README of output files (SNP2GENE) from FUMA web application Author: Kyoko Watanabe (k.watanabe@vu.nl) Version: 1.0.0 (2 Feb 2017) Version: 1.1.2 (27 Apr 2017) Version: 1.3.0 (21 Feb 2018) Version: 1.3.1 (27 Apr 2018) Version: 1.3.4 (8 Feb 2019) Version: 1.3.5 (27 May 2019) Version: 1.3.5d (14 Oct 2019) ###################### # gwascatalog.txt # List of SNPs reported in GWAScatalog which are candidate SNPs of your GWAS summary statistics. ###################### Genomic locus : Index of genomic risk loci. IndSigSNP : One of the independent significant SNPs of the SNP in GWAScatalog. chr : chromosome bp : position on hg19 snp : rsID of reported SNP in GWAS catalog PMID : PubMed ID Trait : The trait reported in GWAScatalog FirthAuth : First author reported in GWAScatalog Date : Date added in GWAScatalog P-value : Reported P-value Journal : Abbreviated journal name Link : PubMed URL Study : Title of paper Trait : Disease or trait examined in study InitialN : Sample size and ancestry description for stage 1 of GWAS (summing across multiple Stage 1 populations, if applicable) ReplicationN : Sample size and ancestry description for subsequent replication(s) (summing across multiple populations, if applicable) Region : Cytogenetic region associated with rs number ReportedGene : Gene(s) reported by author MappendGene : Gene(s) mapped to the strongest SNP. If the SNP is located within a gene, that gene is listed. If the SNP is intergenic, the upstream and downstream genes are listed, separated by a hyphen. UpGene : Entrez Gene ID for nearest upstream gene to rs number, if not within gene DownGene : Entrez Gene ID for nearest downstream gene to rs number, if not within gene SNP_Gene_ID* : Entrez Gene ID, if rs number within gene; multiple genes denotes overlapping transcripts UpGeneDist : distance in kb for nearest upstream gene to rs number, if not within gene DownGeneDist : distance in kb for nearest downstream gene to rs number, if not within gene Strongest : SNP(s) most strongly associated with trait + risk allele (? for unknown risk allele). May also refer to a haplotype. SNPs : Strongest SNP; if a haplotype it may include more than one rs number (multiple SNPs comprising the haplotype) merged : denotes whether the SNP has been merged into a subsequent rs record (0 = no; 1 = yes;) SNP_ID_cur : current rs number (will differ from strongest SNP when merged = 1) Content : SNP functional class intergenic : denotes whether SNP is in intergenic region (0 = no; 1 = yes) RistAF : Reported risk/effect allele frequency associated with strongest SNP in controls (if not available among all controls, among the control group with the largest sample size). If the associated locus is a haplotype the haplotype frequency will be extracted. P : Reported p-value for strongest SNP risk allele (linked to dbGaP Association Browser). Note that p-values are rounded to 1 significant digit (for example, a published p-value of 4.8 x 10-7 is rounded to 5 x 10-7). Pmlog : -log(p-value) Ptext : Information describing context of p-value (e.g. females, smokers). OrBeta : Reported odds ratio or beta-coefficient associated with strongest SNP risk allele. Note that if an OR <1 is reported this is inverted, along with the reported allele, so that all ORs included in the Catalog are >1. Appropriate unit and increase/decrease are included for beta coefficients. 95CI : Reported 95% confidence interval associated with strongest SNP risk allele, along with unit in the case of beta-coefficients. If 95% CIs are not published, we estimate these using the standard error, where available. Platform : Genotyping platform manufacturer used in Stage 1; also includes notation of pooled DNA study design or imputation of SNPs, where applicable CNV : Study of copy number variation (yes/no)