However, even rich outputs of these packages lack information about LD, eQTL, AF and haplotype blocks. Among a plethora of annotation packages on Bioconductor ( and CRAN ( myvariant 3, biomaRt 4, rentrez 5 can retrieve information about annotated SNPs. Two examples of this would be saving the results in different file formats (TXT, CSV, XLSX, etc.,) or taking advantage of their highly-optimized search engines from custom scripts. The user needs to advise that in a number of situations, extra precautions must be made. These tools are all web-based and require the user to do the following: open a web page, manually enter information, and obtain the results.

These tools offer a link of detected genetic variants to additional post-GWAS information about linkage disequilibrium (LD), expression quantitative trait loci (eQTL), allele frequencies (AF), protein functions, and chromatin states (for annotated single-nucleotide polymorphisms (SNP)). To better understand the biological mechanisms involved in complex trait regulations, web-based tools, such as HaploReg 1 and RegulomeDB 2, were proposed.

Genome wide association studies (GWAS) have produced a significant amount of data.

Install endnote rc2