Table 3.
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 |
SNPs with gene-wise FDR adjusted empirical p-value <0.05 are in boldface.
For empirical p-value, 10,000 replicates were generated.
Positive SNPs from stage 1 are highlighted in gray. SNPs without the gray highlight were added in stage 2 for fine mapping.