Chunk #11 — Materials and Methods — Functional mapping and annotation of GWAS meta-analysis

Source

Genome-Wide Association Study Meta-Analysis of the Alcohol Use Disorders Identification Test (AUDIT) in Two Population-Based Cohorts.

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We used FUMA v1.2.8 (22) to study the functional consequences of the index SNPs, and of the SNPs contained in each credible set, which included ANNOVAR categories, Combined Annotation Dependent Depletion (CADD) scores, RegulomeDB scores, eQTLs, and chromatin states. We also studied the regulatory consequences of the index SNPs using the Variant Effect Predictor (VEP; Ensembl GRCh37).