Schema for snp130
  Database: hg18    Primary Table: snp130    Row Count: 18,833,531   Data last updated: 2009-08-18
Format description: Polymorphism data from dbSnp database or genotyping arrays
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(31) Reference sequence chromosome or scaffold
chromStart 259int(10) unsigned Start position in chrom
chromEnd 260int(10) unsigned End position in chrom
name rs72477211varchar(15) dbSNP Reference SNP identifier
score 0smallint(5) unsigned Not used
strand +enum('+', '-') Which DNA strand contains the observed alleles
refNCBI Cblob Reference genomic sequence from dbSNP
refUCSC Cblob Reference genomic sequence from UCSC lookup of chrom,chromStart,chromEnd
observed A/Gvarchar(255) The sequences of the observed alleles from rs-fasta files
molType genomicenum('unknown', 'genomic', 'cDNA') Sample type from exemplar submitted sequence (ss)
class singleenum('unknown', 'single', 'in-del', 'het', 'microsatellite', 'named', 'mixed', 'mnp', 'insertion', 'deletion') Class of variant (single, in-del, named, mixed, etc.)
valid unknownset('unknown', 'by-cluster', 'by-frequency', 'by-submitter', 'by-2hit-2allele', 'by-hapmap', 'by-1000genomes') Validation status of the SNP
avHet 0float Average heterozygosity from all observations
avHetSE 0float Standard Error for the average heterozygosity
func unknownset('unknown', 'coding-synon', 'intron', 'near-gene-3', 'near-gene-5', 'nonsense', 'missense', 'frameshift', 'untranslated-3', 'untranslated-5') Functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.)
locType exactenum('range', 'exact', 'between', 'rangeInsertion', 'rangeSubstitution', 'rangeDeletion') Type of mapping inferred from size on reference; may not agree with class
weight 3int(10) unsigned The quality of the alignment: 1 = unique mapping, 2 = non-unique, 3 = many matches

Connected Tables and Joining Fields
        hg18.gwasCatalog.name (via snp130.name)
      hg18.lsSnpPdb.snpId (via snp130.name)
      hg18.snp130CodingDbSnp.name (via snp130.name)
      hg18.snp130Exceptions.name (via snp130.name)
      hg18.snp130OrthoPt2Pa2Rm2.name (via snp130.name)
      hg18.snp130Seq.acc (via snp130.name)
      hg18.snpArrayIlluminaHuman660W_Quad.name (via snp130.name)
      hg18.snpArrayIlluminaHumanCytoSNP_12.name (via snp130.name)
      hg18.snpArrayIlluminaHumanOmni1_Quad.name (via snp130.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandrefNCBIrefUCSCobservedmolTypeclassvalidavHetavHetSEfunclocTypeweight
585chr1259260rs724772110+CCA/Ggenomicsingleunknown00unknownexact3
585chr1433433rs562890600+---/Cgenomicinsertionunknown00unknownbetween1
585chr1491492rs559989310+CCC/Tgenomicsingleunknown00unknownexact1
585chr1518519rs626365080+GGC/Ggenomicsingleunknown00unknownexact1
585chr1582583rs581081400+GGA/Ggenomicsingleunknown00unknownexact1
585chr1690691rs102184920+GGA/Ggenomicsingleby-cluster00unknownexact1
585chr1766767rs102184930+GGA/Ggenomicsingleby-cluster00unknownexact1
585chr1789790rs102185270+AAA/Ggenomicsingleby-cluster00unknownexact1
585chr1800801rs288539870+GGA/Ggenomicsingleunknown00unknownexact1
585chr1876877rs284847120+GGA/Ggenomicsingleunknown00unknownexact1

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.