Table 3.
Statistically significant associations from the mixed ancestry analysis.
| Gene | Lead model | Lead phenotype | UKB carrier n (%)a | UKB p value | HNP carrier n (%)a | HNP p value | Meta p value | Eur carrier n (%)a,b | Eur p valueb |
|---|---|---|---|---|---|---|---|---|---|
| UGT1A1 | Coding | Total bilirubin | 90 (0.19%) | 3.4 × 10−14 | 19 (0.15%) | 1.5 × 10−2 | 4.3 × 10−15 | 77 (0.16%) | 5.5 × 10−9 |
| FCGRT | Coding | Albumin | 72 (0.16%) | 4.9 × 10−12 | 28 (0.22%) | 2.4 × 10−2 | 8.5 × 10−13 | 72 (0.16%) | 9.2 × 10−8 |
| TMPRSS6 | Coding | Mean corpuscular haemoglobin | 389 (0.8%) | 1.5 × 10−11 | 105 (0.78%) | 5.0 × 10−2 | 5.8 × 10−12 | 369 (0.73%) | 6.3 × 10−9 |
| SLCO1B3 | Coding | Total bilirubin | 531 (1.14%) | 6.7 × 10−10 | 135 (1.06%) | 1.6 × 10−2 | 4.5 × 10−11 | 574 (1.18%) | 1.4 × 10−8 |
| OCA2 | Coding | Hair colour: Blonde | 32 (0.61%)/65 (0.15%)a | 1.5 × 10−14 | 31 (0.66%)/46 (0.13%)a | 2.5 × 10−15c | |||
| TYRP1 | Coding | Hair colour: Blonde | 65 (1.24%)/231 (0.52%)a | 3.4 × 10−12 | 55 (1.18%)/180 (0.5%)a | 6.6 × 10−9 | |||
| SEC23B | Coding | Red blood cell distribution width | 341 (0.7%) | 1.9 × 10−10 | 279 (0.71%) | 3.4 × 10−10 |
All results shown are from the LMM with all ethnicities. When multiple phenotypes and/or models (coding, LoF) were significantly associated with a gene, only the lead phenotype and model are shown. All results can be found in Supplementary Data 2
aFor binary traits, the information shown is case n (%)/ctrl n (%)
bEur carrier and Eur p value columns: For the phenotypes measured in both cohorts, the European meta-analysis values are shown. For the phenotypes measured only in UKB (blank for HNP), the UKB Eur values are shown
cWhile OCA2 was significantly associated with hair colour in the European ancestry subset, that subset had only nine expected case carriers, and so it failed our screening. In the Fisher’s exact test in unrelated individuals with no carrier cutoff, the p value is 1.3 × 10−8