Schema for snp150Common
  Database: hg38    Primary Table: snp150Common    Row Count: 15,124,099   Data last updated: 2017-04-18
Format description: Polymorphism data from dbSNP
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
chrom chr1varchar(31) Reference sequence chromosome or scaffold
chromStart 10177int(10) unsigned Start position in chrom
chromEnd 10177int(10) unsigned End position in chrom
name rs367896724varchar(15) dbSNP Reference SNP (rs) identifier
score 0smallint(5) unsigned Not used
strand +enum('+', '-') Which DNA strand contains the observed alleles
refNCBI -blob Reference genomic sequence from dbSNP
refUCSC -blob Reference genomic sequence from UCSC lookup of chrom,chromStart,chromEnd
observed -/Cvarchar(255) The sequences of the observed alleles from rs-fasta files
molType genomicenum('unknown', 'genomic', 'cDNA', 'mito') Sample type from exemplar submitted SNPs (ss)
class insertionenum('single', 'in-del', 'microsatellite', 'named', 'mnp', 'insertion', 'deletion') Class of variant (single, in-del, named, mixed, etc.)
valid by-cluster,by-frequency,by-...set('unknown', 'by-cluster', 'by-frequency', 'by-submitter', 'by-2hit-2allele', 'by-hapmap', 'by-1000genomes') Validation status of the SNP
avHet 0.488846float Average heterozygosity from all observations. Note: may be computed on small number of samples.
avHetSE 0.073843float Standard Error for the average heterozygosity
func near-gene-5set('unknown', 'coding-synon', 'intron', 'near-gene-3', 'near-gene-5', 'ncRNA', 'nonsense', 'missense', 'stop-loss', 'frameshift', 'cds-indel', 'untranslated-3', 'untranslated-5', 'splice-3', 'splice-5') Functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.)
locType betweenenum('range', 'exact', 'between', 'rangeInsertion', 'rangeSubstitution', 'rangeDeletion', 'fuzzy') Type of mapping inferred from size on reference; may not agree with class
weight 1int(10) unsigned The quality of the alignment: 1 = unique mapping, 2 = non-unique, 3 = many matches
exceptions  set('RefAlleleMismatch', 'DuplicateObserved', 'MixedObserved', 'FlankMismatchGenomeLonger', 'FlankMismatchGenomeEqual', 'FlankMismatchGenomeShorter', 'NamedDeletionZeroSpan', 'NamedInsertionNonzeroSpan', 'SingleClassLongerSpan', 'SingleClassZeroSpan', 'SingleClassTriAllelic', 'SingleClassQuadAllelic', 'ObservedWrongFormat', 'ObservedTooLong', 'ObservedContainsIupac', 'ObservedMismatch', 'MultipleAlignments', 'NonIntegerChromCount', 'AlleleFreqSumNot1', 'SingleAlleleFreq', 'InconsistentAlleles') Unusual conditions noted by UCSC that may indicate a problem with the data
submitterCount 2smallint(5) unsigned Number of distinct submitter handles for submitted SNPs for this ref SNP
submitters 1000GENOMES,BILGI_BIOE,longblob List of submitter handles
alleleFreqCount 2smallint(5) unsigned Number of observed alleles with frequency data
alleles -,C,longblob Observed alleles for which frequency data are available
alleleNs 2878.000000,2130.000000,longblob Count of chromosomes (2N) on which each allele was observed. Note: this is extrapolated by dbSNP from submitted frequencies and total sample 2N, and is not always an integer.
alleleFreqs 0.574681,0.425319,longblob Allele frequencies
bitfields maf-5-some-pop,maf-5-all-popsset('unknown', 'clinically-assoc', 'maf-5-some-pop', 'maf-5-all-pops', 'has-omim-omia', 'microattr-tpa', 'submitted-by-lsdb', 'genotype-conflict', 'rs-cluster-nonoverlapping-alleles', 'observed-mismatch') SNP attributes extracted from dbSNP's SNP_bitfield table

Connected Tables and Joining Fields
        hg38.snp150.exceptions (via snp150Common.exceptions)
      hg38.snp150ExceptionDesc.exception (via snp150Common.exceptions)
      hg38.snp150Flagged.exceptions (via snp150Common.exceptions)
      hg38.snp150Mult.exceptions (via snp150Common.exceptions)
      hg38.snp150.name (via snp150Common.name)
      hg38.snp150CodingDbSnp.name (via snp150Common.name)
      hg38.snp150Flagged.name (via snp150Common.name)
      hg38.snp150Mult.name (via snp150Common.name)
      hg38.snp150OrthoPt5Pa2Rm8.name (via snp150Common.name)
      hg38.snp150Seq.acc (via snp150Common.name)

Sample Rows
 
binchromchromStartchromEndnamescorestrandrefNCBIrefUCSCobservedmolTypeclassvalidavHetavHetSEfunclocTypeweightexceptionssubmitterCountsubmittersalleleFreqCountallelesalleleNsalleleFreqsbitfields
585chr11017710177rs3678967240+---/Cgenomicinsertionby-cluster,by-frequency,by-1000genomes0.4888460.073843near-gene-5between121000GENOMES,BILGI_BIOE,2-,C,2878.000000,2130.000000,0.574681,0.425319,maf-5-some-pop,maf-5-all-pops
585chr11035210352rs5555000750+---/Agenomicinsertionby-cluster,by-frequency,by-1000genomes0.4921880.06201near-gene-5between121000GENOMES,SSMP,2-,A,2817.000000,2191.000000,0.562500,0.437500,maf-5-some-pop,maf-5-all-pops
585chr11100711008rs5752721510+CCC/Ggenomicsingleby-frequency,by-1000genomes0.1606090.233472near-gene-5exact111000GENOMES,2C,G,4567.000000,441.000000,0.911941,0.088059,maf-5-some-pop
585chr11101111012rs5444190190+CCC/Ggenomicsingleby-frequency,by-1000genomes0.1606090.233472near-gene-5exact111000GENOMES,2C,G,4567.000000,441.000000,0.911941,0.088059,maf-5-some-pop
585chr11310913110rs5405380260+GGA/Ggenomicsingleby-frequency,by-1000genomes0.0520820.152737intronexact121000GENOMES,JJLAB,2A,G,134.000000,4874.000000,0.026757,0.973243,maf-5-some-pop
585chr11311513116rs626352860+TTG/Tgenomicsingleby-cluster,by-frequency,by-1000genomes0.1752540.238565intronexact141000GENOMES,BCMHGSC_JDW,ENSEMBL,GMI,2G,T,486.000000,4522.000000,0.097045,0.902955,maf-5-some-pop
585chr11311713118rs620286910-AAC/Tgenomicsingleby-cluster,by-frequency,by-1000genomes0.1752540.238565intronexact141000GENOMES,BCMHGSC_JDW,ENSEMBL,GMI,2C,T,486.000000,4522.000000,0.097045,0.902955,
585chr11327213273rs5317308560+GGC/Ggenomicsingleby-cluster,by-frequency,by-1000genomes0.1720280.23753ncRNAexact151000GENOMES,EVA_MGP,JJLAB,PADH-LAB_SPU,WEILL_CORNELL_DGM,2C,G,476.000000,4532.000000,0.095048,0.904952,maf-5-some-pop
585chr11341713417rs7770385950+---/GAGAgenomicinsertionby-cluster,by-frequency0.2877960.247126ncRNAbetween1MixedObserved4EVA_EXAC,EVA_GENOME_DK,PADH-LAB_SPU,TMC_SNPDB,2-,GAGA,1014.000000,214.000000,0.825733,0.174267,maf-5-some-pop,maf-5-all-pops
585chr11446314464rs5461694440+AAA/Tgenomicsingleby-cluster,by-frequency,by-1000genomes0.173320.23795near-gene-3,ncRNAexact131000GENOMES,JJLAB,WEILL_CORNELL_DGM,2A,T,4528.000000,480.000000,0.904153,0.095847,maf-5-some-pop

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