Table 1.
Genome-wide significant loci from KnockoffTrio analysis
| Gene | Chr | Position | Variant | Allele | MAF | p | Z | W | q | BH q |
|---|---|---|---|---|---|---|---|---|---|---|
| AGP (FDR = 0.1) | ||||||||||
| NRXN1 | 2 | 50805721 | rs9284756 | A | 0.03 | 7.10E−6 | 4.49 | 4.37 | 0.10 | 0.28 |
| ARHGEF10 | 8 | 1920247–1920676 | rs17756915-rs11136442 | – | 0.41 | 1.38E−5 | – | 4.47 | 0.10 | 0.31 |
| LMNTD1-RASSF8 | 12 | 25946268 | rs4963941 | A | 0.10 | 2.56E−6 | 4.70 | 4.84 | 0.10 | 0.28 |
| ALPK3-SLC28A1 | 15 | 84881866 | rs12917429 | T | 0.21 | 6.19E−6 | −4.52 | 4.45 | 0.10 | 0.28 |
| MACROD2 | 20 | 14781064 | rs6074798 | A | 0.49 | 1.02E−6 | 4.89 | 4.83 | 0.10 | 0.28 |
| SFARI: SPARK (FDR = 0.1) | ||||||||||
| ZNF589 | 3 | 48262179 | rs11709691 | G | 0.28 | 4.87E−6 | −4.57 | 5.03 | 0.06 | 0.14 |
| CADM2 | 3 | 85395534–85410981 | rs75005531-rs1549979 | – | 0.22 | 1.30E−5 | – | 4.76 | 0.09 | 0.26 |
| CHSY3-HINT1 | 5 | 130661503 | rs17714209 | C | 0.28 | 8.25E−6 | 4.46 | 4.99 | 0.06 | 0.20 |
| PDGFA-PRKAR1B | 7 | 536383 | rs62431385 | C | 0.10 | 7.20E−8 | −5.39 | 6.71 | 0.02 | 0.06 |
| DOCK4 | 7 | 111986531 | rs73210911 | A | 0.12 | 1.59E−7 | −5.24 | 6.51 | 0.02 | 0.06 |
| MTRNR2L6-PRSS1 | 7 | 142688332 | rs13223009 | C | 0.02 | 8.42E−6 | −4.45 | 4.71 | 0.09 | 0.20 |
| LARP4B-GTPBP4 | 10 | 975370 | rs117732138 | A | 0.02 | 1.60E−6 | 4.80 | 5.48 | 0.02 | 0.07 |
| IDI2 | 10 | 1020654 | rs77782977 | C | 0.02 | 7.95E−7 | 4.94 | 5.84 | 0.02 | 0.06 |
| PCDH20-PCDH9 | 13 | 63204555 | rs12184522 | T | 0.23 | 4.21E−7 | 5.06 | 6.00 | 0.02 | 0.06 |
| SFARI: SPARK (FDR = 0.2) | ||||||||||
| SPINK8 | 3 | 48316110–48329279 | rs74735576-rs13090538 | – | 0.17 | 1.58E−5 | – | 4.39 | 0.17 | 0.28 |
| SLC22A23/PSMG4 | 6 | 3285062 | rs41301847 | G | 0.02 | 1.85E−5 | 4.28 | 4.41 | 0.17 | 0.31 |
| BAG4 | 8 | 38205717 | rs7836805 | A | 0.24 | 2.83E−5 | −4.19 | 4.43 | 0.17 | 0.40 |
| CCNB1IP1-PARP2 | 14 | 20334133 | rs72671266 | T | 0.02 | 2.45E−5 | −4.22 | 4.30 | 0.19 | 0.38 |
| SFARI: SSC (FDR = 0.1) | ||||||||||
| KCNRG-DLEU7 | 13 | 50197099 | rs2703087 | A | 0.04 | 1.88E−7 | 5.21 | 6.54 | 0.10 | 0.70 |
| SFARI: SSC (FDR = 0.2) | ||||||||||
| KCNIP4 | 4 | 20917151 | rs185413018 | T | 0.02 | 5.59E−7 | 5.00 | 6.00 | 0.13 | 0.70 |
Only the top signal is shown if multiple signals were identified for a locus. Gene: A single gene name indicates the signal is within or overlaps with the gene. “Gene1/Gene2” indicates the signal overlaps with two genes. “Gene1-Gene2” indicates the signal is between two genes. MAF: minor allele frequency of a variant, or average minor allele frequency if a signal contains multiple variants. p: KnockoffTrio’s ACAT-combined p values. For single variants, ACAT-combined p values are equivalent to FBAT p values. Z: FBAT Z scores for single variants. W: KnockoffTrio’s feature statistics. q: KnockoffTrio’s q values. BH q: Benjamini-Hochberg q values.