Table 3.
Methylome-wide association results for the four genes that had epigenetically and transcriptionally AD-associated probes.
| ProbeID | Chr | ProbePos | Gene | SNP | Pos | A1 | Freq | PGWAS | PmQTL | bSMR | SESMR | PSMR | PHEIDI | NHEIDI | Current? | Previous? | Region? |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Blood-based Analyses | |||||||||||||||||
| cg03063511 | 2p13.1 | 73930386 | DGUOK | rs6737156 | 73932607 | C | 0.036 | 5.62E-03 | 2.71E-227 | −0.247 | 0.041 | 2.74E-09 | 1.09E-01 | 11 | N | N | N |
| cg02850715 | 11q24.3 | 130159317 | ST14 | rs34008994 | 130165703 | T | 0.096 | 1.55E-04 | 1.21E-26 | −0.812 | 0.138 | 4.14E-09 | 7.87E-01 | 20 | N | N | G |
| cg21029769 | 11q24.3 | 130159620 | ST14 | rs34008994 | 130165703 | T | 0.096 | 1.55E-04 | 4.09E-18 | −1.006 | 0.184 | 4.58E-08 | 9.16E-01 | 20 | N | N | G |
| cg06998361 | 16q21 | 58110599 | C16orf80 | rs10445026 | 58109349 | G | 0.069 | 5.00E-04 | 5.61E-97 | −0.442 | 0.069 | 1.35E-10 | 2.53E-01 | 20 | N | S | S |
| Brain-specific Analyses | |||||||||||||||||
| cg11003133 | 1q23.1 | 159076601 | AIM2 | rs16841642 | 159077008 | G | 0.952 | 5.30E-03 | 6.30E-82 | −0.312 | 0.062 | 4.62E-07 | 3.40E-01 | 18 | N | S | N |
| cg06998361 | 16q21 | 58110599 | C16orf80 | rs74019790 | 58107923 | T | 0.931 | 5.00E-04 | 4.77E-20 | −0.591 | 0.109 | 5.49E-08 | 6.81E-01 | 11 | N | S | S |
Genomic coordinates are based on Human Genome version 38 (hg38). Chr: chromosomal region (i.e., cytogenetic band); ProbePos: probe position; Gene: the gene or closest gene corresponding to the probe; SNP: top methylation quantitative trait locus (mQTL); Pos: SNP position; A1/Freq: SNP’s effect allele and its frequency; PGWAS: p-value of the SNP in genome-wide association meta-analysis; PmQTL: p-value of the SNP in mQTLs analysis; bSMR, SESMR, and PSMR: beta coefficient, its standard error, and p-value of the probe in summary data-based Mendelian randomization (SMR) test; PHEIDI: p-value of the heterogeneity in dependent instruments (HEIDI) test; NHEIDI: number of single-nucleotide polymorphisms used for HEIDI test; Current?: whether there is any AD-associated SNP within ±1 Mb of the probe in the current genome-wide meta-analysis (N: None, G: SNP with PGWAS < 5E-08, and S: SNP with 5E-08 ≤ PGWAS < 5E-06); Previous?: whether there is any AD-associated SNP within ±1 Mb of the probe in previous GWAS (N: None, G: SNP with PGWAS < 5E-08, and S: SNP with 5E-08 ≤ PGWAS < 5E-06); Region?: whether there is any AD-associated SNP within the chromosomal region (i.e., cytogenetic band) corresponding to the probe (N: None, G: SNP with PGWAS < 5E-08, and S: SNP with 5E-08 ≤ PGWAS < 5E-06).