Extended Data Table 2. Genome-wide significant (P<5×10−8) associations in AFR GWAS of schizophrenia.
For conditionally independent SNPs, the chromosome and genomic coordinates (GRCh38), Tested or effect allele, and population frequency in the gnomAD browser (v4.1.0) are displayed. Beta and Std Error are the allelic effect size and its standard error; Plogit is its statistical significance from the basic logistic regression model; PFE is its significance based inverse variance weighted (fixed effects); PRE2 is its significance based on Han and Eskin’s random effects heterogeneity model, and Phet is the significance of Cochran’s heterogeneity test.
| SNP | Chr | GRCh38 position | Tested | Freq | Phase 1 | Phase 2 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
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| Beta | Std Error | P logit | Beta | Std Error | P FE | P RE2 | P het | |||||
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| chr3:112442573:A:C | 3 | 112,442,573 | A | 0.352 | −0.122 | 0.022 | 3.79×10−8 | −0.061 | 0.016 | 2.13×10−4 | 3.47×10−6 | 6.02×10−3 |
| chr3:114552436:T:A | 3 | 114,552,436 | A | 0.141 | 0.178 | 0.031 | 1.11×10−8 | 0.100 | 0.023 | 1.03×10−5 | 3.27×10−7 | 5.50×10−3 |
| chr7:132080559:C:T | 7 | 132,080,559 | T | 0.158 | 0.153 | 0.029 | 1.36×10−7 | 0.120 | 0.021 | 1.91×10−8 | 3.34×10−8 | 0.202 |
| chr8:72154435:G:A | 8 | 72,154,435 | A | 0.156 | −0.126 | 0.030 | 2.90×10−5 | −0.123 | 0.022 | 2.26×10−8 | 3.99×10−8 | 0.899 |
| chr16:10063406:C:A | 16 | 10,063,406 | A | 0.383 | 0.121 | 0.022 | 1.84×10−8 | 0.059 | 0.016 | 1.84×10−4 | 2.51×10−6 | 3.86×10−3 |
| chr17:6264499:G:A | 17 | 6,264,499 | A | 0.010 | 0.546 | 0.097 | 1.63×10−8 | · | · | · | · | · |
| chr17:48458465:TCA:T | 17 | 48,458,465 | T | 0.009 | 0.641 | 0.108 | 2.48×10−9 | · | · | · | · | · |
| chrl 8:59852986:G:A | 18 | 59,852,986 | A | 0.272 | −0.138 | 0.025 | 2.53×10−8 | −0.102 | 0.018 | 2.02×10−8 | 2.71×10−8 | 0.349 |