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. Author manuscript; available in PMC: 2018 Aug 1.
Published in final edited form as: Neurobiol Aging. 2017 May 3;56:150–158. doi: 10.1016/j.neurobiolaging.2017.04.018

Table 3.

Nonchromosome 21 SNPs that are associated with Alzheimer’s disease at empirical p < 0.05

Chr Gene SNPa BP (Hg19) Risk allele Allele freq OR (L95-U95) Empirical p (pointwise)b BH adjusted empirical p (genewise)
8 MSRAc rs17692624 10,070,368 C 0.233 0.589 0.374 0.927 0.0230 0.8470
9 DAPK1 rs2058882 90,114,746 G 0.2 1.579 1.003 2.486 0.0474 0.9415
10 PITRM1 rs9423705 3,200,155 G 0.339 1.440 1.002 2.070 0.0498 0.4050
10 SORCS1 rs10748921 108,390,100 C 0.333 0.648 0.424 0.990 0.0469 0.5532
10 SORCS1 rs1538417 108,583,599 A 0.283 1.536 1.025 2.301 0.0361 0.5532
10 SORCS1 rs10787011 108,863,228 G 0.359 1.482 1.022 2.150 0.0371 0.5532
10 SORCS1 rs7897974 108,893,522 A 0.458 0.685 0.475 0.988 0.0426 0.5532
10 SORCS1 rs7099998 108,928,558 G 0.2 0.566 0.345 0.929 0.0230 0.5532
11 SORL1 rs11605969 121,430,872 A 0.153 1.683 1.032 2.747 0.0387 0.8816
17 TNK1 rs7219773 7,283,144 A 0.42 1.549 1.065 2.251 0.0257 0.0596
17 TNK1 rs12948090 7,285,104 A 0.416 1.458 1.013 2.098 0.0442 0.0596
17 TNK1 rs1554948 7,286,326 A 0.413 1.604 1.106 2.327 0.0135 0.0596
17 TNK1 rs3744549 7,293,715 G 0.251 0.655 0.429 0.998 0.0477 0.0596
19 LDLR rs2738466 11,242,765 G 0.423 1.537 1.010 2.341 0.0442 0.2063
19 ZNF224 rs4803675 44,589,716 G 0.388 1.522 1.054 2.198 0.0275 0.1925
19 MARK4 rs12976518 45,759,344 G 0.475 1.636 1.141 2.347 0.0089 0.0534
19 MARK4 rs2377324 45,768,946 G 0.282 0.551 0.355 0.854 0.0089 0.0534
19 MARK4 rs2306660 45,802,863 G 0.245 0.599 0.378 0.948 0.0298 0.0715
20 CST3 rs35610040 23,616,469 G 0.179 1.774 1.106 2.844 0.0165 0.0297
20 CST3 rs3787498 23,616,781 A 0.172 1.909 1.180 3.086 0.0085 0.0211
20 CST3 rs3827142 23,617,007 A 0.179 1.907 1.182 3.078 0.0079 0.0211
20 CST3 rs5030707 23,618,656 C 0.167 1.974 1.230 3.167 0.0049 0.0211
20 CST3 rs3827143 23,619,617 G 0.226 1.748 1.141 2.677 0.0094 0.0211
20 CST3 rs2254635 23,622,758 A 0.203 1.655 1.043 2.626 0.0316 0.0406
20 CST3 rs2405367 23,622,880 A 0.189 1.703 1.080 2.686 0.0200 0.0300
a

SNPs with gene-wise FDR adjusted empirical p-value <0.05 are in boldface.

b

For empirical p-value, 10,000 replicates were generated.

c

Positive SNPs from stage 1 are highlighted in gray. SNPs without the gray highlight were added in stage 2 for fine mapping.