Table 1 Description of functional weighting methods.
Method name | Classification | Level | Citation | Significance threshold |
|---|---|---|---|---|
Suggestive | NA | Variant | NA | p < 1e−5 |
GenoCanyon10K | Annotation | Variant | Lu et al. Sci. Rep. 2015 | Prediction Score >0.5 |
GenoSkyline | Annotation | Variant | Lu et al. PLoS Genet. 2017 | Prediction Score >0.5 |
Sveinbjornsson | Annotation | Variant | Sveinbjornsson et al. Nat. Genet. 2016 | Annotation-based threshold |
LSMM | Annotation | Variant | Ming et al. Bioinformatics 2018 | FDR < 0.05 |
GPA | Pleiotropy | Variant | Chung et al. PLoS Genet. 2014 | FDR < 0.05 |
MTAG | Pleiotropy | Variant | Turley et al. Nat. Genet. 2018 | p < 5e−8 |
fGWAS | eQTL | Variant | Pickrell. AJHG 2014 | PPA > 0.9 |
Weighted eQTL | eQTL | Variant | Li et al. Front. Genet. 2013 | p < 5e−8 |
COLOC | eQTL | eQTL | Giambartolomei et al. PLoS Genet. 2014 | Approximate Bayes Factor >0.75 |
MOLOC | eQTL | eQTL | Giambartolomei et al. Bioinformatics 2018 | Posterior Probability >0.80 |
Jepeg | eQTL | eQTL | Lee et al. Bioinformatics 2014 | Bonferroni-adjusted Jepeg p-value |
Sherlock | eQTL | eQTL | He et al. AJHG 2013 | Log Bayes Factor >= 4.0 |
SMR | eQTL | eQTL | Zhu et al. Nat. Genet. 2016 | FDR q-value < 0.05; Heidi p-value < 0.05 |
TWAS/FUSION | eQTL | eQTL | Gusev et al. Nat. Gen. 2016 | Bonferroni-adjusted TWAS p-value |
fastENLOC | eQTL | eQTL | Wen et al. PLoS Genet. 2017 | RCP > = 0.50 |
EUGENE | eQTL | eQTL | Ferreira et al. JACI 2017 | p-value corresponding to largest FDR < 0.05 |
UTMOST | eQTL | eQTL | Hu et al. Nat. Genet. 2019 | Bonferroni-adjusted UTMOST p-value |
