Table 2.
Credible Set of Causal Variants in the Neandertal Haplotype.
| Chr | Position | Ref | Alt | Anc. | Archaic | rsID | OR | P value | PIP | CADD | Reg. feature |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 7 | 37,984,972 | G | A | G | G/A | rs17171240 | 1.79 | 6.4 × 10−132 | 0.21 | 7.3 | Open chromatin |
| 7 | 37,984,802 | G | A | A | G/A | rs2044830 | 1.79 | 7.4 × 10−132 | 0.18 | 10.0 | Open chromatin |
| 7 | 37,984,011 | T | C | T | T/C | rs117329120 | 1.79 | 8.2 × 10−132 | 0.16 | 1.1 | No overlap |
| 7 | 37,983,798 | A | G | A | A/G | rs117575966 | 1.79 | 8.7 × 10−132 | 0.15 | 2.2 | No overlap |
| 7 | 37,964,710 | G | A | G | G/A | rs117387543 | 1.78 | 2.0 × 10−131 | 0.07 | 1.5 | No overlap |
| 7 | 37,964,701 | A | G | A | A/G | rs114929416 | 1.78 | 2.0 × 10−131 | 0.06 | 1.7 | No overlap |
| 7 | 37,964,907 | A | G | A | A/G | rs79590116 | 1.78 | 2.0 × 10−131 | 0.06 | 4.5 | No overlap |
| 7 | 37,966,121 | T | A | T | T/A | rs75182114 | 1.77 | 2.4 × 10−131 | 0.06 | 0.1 | No overlap |
| 7 | 37,976,920 | T | G | T | T/G | rs74335252 | 1.79 | 2.5 × 10−131 | 0.05 | 2.1 | No overlap |
95% credible set derived from fine-mapping assuming one causal variant (Locuszoom; Pruim et al. 2010, Boughton et al. 2021). Archaic refers to alleles present in the Vindija, Chagyrskaya, and Altai Neandertal and Denisova genomes (Meyer et al. 2012, Prüfer et al. 2014, 2017, Mafessoni et al. 2020). Regulatory features are derived from Ensembl (Zerbino et al. 2015). Coordinates are in hg38.
Ref., reference allele; Alt., alternative allele; Anc., ancestral allele; OR, odds ratio; PIP, posterior inclusion probability based on fine-mapping; CADD, Combined Annotation Dependent Depletion score (Rentzsch et al. 2019).