HaploReg consists of a PHP interface to a MySQL database. The initial database table was populated using genomic coordinates and sequences for 16 151 841 biallelic SNPs and small indels from the pilot release of the 1000 Genomes Project (17). In some cases, such as novel indels, the variant call format (VCF) file from the pilot release did not have a RefSNP identifier (rsid); for the purpose of creating a unique identifier for this database, these variants were assigned the label of ‘chromosome:position’ in hg18 coordinates. To provide backward compatibility with obsolete rsids, dbSNP release 132 was checked for variants at the same position as 1000 Genomes pilot variants with multiple rsids (18). In addition, annotations of functional consequences were extracted from dbSNP.
