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) ###################### # genes.txt # The list of genes mapped by SNPs in snps.txt based on the user defined mapping parameters. # Columns with posMap or eqtlMap in the parentheses are only available when positional or eQTL mapping is performed, respectively. ###################### Gene : ENSG ID Symbol : Gene Symbol entrezID : entrez ID GenomicLocus : Index of genomic loci where mapped SNPs are from. This could contain more than one interval in the case that eQTLs are mapped to genes from distinct genomic risk loci. chr : chromosome start : Starting position of the gene end : Ending position of the gene strand : Strand of the gene status : Status of the gene from Ensembl (not available for > v85) type : Gene biotype from Ensembl HUGO : HUGO (HGNC) gene symbol pLI : pLI score from ExAC database. The probability of being loss-of-function intolerant. The higher the score is, the more intolerant to loss-of-function mutations the gene is. ncRVIS : Non-coding residual variation intolerance score. The higher the score is, the more intolerant to non-coding variation the gene is. posMapSNPs (posMap): The number of SNPs mapped to gene based on positional mapping (after functional filtering if parameters are given). posMapMaxCADD (posMap): The maximum CADD score of mapped SNPs by positional mapping. eqtlMapSNPs (eqtlMap): The number of SNPs mapped to the gene based on eQTL mapping. eqtlMapminP (eqtlMap): The minimum eQTL P-value of mapped SNPs. eqtlMapmin! (eqtlMap): The minimum eQTL FDR of mapped SNPs. eqtlMapts (eqtlMap): Tissue types of mapped eQTL SNPs. eqtlDirection (eqtlMap): Consecutive direction of mapped eQTL SNPs after aligning risk increasing alleles in GWAS and tested alleles in eQTL data source. "NA" if risk increase alleles are not defined either because signed effect is not provided in the input GWAS file or all of eQTL SNPs are not in the input GWAS file but included from reference panel for the gene. ciMap (ciMap): "Yes" if the gene is mapped by chromatin interaction mapping, "No" otherwise. ciMapts (ciMap): Tissue/cell types of mapped chromatin interactions. minGwasP : The minimum P-value of mapped SNPs. ciMap : If the gene is mapped by chromatin interaction "Yes", otherwise "No". IndSigSNPs : rsID of the all independent significant SNPs of mapped SNPs.