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Table 1 Individually genotyped SNPs that show significant association with LOAD.

From: A genome-wide association study for late-onset Alzheimer's disease using DNA pooling

SNP ID Chrom Position Gene Symbol SNP Type Minor Allele Pooled fcas Pooled fcon Ind fcas Ind fcon Ind f 1958 Comb Z-test pools p Cases vs MRC Cons p Cases vs All Cons
Rs6859 α 19 50073874 PVRL2 T/C A 0.423 0.324 0.519 0.419 0.417 6.00E-07 1.73E-10 6.09E-14
Rs157580 α 19 50087106 TOMM40 A/G G 0.653 0.583 0.693 0.595 0.616 6.43E-05 8.24E-11 3.87E-11
Rs8106922α 19 50093506 TOMM40 A/G G 0.622 0.507 0.698 0.599 0.596 5.89E-09 1.21E-10 3.96E-14
Rs405509 α 19 50100676 APOE A/C G 0.547 0.468 0.558 0.463 0.521 7.33E-06 2.08E-09 4.77E-06
Rs439401 α 19 50106291 APOE T/C T 0.303 0.372 0.276 0.361 0.357 8.97E-05 7.97E-09 9.15E-11
Rs727153 ‡ 4 156012026 intergenic T/C C 0.425 0.515 0.475 0.540 0.535 0.0009 0.00002 3.37E-06
Rs3754675 2 101008361 NPAS2 T/C C 0.814 0.741 0.939 0.905 0.936 5.70E-06 0.00003 0.0144
Rs4699852 4 95699967 intergenic T/C A 0.392 0.468 0.431 0.493 0.451 0.0008 0.00004 0.0032
Rs2905990 5 11160513 CTNND2 A/G T 0.298 0.369 0.300 0.356 0.327 3.79E-05 0.00009 0.0014
Rs9600764 13 76208794 intergenic T/C G 0.904 0.860 0.974 0.953 0.964 9.98E-05 0.00019 0.0027
Rs1032412 2 163464614 KCNH7 A/G G 0.536 0.484 0.726 0.673 0.711 0.0024 0.00019 0.0097
Rs12510838 4 73326573 NPFFR2 A/G G 0.627 0.558 0.828 0.783 0.810 0.0008 0.00024 0.0047
Rs7140253 14 106305044 intergenic T/C G 0.772 0.711 0.898 0.862 0.875 3.18E-05 0.00024 0.0007
Rs1455280 4 61600197 intergenic T/C G 0.870 0.820 0.900 0.864 0.882 0.0001 0.00027 0.0026
Rs13397414 2 154056922 intergenic A/G G 0.529 0.428 0.895 0.859 0.867 3.44E-09 0.00028 0.0003
Rs587259 19 39348246 LSM14A T/C T 0.515 0.450 0.397 0.344 0.364 0.0002 0.00028 0.0009
Rs13115107 4 183493069 intergenic T/C G 0.466 0.537 0.687 0.736 0.722 0.0001 0.00032 0.0005
Rs1373900 2 193561888 intergenic T/C T 0.259 0.322 0.329 0.380 0.346 5.38E-05 0.00037 0.0087
Rs1911014 4 127131703 intergenic A/G A 0.145 0.205 0.124 0.162 0.155 3.56E-06 0.00037 0.0003
Rs17228994 5 14095376 intergenic A/C C 0.668 0.736 0.849 0.885 0.870 3.60E-05 0.00060 0.0025
Rs407146 16 13223156 LOC729993 A/C T 0.294 0.239 0.416 0.365 0.399 0.0007 0.00060 0.0137
Rs7937776 11 94336790 HSPC148 A/G C 0.576 0.642 0.797 0.837 0.826 0.0006 0.00067 0.0007
Rs3819902 21 42973084 PDE9A A/G C 0.623 0.555 0.914 0.883 0.887 0.0009 0.00068 0.0004
Rs16916856 8 52901703 PCMTD1 T/C C 0.745 0.677 0.887 0.852 0.868 7.80E-06 0.00069 0.0036
Rs393195 19 49184982 ZNF155 A/C G 0.600 0.525 0.760 0.715 0.745 0.0002 0.00071 0.0147
Rs12146414 10 17108257 CUBN A/G G 0.829 0.759 0.933 0.905 0.920 1.37E-05 0.00086 0.0067
Rs7798395 7 70326814 WBSCR17 T/C C 0.691 0.777 0.923 0.948 0.941 2.20E-06 0.00090 0.0011
Rs741477 ‡ 2 64977962 intergenic A/G G 0.852 0.795 0.898 0.867 0.858 5.44E-05 0.00124 3.05E-05
Rs10161338‡ 12 114328023 intergenic T/C C 0.759 0.682 0.902 0.872 0.875 3.52E-05 0.00176 0.0009
Rs10406335‡ 19 49325793 ZNF225 A/G G 0.637 0.571 0.905 0.878 0.876 0.0003 0.00390 0.0009
Rs9324088 ‡ 14 106041164 intergenic T/C G 0.616 0.544 0.751 0.718 0.699 0.0003 0.01295 0.0002
  1. Pooled fcas: Predicted Allele Frequency in MRC Case Pools. Pooled fcon – Predicted Allele Frequency in MRC Control Pools
  2. Ind fcas: Actual Allele Frequency in MRC Cases.
  3. Ind fcon: Actual Allele Frequency in MRC Controls.
  4. Ind f1958: Allele Frequency in 1958 Birth Cohort
  5. Comb Z-test pools: the p-value of combined Z-test for allelic association in pooled data.
  6. p Cases vs MRC Cons: refers to p-value for allelic association in LOAD case subjects vs LOAD MRC control subjects matched for age, gender ethnicity.
  7. p Cases vs All_Cons: refers to p-value for allelic association in LOAD case subjects vs MRC LOAD control subjects combined with genotype data obtained from the 1958 Birth Cohort
  8. α : SNPs in the region of APOE
  9. ‡ : SNPs that show an approximately 10 fold increase in significance when additional controls from the 1958 Birth Cohort are combined with controls from the MRC sample (p Cases vs All Cons)