Skip to main content

Table 1 Worldwide risk allele frequencies and global Fst for 25 disease-associated SNPs typed in the CEPH-HGDP panel.

From: Worldwide population differentiation at disease-associated SNPs

          Risk allele frequency
SNP1 Disease2 Replication Chr Position3 Gene4 Global Fst P P cor 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. 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. 2 CD = Crohn's disease; T2D = type 2 diabetes; T1D = type 1 diabetes; CAD = coronary artery disease; RA = rheumatoid arthritis; OB = obesity.
  3. 3 Positions refer to NCBI Build 35 coordinates.
  4. 4 Blank cells indicate that the SNP does not fall within or near a known coding gene.