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Table 4 Total number of genes with SNPs (after QC) and number of genes with SNPs at p < α

From: Exome localization of complex disease association signals

    observed 95% confidence interval
   Total p < 0.1 p < 0.01 p < 0.001 p < 0.1 p < 0.01 p < 0.001
  CD 16,381 6,941 1,306 222 6,712-7007 1192-1367 131-188
  T1D 16,387 7,108 1,547 389 6,709-7004 1191-1366 131-188
  T1D-MHC 16,206 6,945 1,400 254 6658-6952 1184-1358 130-187
Gene T2D 16,375 7,002 1,289 172 6702-6999 1189-1364 130-188
± 100 kb RA 16,381 7,064 1,493 281 6708-7003 1190-1366 131-188
  RA-MHC 16,203 6,933 1,400 203 6658-6952 1184-1359 130-187
  HT 16,382 7,057 1,328 191 6707-7003 1191-1366 130-188
  CAD 16,377 6,993 1,267 173 6704-7002 1191-1365 130-188
  BD 16,377 7,019 1,352 187 6699-6995 1188-1363 130-188
  CD 2,264 291 33 11 234-296 17-38 0-6
  T1D 2,263 316 61 24 234-296 17-38 0-6
  T1D-MHC 2,236 295 41 8 232-293 17-38 0-6
  T2D 2,259 263 30 1 234-294 17-38 0-6
Exon RA 2,265 293 38 12 235-296 17-38 0-6
  RA-MHC 2,238 278 28 4 232-293 17-38 0-6
  HT 2,265 300 31 3 234-295 17-38 0-6
  CAD 2,260 296 34 5 234-294 17-38 0-6
  BD 2,258 281 46 2 233-294 17-38 0-6
  1. Numbers are derived for all seven diseases and for T1D and RA after removal of the MHC region (T1D-MHC and RA-MHC). We consider SNPs that are located within less then 100 kb of a gene and SNPs that are only located within an exon. We derived 95% confidence intervals for the number of genes with p < α based on 100,000 permutations of the disease status.