SNV-to-Gene Mappings

Collection of MAGMA SNV-to-Gene mappings.<br>Refer to MAGMA user manual for general details on file format (https://ctg.cncr.nl/software/magma).<br>File names are descriptive. For example:<br>GENEBODY_U2D2_EPM-GENEHANCER_MHC_G1000EUR_MAF1<br>(1) GENEBODY - map SNVs to genes with which they overlap (irrespective of whether the overlap is with an intron or an exon).(2) U2D2 - U (flank upstream of the transcription start-site) and D (flank downstream of the transcription end-site) where the integers specify the corresponding flank's size in kb.(3) EPM-GENEHANCER - name of dataset of regulatory interactions used for augmentation, following the naming system used in our publication (NONE means no augmentation with RIs).(4) MHC - specifies that the file still contains genes and SNVs overlapping with the MHC region. We did not consider such genes (--gene-exclude modifier in MAGMA gene-set analysis command) or SNVs (remove SNVs overlapping with MHC region from summary statistics) in our analyses. Their presence in these files simply adds flexibility by giving the opportunity to include the MHC region without having to build new mappings.(5) G1000EUR - we used the 1000 Genomes Project European Reference Population files (that is, those downloadable from the MAGMA website) for mapping SNVs to genes (see next point as well).(6) MAF1 - specifically, we used SNVs with a minor allele frequency (MAF) of 1% from the relevant MAGMA binary files to build our mappings. One can use a software such as PLINK to filter the binary files according to properties such as MAF (https://zzz.bwh.harvard.edu/plink/). <br>All files share the suffix: .aggregated.genes.annot<br><b>NOTE:</b> in our file names we used "Cardiac Muscle Cells" as a synonym for the term "Heart Muscle Cells" used in our publication. Likewise, in our file names we used "Hematopoeitic Cells" as a synonymfor "Blood Cells" used in our publication (...and yes, the correct spelling is hematopoietic).