (0.008) | 4.345 | 1.39E-05 | 0.00% | 0.569
 |  |  |  | Stage 2 | 51478 | -0.001 (0.006) | -0.087 | 9.31E-01 | 0.00% | 0.999
 |  |  |  | Stage 1+2 Combined | 89133 | 0.013 (0.005) | 2.853 | 4.33E-03 | 0.00% | 0.889
IPO8 (12p11.21) | rs6487924 (C/T) | WHR | 0.242 | Stage 1 | 37713 | 0.038 (0.009) | 4.408 | 1.04E-05 | 24.48% | 0.117
 |  |  |  | Stage 2 | 48021 | -0.005 (0.007) | -0.649 | 5.17E-01 | 18.50% | 0.17
 |  |  |  | Stage 1+2 Combined | 85735 | 0.014 (0.005) | 2.531 | 1.14E-02 | 32.63% | 0.00754
IPO8 (12p11.21) | rs6487924 (C/T) | WC | 0.242 | Stage 1 | 38623 | 0.037 (0.009) | 4.216 | 2.49E-05 | 0.00% | 0.741
 |  |  |  | Stage 2 | 47838 | 0.001 (0.007) | 0.167 | 8.68E-01 | 0.00% | 0.496
 |  |  |  | Stage 1+2 Combined | 86461 | 0.017 (0.005) | 3.066 | 2.17E-03 | 4.85% | 0.367
HMGA2* (12q15) | rs7970350 (C/T) | WC | 0.482 | Stage 1 | 38598 | 0.038 (0.007) | 5.081 | 3.74e-07 | 0 | 0.827
 |  |  |  | Stage 2 | 50118 | 0.014 (0.006) | 2.227 | 0.0259 | 0.1504 | 0.229
 |  |  |  | Stage 1+2 Combined | 88717 | 0.024 (0.005) | 5.18 | 2.22e-07 | 0.0581 | 0.348
[NAME] (14p13) | rs8014476 (G/A) | WHR | 0.067 | Stage 1 | 37722 | 0.073 (0.018) | 4.473 | 7.70E-06 | 24.29% | 0.119
 |  |  |  | Stage 2 | 45852 | -0.002 (0.015) | 0.145 | 8.84E-01 | 15.07% | 0.225
 |  |  |  | Stage 1+2 Combined | 83575 | 0.030 (0.011) | 3.220 | 1.28E-03 | 27.50% | 0.0265
TCF12 (15q21) | rs2414500 (G/A) | WC | 0.45 | Stage 1 | 38536 | 0.033 (0.008) | 4.342 | 1.41E-05 | 0.00% | 0.791
 |  |  |  | Stage 2 | 39527 | -0.001 (0.007) | -0.159 | 8.74E-01 | 7.48% | 0.349
 |  |  |  | Stage 1+2 Combined | 78064 | 0.016 (0.005) | 3.078 | 2.08E-03 | 8.28% | 0.297
MKL2 (16p13.3) | rs7194591 (G/C) | WC | 0.067 | Stage 1 | 34107 | 0.103 (0.023) | 4.613 | 3.97e-06 | 0.0725 | 0.357
 |  |  |  | Stage 2 | 35617 | 0.005 (0.023) | -0.044 | 0.965 | 0.2584 | 0.103
 |  |  |  | Stage 1+2 Combined | 69725 | 0.056 (0.016) | 3.336 | 0.000849 | 0.2635 | 0.0399
CYP2A6 (19q13.2) | rs406796 (G/A) | WHR | 0.267 | Stage 1 | 37718 | 0.039 (0.008) | 4.875 | 1.09E-06 | 0.00% | 0.522
 |  |  |  | Stage 2 | 56821 | 0.003 (0.006) | 0.463 | 6.43E-01 | 0.00% | 0.811
 |  |  |  | Stage 1+2 Combined | 94540 | 0.017 (0.005) | 3.557 | 3.75E-04 | 2.14% | 0.427
PCSK2 (20p11.2) | rs16998899 (A/C) | WHR | 0.059 | Stage 1 | 37714 | 0.070 (0.016) | 4.319 | 1.57E-05 | 14.23% | 0.249
 |  |  |  | Stage 2 | 51742 | 0.001 (0.013) | 0.025 | 9.80E-01 | 0.00% | 0.826
 |  |  |  | Stage 1+2 Combined | 89457 | 0.031 (0.010) | 2.921 | 3.49E-03 | 9.75% | 0.258
Nearby gene:  gene(s) nearest SNP used in analyses
Alleles:  the first allele listed in the parenthesis is the effect allele
MAF: minor allele frequency in the HapMap CEU data
Effect size (b), standard error (SE)
Stage 1:  data from stage 1 GIANT meta-analysis
Stage 2 is the meta analysos of Stage 2a:  data from in silico studies and Stage 2b:  data from de novo genotyped studies
Stage 1+2: data from stage 1 GIANT analyzed with [NAME] genotyped and in silico studies from stage 2
* SNPs added on the basis of candidacy of nearby genes
Total sample sizes do not always reflect the sum of component studies due to rounding errors in non-integeric sample sizes arising from the weighting procedure.