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Set-Cookie: hguid.genome-euro=432629880_9e8eCUA16XydNqjrXDpDaWgtge3j; path=/; domain=.ucsc.edu; expires=Thu, 31-Dec-2037 23:59:59 GMT Content-Type:text/html Schema for snp150Flagged
Schema for snp150Flagged
  Database: hg38    Primary Table: snp150Flagged    Row Count: 203,915   Data last updated: 2017-04-18
Format description: Polymorphism data from dbSNP
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 592smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(31) values Reference sequence chromosome or scaffold
chromStart 948135int(10) unsigned range Start position in chrom
chromEnd 948136int(10) unsigned range End position in chrom
name rs267598747varchar(15) values dbSNP Reference SNP (rs) identifier
score 0smallint(5) unsigned range Not used
strand +enum('+', '-') values Which DNA strand contains the observed alleles
refNCBI Gblob values Reference genomic sequence from dbSNP
refUCSC Gblob values Reference genomic sequence from UCSC lookup of chrom,chromStart,chromEnd
observed A/Gvarchar(255) values The sequences of the observed alleles from rs-fasta files
molType genomicenum('unknown', 'genomic', 'cDNA', 'mito') values Sample type from exemplar submitted SNPs (ss)
class singleenum('single', 'in-del', 'microsatellite', 'named', 'mnp', 'insertion', 'deletion') values Class of variant (single, in-del, named, mixed, etc.)
valid by-clusterset('unknown', 'by-cluster', 'by-frequency', 'by-submitter', 'by-2hit-2allele', 'by-hapmap', 'by-1000genomes') values Validation status of the SNP
avHet 0float range Average heterozygosity from all observations. Note: may be computed on small number of samples.
avHetSE 0float range Standard Error for the average heterozygosity
func coding-synonset('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') values Functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.)
locType exactenum('range', 'exact', 'between', 'rangeInsertion', 'rangeSubstitution', 'rangeDeletion', 'fuzzy') values Type of mapping inferred from size on reference; may not agree with class
weight 1int(10) unsigned range 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') values Unusual conditions noted by UCSC that may indicate a problem with the data
submitterCount 1smallint(5) unsigned range Number of distinct submitter handles for submitted SNPs for this ref SNP
submitters YSAMUELS,longblob   List of submitter handles
alleleFreqCount 0smallint(5) unsigned range Number of observed alleles with frequency data
alleles  longblob   Observed alleles for which frequency data are available
alleleNs  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  longblob   Allele frequencies
bitfields clinically-assoc,submitted-...set('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') values SNP attributes extracted from dbSNP's SNP_bitfield table

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

Sample Rows
 
binchromchromStartchromEndnamescorestrandrefNCBIrefUCSCobservedmolTypeclassvalidavHetavHetSEfunclocTypeweightexceptionssubmitterCountsubmittersalleleFreqCountallelesalleleNsalleleFreqsbitfields
592chr1948135948136rs2675987470+GGA/Ggenomicsingleby-cluster00coding-synonexact11YSAMUELS,0clinically-assoc,submitted-by-lsdb
592chr1955963955964rs2675987480+GGA/C/Ggenomicsingleby-cluster,by-frequency0.0000330.004069coding-synonexact1SingleClassTriAllelic,InconsistentAlleles2EVA_EXAC,YSAMUELS,2C,G,2.000000,120776.000000,0.000017,0.999983,clinically-assoc,submitted-by-lsdb
592chr1970787970788rs2675987590+GGA/Ggenomicsingleby-cluster00intron,ncRNA,missenseexact11YSAMUELS,0clinically-assoc,submitted-by-lsdb
592chr110141421014143rs7862010050+CCC/Tgenomicsingleunknown00nonsenseexact11CLINVAR,0clinically-assoc,has-omim-omia,submitted-by-lsdb
592chr110143191014319rs6726013450+---/Ggenomicinsertionunknown00frameshiftbetween11CLINVAR,0clinically-assoc,has-omim-omia,submitted-by-lsdb
592chr110143581014359rs6726013120+GGG/Tgenomicsingleby-cluster0.0000170.002892nonsenseexact12CLINVAR,EVA_EXAC,2G,T,119543.000000,1.000000,0.999992,0.000008,clinically-assoc,has-omim-omia,submitted-by-lsdb
592chr110223121022313rs8792537870+AAA/Tgenomicsingleunknown00ncRNA,missenseexact11CLINVAR,0clinically-assoc,submitted-by-lsdb
592chr110415811041582rs5877772990+CCC/Tgenomicsingleby-cluster00ncRNA,nonsenseexact12ILLUMINA,OMIM-CURATED-RECORDS,0clinically-assoc,has-omim-omia,submitted-by-lsdb
592chr110415821041583rs1503597240+AAA/Ggenomicsingleby-cluster,by-frequency,by-1000genomes0.0091830.067134ncRNA,missenseexact1111000GENOMES,CLINVAR,EVA-GONL,EVA_DECODE,EVA_EXAC,EXOME_CHIP,ILLUMINA,JJLAB,NHLBI-ESP,TOPMED,WEILL_CORNELL_DGM,2A,G,111119.000000,555.000000,0.995030,0.004970,clinically-assoc,submitted-by-lsdb
592chr110421401042140rs8792537880+---/Cgenomicinsertionunknown00ncRNA,frameshiftbetween1MixedObserved1CLINVAR,0clinically-assoc,submitted-by-lsdb

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