Table 3.
Fine mapping and variant prioritization of AM loci associated with AD in AA samples
| A. Fine mapping of AM loci | ||||||||
|---|---|---|---|---|---|---|---|---|
| SNP | CHR | POS | OR | P_assoc | P_thrs | P_cc_adj | P_c_adj | |
| rs74864956 | 4 | 48432376 | 0.557 | 3.92E−3 | 2.35E−5 | 0.43 | 2.40E−09 | |
| rs3130569 | 6 | 31102955 | 1.268 | 3.24E−3 | 3.24E−5 | 0.96 | 2.81E−08 | |
| rs148783322 | 7 | 76919259 | 1.474 | 2.33E−3 | 4.81E−4 | 0.014 | 2.05E−08 | |
| rs563250505 | 15 | 22357139 | 1.723 | 3.86E−3 | 8.47E−4 | 0.163 | 6.24E−11 | |
| rs79548864 | 20 | 22654011 | 1.463 | 7.56E−3 | 4.46E−4 | 0.91 | 9.31E−07 | |
| B. Prioritization of AM loci | ||||||||
| SNP | CHR | POS | AFR_AF | EUR_AF | DELTA | CADD | RDB | GENE |
| rs375259 | 4 | 48343550 | 0.056 | 0.3439 | 0.2879 | 16.65 | 2b | SLAIN2 |
| rs3807033 | 6 | 30043955 | 0.4425 | 0.0825 | 0.36 | 18.8 | 1f | RNF39 |
| rs77580993 | 6 | 30059592 | 0.5068 | 0.1889 | 0.3179 | 17.42 | 2b | – |
| rs7765810 | 6 | 30063496 | 0.5091 | 0.1779 | 0.3312 | 17.96 | 1a | – |
| rs2277764 | 20 | 22566124 | 0.351 | 0.0606 | 0.2904 | 17.77 | 2b | FOXA2 |
A. Fine mapping association test. CHR, chromosome; POS, base-pair position; OR, odds ratio; P_assoc, association p value; P_thrs, p value threshold for significant association after multiple testing adjustment; P_cc_adj, inflation-adjusted case-control p value; P_c_adj, inflation-adjusted case-only p value. B. Prioritized variants in AM loci. AFR_AF and EUR_AF, Minor allele frequency in African and European populations, respectively; RDB, RegulomeDB score; CADD, CADD score; DELTA, absolute difference in AFR_AF and EUR_AF.