Table 2.
Inverse-variance-weighted meta-analysis of loci lead variants with similar effect in FinnGen and UKB
| LOCUS | RSID | Nearest gene | Consequence | MAF | Phenotype | OR | 95% CI | P-value |
|---|---|---|---|---|---|---|---|---|
| 9q33.3* | rs3758213-T | NEK6 | intronic | 38.2% | VAR | 0.95 | (0.93–0.97) | 4.81E-08 |
| 11q13.5 | rs11236795-T | EMSY | intergenic | 26.2% | VAR | 0.93 | (1.06–1.14) | 6.16E-12 |
| 1q21.3* | rs2089081-T | ARNT | intronic | 44.5% | NP | 1.10 | (1.11–1.20) | 9.55E-10 |
| 2q12.1 | rs56117144-C | IL18RAP | intergenic | 28.8% | NP | 1.15 | (0.76–0.87) | 8.32E-16 |
| 2q22.3* | rs66484168-G | ZEB2 | intergenic | 8.8% | NP | 0.81 | (0.76–0.87) | 2.95E-12 |
| 5q22.1 | rs34962275-G | WDR36 | downstream | 31.3% | NP | 1.20 | (1.16–1.25) | 7.60E-28 |
| 5q31.1a | rs11738827-T | CDC42SE2 | intronic | 27.3% | NP | 0.88 | (0.85–0.92) | 7.82E-13 |
| 5q31.1b | rs56399423-C | SLC22A4 | intronic | 31.7% | NP | 0.87 | (0.83–0.90) | 4.65E-18 |
| 9p24.1 | rs2095044-T | IL33 | upstream | 23.9% | NP | 1.34 | (1.29–1.39) | 1.20E-58 |
| 10p14a | rs10905284-C | GATA3 | intronic | 42.0% | NP | 0.88 | (0.85–0.91) | 2.44E-15 |
| 10p14b | rs962993-T | GATA3 | regulatory | 30.3% | NP | 0.83 | (0.80–0.86) | 2.58E-28 |
| 12q13.2 | rs705702-G | RAB5B | upstream | 30.3% | NP | 1.15 | (1.10–1.19) | 5.24E-16 |
| 16p13.13 | rs34540843-G | CLEC16A | intronic | 21.2% | NP | 0.86 | (0.83–0.90) | 4.90E-14 |
| 19q13.2 | rs338593-T | CYP2S1 | intronic | 42.8% | NP | 0.87 | (0.84–0.90) | 2.25E-18 |
| 1p36.23 | rs12082271-T | SLC45A1 | upstream | 30.2% | CDTA | 0.94 | (0.91–0.96) | 2.65E-09 |
| 2p13.2* | rs35668054-T | DYSF | regulatory | 9.5% | CDTA | 1.10 | (1.06–1.14) | 2.30E-08 |
| 2q33.3 | rs189411872-G | ADAM23 | intronic | 1.3% | CDTA | 1.53 | (1.39–1.68) | 1.13E-20 |
| 4q24a | rs4648052-T | NFKB1 | intronic | 39.9% | CDTA | 0.94 | (0.91–0.96) | 1.99E-11 |
| 4q24b | rs5860793-D | TET2 | intergenic | 28.4% | CDTA | 0.93 | (0.90–0.95) | 1.60E-12 |
| 8p11.21* | rs73631760-C | SLC20A2 | intronic | 9.4% | CDTA | 1.11 | (1.07–1.15) | 1.65E-09 |
| 9q34.2 | rs612169-G | ABO | intronic | 43.6% | CDTA | 1.07 | (1.04–1.09) | 6.45E-11 |
| 12p13.31 | rs10849448-A | LTBR | 5’ UTR | 24.5% | CDTA | 1.11 | (1.08–1.14) | 3.77E-19 |
| 19p13.3 | rs74178437-G | ZBTB7A | intronic | 26.3% | CDTA | 0.94 | (0.91–0.96) | 3.83E-09 |
| 22q12.2 | rs713875-G | HORMAD2 | intronic | 47.9% | CDTA | 1.09 | (1.07–1.12) | 2.40E-20 |
| 3q12.3* | rs1456200-A | NFKBIZ | upstream | 37.5% | PA | 1.13 | (1.08–1.17) | 8.69E-09 |
| 3q21.2 | rs1980080-C | SLC12A8 | intronic | 34.7% | PA | 1.15 | (1.09–1.20) | 8.57E-11 |
| 13q21.33 | rs9542155-T | KLHL1 | intronic | 35.6% | PA | 1.16 | (1.11–1.21) | 4.11E-14 |
| 15q22.33 | rs17293632-T | SMAD3 | intronic | 26.2% | VAR** | 1.07 | (1.05–1.10) | 2.09E-11 |
| 7p12.2* | rs55935382-A | IKZF1 | intergenic | 31.4% | CDTA** | 0.94 | (0.92–0.97) | 1.16E-08 |
MAF minor allele frequency in FinnGen. “Consequence” reports the most severe predicted variant impact: 5’ UTR Untranslated region in 5’ end of gene, non-coding exon of non-coding gene, regulatory regulatory region. Odds ratios (OR) were estimated using logistic regression (Methods). P-values were calculated using upper tail chi-square testing (one degree of freedom) from a t-statistic under a normal approximation. 95% CI were derived using normal approximation. Loci shared among phenotypes are denoted for the phenotype with the lowest p value, such that, e.g., 2q12.1 was MTS associated with VAR, CRS, and NP, and is shown here for NP. *locus has no previous association with IURDs **detected from cross-trait analysis and meta-analyzed using the specific IURD with smallest p value in FinnGen.