Can I assume that rs numbers in the SNPContigLoc table, but not in the SNPContigLocusId table are intergenic regions?
There are several reasons why a SNP could be in the SNPContigLoc table, but not in the SNPContigLocusId table:1.The SNP is intragenic.2.The SNP has multiple hits on the genome. We only annotate those SNPs that are uniquely placed on a genome.3.The SNP’s flanking sequence is in cDNA context and has resulted in poor alignment to genome, but the SNP still could be in a gene (this case is not common).
