Genome-wide significant loci associated with GATA1s mutation VAF in newborns with DS
| SNP . | Chr: position . | Gene∗ . | Ref . | Alt . | MAF† . | Multiancestry (N = 429), GATA1s mutation VAF . | Multiancestry (N = 429), GATA1s mutation status (yes/no) . | White-only (n = 270), GATA1s mutation VAF . | White-only (n = 270), GATA1s mutation status (yes/no) . | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| β‡ (95% CI) . | P value . | OR (95% CI) . | P value . | β‡ (95% CI) . | P . | OR (95% CI) . | P value . | ||||||
| Significant hit (P < 5 × 10−8) from multiancestry analysis | |||||||||||||
| rs115118904 | 2: 48 707 683 | LHCGR | T | C | 0.056/0.057 | 3.26 (2.13-4.40) | 3.22 × 10–8 | 4.69 (2.50-8.76) | 1.26 × 10−6 | 2.96 (1.59-4.32) | 3.14 × 10–5 | 3.93 (1.83-8.43) | 4.40 × 10−4 |
| Significant hits (P < 5 × 10−8) from White-only analysis | |||||||||||||
| rs66519478 | 1: 218 903 556 | LYPLAL1 | G | A | 0.17/0.13 | 1.82 (1.06-2.57) | 3.39 × 10−6 | 2.68 (1.76-4.09) | 4.77 × 10−6 | 2.85 (1.90-3.80) | 1.25 × 10−8 | 4.57 (2.54-8.24) | 4.19 × 10−7 |
| rs7528768 | 1: 218 905 645 | LYPLAL1 | C | T | 0.17/0.13 | 1.74 (0.99-2.49) | 7.89 × 10−6 | 2.58 (1.69-3.93) | 1.01 × 10−5 | 2.85 (1.90-3.80) | 1.25 × 10−8 | 4.57 (2.53-8.24) | 4.19 × 10−7 |
| rs1972029 | 1: 218 909 006 | LYPLAL1 | G | A | 0.17/0.13 | 1.68 (0.91-2.44) | 2.11 × 10−5 | 2.48 (1.62-3.79) | 2.76 × 10−5 | 2.77 (1.80-3.72) | 3.84 × 10−8 | 4.26 (2.38-7.63) | 1.09 × 10−6 |
| rs12647008 | 4: 56 189 001 | CRACD | A | T | 0.10/0.041 | 1.21 (0.14-2.26) | .025 | 2.03 (1.14-3.64) | .017 | 5.83 (3.96-7.69) | 3.28 × 10−9 | 24.00 (5.90-97.6) | 8.94 × 10−6 |
| SNP . | Chr: position . | Gene∗ . | Ref . | Alt . | MAF† . | Multiancestry (N = 429), GATA1s mutation VAF . | Multiancestry (N = 429), GATA1s mutation status (yes/no) . | White-only (n = 270), GATA1s mutation VAF . | White-only (n = 270), GATA1s mutation status (yes/no) . | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| β‡ (95% CI) . | P value . | OR (95% CI) . | P value . | β‡ (95% CI) . | P . | OR (95% CI) . | P value . | ||||||
| Significant hit (P < 5 × 10−8) from multiancestry analysis | |||||||||||||
| rs115118904 | 2: 48 707 683 | LHCGR | T | C | 0.056/0.057 | 3.26 (2.13-4.40) | 3.22 × 10–8 | 4.69 (2.50-8.76) | 1.26 × 10−6 | 2.96 (1.59-4.32) | 3.14 × 10–5 | 3.93 (1.83-8.43) | 4.40 × 10−4 |
| Significant hits (P < 5 × 10−8) from White-only analysis | |||||||||||||
| rs66519478 | 1: 218 903 556 | LYPLAL1 | G | A | 0.17/0.13 | 1.82 (1.06-2.57) | 3.39 × 10−6 | 2.68 (1.76-4.09) | 4.77 × 10−6 | 2.85 (1.90-3.80) | 1.25 × 10−8 | 4.57 (2.54-8.24) | 4.19 × 10−7 |
| rs7528768 | 1: 218 905 645 | LYPLAL1 | C | T | 0.17/0.13 | 1.74 (0.99-2.49) | 7.89 × 10−6 | 2.58 (1.69-3.93) | 1.01 × 10−5 | 2.85 (1.90-3.80) | 1.25 × 10−8 | 4.57 (2.53-8.24) | 4.19 × 10−7 |
| rs1972029 | 1: 218 909 006 | LYPLAL1 | G | A | 0.17/0.13 | 1.68 (0.91-2.44) | 2.11 × 10−5 | 2.48 (1.62-3.79) | 2.76 × 10−5 | 2.77 (1.80-3.72) | 3.84 × 10−8 | 4.26 (2.38-7.63) | 1.09 × 10−6 |
| rs12647008 | 4: 56 189 001 | CRACD | A | T | 0.10/0.041 | 1.21 (0.14-2.26) | .025 | 2.03 (1.14-3.64) | .017 | 5.83 (3.96-7.69) | 3.28 × 10−9 | 24.00 (5.90-97.6) | 8.94 × 10−6 |
Genome-wide significant loci (P < 5 × 10−8) highlighted in bold.
95% CI, 95% confidence interval; Alt, alternative allele; Chr, chromosome; MAF, minor allele frequency in ODSCS; OR, odds ratio; Ref, reference allele.
Corresponds to the nearest gene.
Multiancestry/White-only.
β estimate corresponds to each 1-unit increase in the logit-transformed VAF.