Table 1.
Genome-wide significant loci
| European ancestries | Asian ancestries | Cross-ancestry | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | Position (bp) | ID | Prioritized gene | A1 | A2 | Freq | Effect (s.e.) | P | Effect (s.e.) | P | Effect (s.e.) | P |
| 9 | 27,563,868 | rs2453555 | C9orf72 | A | G | 0.248 | 0.174 (0.013) | 1.0 × 10−43 | 0.017 (0.066) | 0.80 | 0.168 (0.012) | 1.5 × 10−41 |
| 19 | 17,752,689 | rs12608932 | UNC13A | C | A | 0.347 | 0.125 (0.012) | 8.8 × 10−25 | 0.074 (0.038) | 0.053 | 0.120 (0.012) | 3.0 × 10−25 |
| 21 | 33,039,603 | rs80265967 | SOD1 | C | A | 0.006 | 1.078 (0.124) | 3.5 × 10−18 | – | – | – | – |
| 14 | 31,045,596 | rs229195 | SCFD1 | A | G | 0.337 | 0.091 (0.012) | 9.2 × 10−15 | – | – | – | – |
| 14 | 31,045,181 | rs229194a | SCFD1 | A | G | 0.337 | 0.091 (0.012) | 9.2 × 10−15 | 0.002 (0.036) | 0.97 | 0.083 (0.011) | 1.5 × 10−13 |
| 3 | 39,508,968 | rs631312 | MOBP, RPSA | G | A | 0.291 | 0.079 (0.012) | 5.2 × 10−11 | 0.084 (0.036) | 0.020 | 0.080 (0.011) | 3.3 × 10−12 |
| 6 | 32,672,641 | rs9275477 | HLA | C | A | 0.096 | −0.143 (0.021) | 5.5 × 10−12 | −0.110 (0.111) | 0.32 | −0.142 (0.02) | 3.5 × 10−12 |
| 12 | 57,975,700 | rs113247976 | KIF5A | T | A | 0.016 | 0.332 (0.049) | 1.4 × 10−11 | – | – | – | – |
| 21 | 45,753,117 | rs75087725 | CFAP410 | A | C | 0.012 | 0.418 (0.063) | 2.7 × 10−11 | – | – | – | – |
| 5 | 150,410,835 | rs10463311 | GPX3, TNIP1 | C | T | 0.253 | 0.079 (0.013) | 3.5 × 10−10 | 0.042 (0.036) | 0.24 | 0.075 (0.012) | 2.7 × 10−10 |
| 20 | 48,438,761 | rs17785991 | SLC9A8, SPATA2 | A | T | 0.353 | 0.074 (0.012) | 3.5 × 10−10 | 0.045 (0.076) | 0.55 | 0.073 (0.012) | 3.2 × 10−10 |
| 12 | 64,877,053 | rs4075094 | TBK1 | A | T | 0.112 | −0.098 (0.018) | 1.7 × 10−8 | −0.216 (0.090) | 0.017 | −0.103 (0.017) | 2.1 × 10−9 |
| 5 | 172,354,731 | rs517339 | ERGIC1 | C | T | 0.397 | −0.065 (0.011) | 8.5 × 10−9 | −0.067 (0.074) | 0.37 | −0.065 (0.011) | 5.6 × 10−9 |
| 4 | 170,583,157 | rs62333164 | NEK1 | A | G | 0.335 | 0.063 (0.012) | 7.0 × 10−8 | 0.203 (0.070) | 3.8 × 10−3 | 0.067 (0.012) | 6.9 × 10−9 |
| 13 | 46,113,984 | rs2985994 | COG3 | C | T | 0.259 | 0.066 (0.013) | 1.9 × 10−7 | 0.100 (0.041) | 0.014 | 0.069 (0.012) | 1.2 × 10−8 |
| 7 | 157,481,780 | rs10280711 | PTPRN2 | G | C | 0.124 | 0.076 (0.017) | 5.8 × 10−6 | 0.132 (0.037) | 2.9 × 10−4 | 0.086 (0.015) | 1.8 × 10−8 |
Details of two-sided SAIGE logistic mixed model regression for the top associated SNPs within each genome-wide significant locus (P < 5 × 10−8). aFor the strongest associated SNP in the SCFD1 locus, rs229195 (MAF = 0.337), details of the LD proxy rs229194 are described (MAF = 0.337, r2 = 0.996 in Asian ancestries), as only the LD proxy was present in the Asian ancestry GWAS. The low-frequency SNPs rs80265967, rs113247976 and rs75087725 were not present in the Asian ancestry GWAS, and no LD proxies (r2 > 0.8) were found. Chr, chromosome; Position, basepair position in the reference genome GRCh37; A1, effect allele; A2, non-effect allele; Freq, frequency of the effect allele in the European ancestry GWAS; s.e., standard error of the effect estimate.