Schema for snp130

Database: hg18 Primary Table: snp130 Row Count: 18,833,531 Data last updated: 2009-08-19
Format description: Polymorphism data from dbSnp database or genotyping arrays
On download server: MariaDB table dump directory

field	example	SQL type	description
`bin`	585	`smallint(5) unsigned`	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(31)`	Reference sequence chromosome or scaffold
`chromStart`	259	`int(10) unsigned`	Start position in chrom
`chromEnd`	260	`int(10) unsigned`	End position in chrom
`name`	rs72477211	`varchar(15)`	dbSNP Reference SNP identifier
`score`	0	`smallint(5) unsigned`	Not used
`strand`	+	`enum('+', '-')`	Which DNA strand contains the observed alleles
`refNCBI`	C	`blob`	Reference genomic sequence from dbSNP
`refUCSC`	C	`blob`	Reference genomic sequence from UCSC lookup of chrom,chromStart,chromEnd
`observed`	A/G	`varchar(255)`	The sequences of the observed alleles from rs-fasta files
`molType`	genomic	`enum('unknown', 'genomic', 'cDNA')`	Sample type from exemplar submitted sequence (ss)
`class`	single	`enum('unknown', 'single', 'in-del', 'het', 'microsatellite', 'named', 'mixed', 'mnp', 'insertion', 'deletion')`	Class of variant (single, in-del, named, mixed, etc.)
`valid`	unknown	`set('unknown', 'by-cluster', 'by-frequency', 'by-submitter', 'by-2hit-2allele', 'by-hapmap', 'by-1000genomes')`	Validation status of the SNP
`avHet`	0	`float`	Average heterozygosity from all observations
`avHetSE`	0	`float`	Standard Error for the average heterozygosity
`func`	unknown	`set('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`	exact	`enum('range', 'exact', 'between', 'rangeInsertion', 'rangeSubstitution', 'rangeDeletion')`	Type of mapping inferred from size on reference; may not agree with class
`weight`	3	`int(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)

Sample Rows

bin	chrom	chromStart	chromEnd	name	strand	refNCBI	refUCSC	observed	molType	class	valid	func	locType	weight
585	chr1	259	260	rs72477211	+	C	C	A/G	genomic	single	unknown	unknown	exact	3
585	chr1	433	433	rs56289060	+	-	-	-/C	genomic	insertion	unknown	unknown	between	1
585	chr1	491	492	rs55998931	+	C	C	C/T	genomic	single	unknown	unknown	exact	1
585	chr1	518	519	rs62636508	+	G	G	C/G	genomic	single	unknown	unknown	exact	1
585	chr1	582	583	rs58108140	+	G	G	A/G	genomic	single	unknown	unknown	exact	1
585	chr1	690	691	rs10218492	+	G	G	A/G	genomic	single	by-cluster	unknown	exact	1
585	chr1	766	767	rs10218493	+	G	G	A/G	genomic	single	by-cluster	unknown	exact	1
585	chr1	789	790	rs10218527	+	A	A	A/G	genomic	single	by-cluster	unknown	exact	1
585	chr1	800	801	rs28853987	+	G	G	A/G	genomic	single	unknown	unknown	exact	1
585	chr1	876	877	rs28484712	+	G	G	A/G	genomic	single	unknown	unknown	exact	1

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