Table 1

Worldwide risk allele frequencies and global Fst for 25 disease-associated SNPs typed in the CEPH-HGDP panel.









Risk allele frequency
SNP1
 Disease2
 Replication
 Chr
 Position3
 Gene4
 Global Fst
 P
 Pcor
 Global
 Africa
 Middle East
 Europe
 Central South Asia
 East Asia
 America
 Oceania
rs10077785
 CD
 [30]
 5
 131829057
0.062
 0.642
 0.511
 0.82
 0.975
 0.809
 0.812
 0.716
 0.898
 0.688
 0.75
rs10210302
 CD
 [30]
 2
 233940839
 ATG16L1
 0.117
 0.315
 0.323
 0.393
 0.268
 0.459
 0.539
 0.541
 0.31
 0.066
 0.018
rs10761659
 CD
 [30]
 10
 64115570
0.251
 0.036
 0.046
 0.542
 0.015
 0.427
 0.507
 0.631
 0.759
 0.811
 0.269
rs10811661
 T2D
 [27]
 9
 22124094
 CDKN2A/2B
 0.126
 0.278
 0.224
 0.782
 0.97
 0.805
 0.833
 0.876
 0.584
 0.836
 0.518
rs10883365
 CD
 [29]
 10
 101277754
0.04
 0.8
 0.65
 0.459
 0.48
 0.541
 0.497
 0.43
 0.449
 0.161
 0.643
rs10946398
 T2D
 [27, 31]
 6
 20769013
 CDKAL1
 0.028
 0.901
 0.697
 0.328
 0.47
 0.338
 0.286
 0.243
 0.382
 0.242
 0.321
rs1111875
 T2D
 [27, 28]
 1
 218111919
0.179
 0.131
 0.183
 0.525
 0.828
 0.664
 0.588
 0.487
 0.232
 0.685
 0.554
rs11171739
 T1D
 [32]
 12
 54756892
0.221
 0.063
 0.049
 0.367
 0.884
 0.343
 0.438
 0.318
 0.219
 0.056
 0.481
rs11805303
 CD
 [33]
 1
 67387537
 IL23
 0.085
 0.483
 0.492
 0.421
 0.27
 0.456
 0.303
 0.513
 0.547
 0.121
 0.446
rs12708716
 T1D
 [32]
 16
 11087374
 KIAA0350
 0.071
 0.57
 0.398
 0.648
 0.411
 0.592
 0.611
 0.645
 0.773
 0.849
 0.571
rs13266634
 T2D
 [27, 28]
 8
 114748339
 SLC30A8
 0.07
 0.575
 0.365
 0.74
 0.941
 0.803
 0.721
 0.756
 0.593
 0.703
 0.911
rs1333049
 CAD
 [34, 35, 36]
 9
 22115503
0.079
 0.516
 0.464
 0.483
 0.157
 0.54
 0.569
 0.536
 0.52
 0.5
 0.161
rs17234657
 CD
 [37]
 5
 40437266
0.112
 0.334
 0.192
 0.07
 0.243
 0.099
 0.126
 0.021
 0.002
 0.008
 0
rs17696736
 T1D
 [32]
 12
 110949538
 C12orf30
 0.237
 0.049
 0.113
 0.165
 0
 0.37
 0.413
 0.13
 0.011
 0.04
 0
rs1801282
 T2D
 [27, 38, 39]
 3
 12368125
 PPARG
 0.021
 0.943
 0.581
 0.923
 1
 0.938
 0.91
 0.877
 0.923
 0.897
 1
rs2542151
 T1D/CD
 [29]
 18
 12769947
0.008
 0.991
 0.77
 0.153
 0.183
 0.127
 0.144
 0.179
 0.154
 0.172
 0.018
rs4402960
 T2D
 [27]
 3
 186994389
 IGF2BP2
 0.077
 0.53
 0.612
 0.371
 0.693
 0.302
 0.354
 0.378
 0.306
 0.218
 0.536
rs5215
 T2D
 [27, 38, 39]
 11
 17365206
 KCNJ11
 0.057
 0.671
 0.697
 0.319
 0.056
 0.268
 0.418
 0.34
 0.377
 0.312
 0.393
rs564398
 T2D
 [27]
 9
 22019547
 CDKN2A/2B
 0.113
 0.332
 0.246
 0.818
 1
 0.848
 0.706
 0.753
 0.862
 0.937
 0.34
rs6679677
 T1D/RA
 [40, 41]
 1
 114015850
 RSBN1
 0.019
 0.95
 0.875
 0.016
 0
 0.019
 0.055
 0.013
 0.004
 0
 0
rs6887695
 CD
 [29]
 5
 158755223
0.028
 0.898
 0.741
 0.362
 0.381
 0.383
 0.281
 0.299
 0.409
 0.371
 0.643
rs7901695
 T2D
 [27, 28, 31]
 10
 114744078
 TCF7L2
 0.213
 0.073
 0.08
 0.281
 0.629
 0.438
 0.325
 0.321
 0.044
 0.087
 0.054
rs9858542
 CD
 [29]
 3
 49676987
 BSN
 0.094
 0.432
 0.318
 0.222
 0.23
 0.301
 0.317
 0.331
 0.077
 0.016
 0.143
rs9939609
 T2D/OB
 [27, 42]
 16
 52378028
 FTO
 0.101
 0.391
 0.446
 0.315
 0.471
 0.41
 0.426
 0.348
 0.157
 0.048
 0.25

1 All SNPs were initially obtained from the WTCCC [26], except rs13266634 which was not well tagged by the Affymetrix GeneChip Human Mapping 500 K platform but was reported elsewhere as a T2D candidate [27, 28].

2 CD = Crohn's disease; T2D = type 2 diabetes; T1D = type 1 diabetes; CAD = coronary artery disease; RA = rheumatoid arthritis; OB = obesity.

3 Positions refer to NCBI Build 35 coordinates.

4 Blank cells indicate that the SNP does not fall within or near a known coding gene.

Myles et al. BMC Medical Genomics 2008 1:22   doi:10.1186/1755-8794-1-22