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)

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# ci.txt
# This file is only available when chromatin interaction mapping is performed.
# The file contains significant interactions of user defined data or user uploaded data filtered.
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GenomicLocus : Index of genomic loci where the significant interaction is overlapped.
region1 : One end of significant chromatin interaction which overlap with at least one candidate SNPs in one of the genomic risk loci.
region2 : The other end of significant chromatin interaction. This region could be located outside the risk loci.
FDR : FDR of interaction.
type : Type of chromatin interaction data, e.g. Hi-C or ChIA-PET
DB : The name of data source.
tissue/cell : Tissue or cell type of the interaction.
intra/inter : Intra- or Inter-chromosomal interaction.
SNPs : rsID of candidate SNPs which are overlapping with the region 1.
genes : ENSG ID of genes whose promoter regions are overlapped with region 2.
ciMapFilt : If the interaction used for mapping 1, otherwise 0. It can be 0 due to one of the following reasons.
	1) region 2 is not mapped to any gene
	2) genes mapped by region 2 are not user selected gene type (such as protein coding genes)
	3) SNPs overlapping region 1 are filtered out by other functional filtering such as CADD score
	4) When filtering based on enhancer and/or promoter is activated, either region 1 is not overlapping with any enhancer or region 2 is not overlapping with any promoter