Schema for snp130OrthoPt2Pa2Rm2

Database: hg18 Primary Table: snp130OrthoPt2Pa2Rm2 Row Count: 11,797,184 Data last updated: 2009-07-08
Format description: Orthologous alleles in chimp, orangutan and rhesus macaque (human only)
On download server: MariaDB table dump directory

field	example	SQL type	description
`bin`	585	`smallint(6)`	Indexing field to speed chromosome range queries.
`chrom`	chr1	`varchar(255)`	Chromosome
`chromStart`	491	`int(10) unsigned`	Start position in chrom
`chromEnd`	492	`int(10) unsigned`	End position in chrom
`name`	rs55998931	`varchar(255)`	Reference SNP identifier from dbSnp
`humanObserved`	C/T	`varchar(255)`	Observed alleles in human SNP
`humanAllele`	C	`char(1)`	Reference allele for human SNP
`humanStrand`	+	`char(1)`	Strand of human SNP annotation
`chimpChrom`	chr15	`varchar(255)`	Chimp chromosome to which the human SNP is mapped
`chimpStart`	100050033	`int(10) unsigned`	Start position on chimpChrom
`chimpEnd`	100050034	`int(10) unsigned`	End position on chimpChrom
`chimpAllele`	C	`char(1)`	Reference allele for chimp SNP
`chimpStrand`	-	`char(1)`	Strand of chimp SNP annotation
`orangChrom`	?	`varchar(255)`	Orang chromosome to which the human SNP is mapped
`orangStart`	0	`int(10) unsigned`	Start position on orangChrom
`orangEnd`	0	`int(10) unsigned`	End position on orangChrom
`orangAllele`	?	`char(1)`	Reference allele for orang SNP
`orangStrand`	?	`char(1)`	Strand of orang SNP annotation
`macaqueChrom`	?	`varchar(255)`	Macaque chromosome to which the human SNP is mapped
`macaqueStart`	0	`int(10) unsigned`	Start position on macaqueChrom
`macaqueEnd`	0	`int(10) unsigned`	End position on macaqueChrom
`macaqueAllele`	?	`char(1)`	Reference allele for macaque SNP
`macaqueStrand`	?	`char(1)`	Strand of macaque SNP annotation

Connected Tables and Joining Fields


	hg18.gwasCatalog.name (via snp130OrthoPt2Pa2Rm2.name) hg18.snp130.name (via snp130OrthoPt2Pa2Rm2.name) hg18.snp130CodingDbSnp.name (via snp130OrthoPt2Pa2Rm2.name) hg18.snp130Exceptions.name (via snp130OrthoPt2Pa2Rm2.name) hg18.snp130Seq.acc (via snp130OrthoPt2Pa2Rm2.name)

Sample Rows

bin	chrom	chromStart	chromEnd	name	humanObserved	humanAllele	humanStrand	chimpChrom	chimpStart	chimpEnd	chimpAllele	chimpStrand	orangChrom	orangStart	orangEnd	orangAllele	orangStrand	macaqueChrom	macaqueStart	macaqueEnd	macaqueAllele	macaqueStrand
585	chr1	491	492	rs55998931	C/T	C	+	chr15	100050033	100050034	C	-	?	0	0	?	?	?	0	0	?	?
585	chr1	518	519	rs62636508	C/G	G	+	chr15	100050006	100050007	C	-	?	0	0	?	?	?	0	0	?	?
585	chr1	582	583	rs58108140	A/G	G	+	chr15	100049942	100049943	G	-	?	0	0	?	?	?	0	0	?	?
585	chr1	690	691	rs10218492	A/G	G	+	chr15	100049866	100049867	G	-	?	0	0	?	?	?	0	0	?	?
585	chr1	789	790	rs10218527	A/G	A	+	chr15	100049806	100049807	A	-	?	0	0	?	?	?	0	0	?	?
585	chr1	800	801	rs28853987	A/G	G	+	chr15	100049795	100049796	G	-	?	0	0	?	?	?	0	0	?	?
585	chr1	876	877	rs28484712	A/G	G	+	chr15	100049727	100049728	G	-	?	0	0	?	?	?	0	0	?	?
585	chr1	884	885	rs28775022	A/G	G	+	chr15	100049719	100049720	G	-	?	0	0	?	?	?	0	0	?	?
585	chr1	10003	10004	rs56336884	A/G	G	+	chr15	100039770	100039771	G	-	?	0	0	?	?	chr13	113700693	113700694	G	-
585	chr1	10068	10069	rs71262675	A/G	C	-	chr15	100039705	100039706	G	+	chr2b	21142624	21142625	G	-	chr13	113700628	113700629	G	+

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