To generate a list of gene (or other) regions for your SNPS you could do the following.
1. get SNP location from SNPloc package
(Assuming you only have SNP id's and not locations.)
All pre-built Bioconductor annotations are listed here:
Search for 'SNPloc' and choose the package that was aligned to the same genome as your SNPs. See the man page for examples of how to extract snps into a GRanges using the rsid.
2. get (or make) TxDb package for regions of interest
Search the annotation site for 'TxDb'. These packages contain gene models from various resources and genome builds (apparent in titles). If you don't see a compatible TxDb you can create you own with a function from GenomicFeatures.
Once you have the TxDb you can extract gene, exons, UTRs or other regions. I'll use the known gene table from UCSC:
library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
There are several extractors, see ?transcriptsBy:
genes <- transcriptsBy(txdb, "gene")
3. overlap SNP locations with regions from TxDb
There are several options for overlaps. You could use findOverlaps() from IRanges or locateVariants() from VariantAnnotation. Alternatively you could use the biomaRt package to extract metadata based on the SNPs.
Hopefully this is enough to get you going. It would be helpful to know what information you have in the 'list' of GWAS generated SNPs. If you run into problems please show an example of what you've tried so we can give a more specific answer.
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