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)

######################
# snps.txt
# All SNPs in LD with any of independent lead SNPs with r2 greater or equal to the defined threshold
######################
uniqID : Unique ID of SNPs consists of chr:position:allele1:allele2 where alleles are alphabetically ordered.
rsID : rsID based on dbSNP build 146.
chr : chromosome
pos : position on hg19
effect_allele : Effect/risk allele if it is provided in the input GWAS summary statistics file. If not, this is the alternative (minor) allele in 1000G.
non_effect_allele : Non-effect/non-risk allele if it is provided in the input GWAS summary statistics file. If not, this is the reference (major) allele in 1000G.
MAF : Minor allele frequency computed based on 1000G.
gwasP : P-value provided in the input GWAS summary statistics file. Non-GWAS tagged SNPs (which do not exist in input file but are extracted from the reference panel) have "NA" instead.
or : Odds ratio provided in the input GWAS summary statistics file if available. Non-GWAS tagged SNPs (which do not exist in input file but are extracted from the reference panel) have "NA" instead.
beta : Beta provided in the input GWAS summary statistics file if available. Non-GWAS tagged SNPs (which do not exist in input file but are extracted from the reference panel) have "NA" instead.
se : Standard error provided in the input GWAS summary statistics file if available. Non-GWAS tagged SNPs (which do not exist in input file but are extracted from the reference panel) have "NA" instead.
r2 : The maximum r2 of the SNP with one of the independent significant SNP (this doesn't have to be top lead SNPs in the genomic loci).
IndSigSNP : rsID of a independent significant SNP which has the maximum r2 of the SNP.
Genomic locus : Index of the genomic risk loci matching with "GenomicRiskLoci.txt".
nearestGene : The nearest Gene of the SNP based on ANNOVAR annotations.
	Note that ANNOVAR annotates "consequence" function by prioritising the most deleterious annotation for SNPs which are locating a genomic region where multiple genes are overlapped.
	Genes are encoded in symbol, if it is available, otherwise Ensembl ID.
	Genes include all transcripts from Ensembl gene build 85 including non-protein coding genes and RNAs.
dist : Distance to the nearest gene. SNPs which are locating in the gene body or 1kb up- or down-stream of TSS or TES have 0.
func : Functional consequence of the SNP on the gene obtained from ANNOVAR. For exonic SNPs, detail annotation (e.g. non-synonymous, stop gain and so on) is available in ANNOVAR table (annov.txt).
CADD : CADD score which is computed based on 63 annotations. The higher score, the more deleterious the SNP is. 12.37 is the suggested threshold by Kicher et al(ref).
RDB : RegulomeDB score which is the categorical score (from 1a to 7). 1a is the highest score that the SNP has the most biological evidence to be regulatory element.
minChrState : The minimum 15-core chromatin state across 127 tissue/cell type.
commonChrState : The most common 15-core chromatin state across 127 tissue/cell types.
posMapFilt : Whether the SNP was used for positional mapping or not. 1 is used, otherwise 0. When positional mapping is not performed, all SNPs have 0.
eqtlMapFilt : Whether the SNP was used for eqtl mapping or not. 1 is used, otherwise 0. When eQTL mapping is not performed, all SNPs have 0.