Table 2.
Significant cis eQTLs that are also associated with AD-risk in the FCA3DS AD case-control series. WES variants within 1Mb of AKAP9 and ABCA7 that remained significant after FDR correction (cis eQTLs) and which had a nominal p-value for association with AD-risk in 420 FCA3DS AD cases and CU controls are shown. rsID: dbSNP ID of the eQTL; Chr: chromosome; Position: hg38; A1: tested allele; A2: reference allele; ß: coefficient of eQTL linear regression model; P: p-value (F-test); Q: FDR q-value. Also shown are the AD-risk association results, including AD-risk odds ratio (OR), p-value (T-test) and MAFs of variants in the 474 FCA3DS AD cases and controls, and ORs and p-values from the Kunkle et al. AD-risk GWAS in NHW.14 Variant annotation shows the gene proximal to the variant, its exonic function (syn: synonymous; nonsyn: nonsynonymous missense variant) and Regulome score25 obtained from ANNOVAR.24
| Plasma eQTL |
AD GWAS - FCA3DS |
AD GWAS - NHW |
Variant Annotation |
||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| cf-mRNA | rs ID | Chr | Position | A1 | A2 | β | P | Q | MAF | OR | P | MAF | OR | P | Gene | Function | Regulome |
| AKAP9 | rs10228334 | 7 | 92084658 | C | T | 1·67 | 4·75E-69 | 1·18E-64 | 0·49 | 1·34 | 3·53E-02 | 0·49 | 1·03 | 5·83E-02 | AKAP9 | syn | 5 |
| rs57122389 | 7 | 92113034 | C | A | 1·69 | 8·45E-69 | 1·39E-64 | 0·48 | 1·42 | 1·36E-02 | 0·49 | 1·03 | 4·78E-02 | CYP51A1 | 3’UTR | 6 | |
| rs6964587 | 7 | 92001306 | G | T | 1·69 | 4·73E-68 | 5·85E-64 | 0·49 | 1·33 | 4·19E-02 | 0·49 | 1·03 | 5·58E-02 | AKAP9 | syn | 5 | |
| rs7793861 | 7 | 92113414 | G | C | -1·60 | 4·57E-58 | 2·83E-54 | 0·49 | 0·76 | 4·69E-02 | 0·48 | 0·97 | 4·70E-02 | CYP51A1 | 3’UTR | 6 | |
| rs11459 | 7 | 92112873 | G | A | -1·56 | 4·73E-55 | 2·34E-51 | 0·47 | 0·76 | 4·66E-02 | 0·46 | 0·97 | 4·18E-02 | CYP51A1 | 3’UTR | 6 | |
| rs6465348 | 7 | 92113288 | G | A | -1·55 | 1·55E-53 | 6·97E-50 | 0·47 | 0·74 | 2·92E-02 | 0·46 | 0·97 | 3·88E-02 | CYP51A1 | 3’UTR | 6 | |
| rs57433727 | 7 | 92400943 | C | T | 0·74 | 4·85E-05 | 2·90E-02 | 0·11 | 1·88 | 3·69E-03 | 0·12 | - | - | ANKIB1 | 3’UTR | 5 | |
| rs61740421 | 7 | 92397766 | T | C | 0·73 | 5·00E-05 | 2·91E-02 | 0·11 | 1·87 | 4·20E-03 | 0·12 | - | - | ANKIB1 | syn | 4 | |
| ABCA7 | rs3752232 | 19 | 1043749 | G | A | -0·51 | 2·10E-07 | 2·74E-04 | 0·25 | 1·65 | 2·99E-03 | 0·26 | 0·93 | 4·87E-02 | ABCA7 | nonsyn | 1f |
| rs4147910 | 19 | 1047079 | G | A | -0·38 | 8·24E-05 | 4·01E-02 | 0·25 | 1·52 | 1·13E-02 | 0·26 | 1·16 | 9·27E-09 | ABCA7 | intronic | 4 | |