Functional consequences of SNPs on genes are obtained by performing ANNOVAR12 (“gene-based annotation”) using Ensembl genes (build 85). Note that SNPs can be annotated to more than one gene in case of intergenic SNPs which are annotated to the two closest up- and down-stream genes. CADD scores, RegulomeDB scores and 15-core chromatin state are annotated to all SNPs in 1000G phase 3 by matching chromosome, position, reference, and alternative alleles. eQTLs are also extracted by matching chromosome, position and alleles of all independent significant SNPs and SNPs which are in LD with one of the independent significant SNPs for each user-selected tissue type, wherein SNPs can have multiple eQTLs for distinct genes and tissue types (Supplementary Note 2). Information on previously known SNP-trait associations reported in the GWAS catalog is also retrieved for all SNPs of interest by matching chromosome and position.
