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Database: hg38 Primary Table: snp150Flagged Row Count: 203,915   Data last updated: 2020-06-15
field | example | SQL type | info |
bin | 592 | smallint(5) unsigned | range |
chrom | chr1 | varchar(31) | values |
chromStart | 948135 | int(10) unsigned | range |
chromEnd | 948136 | int(10) unsigned | range |
name | rs267598747 | varchar(15) | values |
score | 0 | smallint(5) unsigned | range |
strand | + | enum('+', '-') | values |
refNCBI | G | blob | values |
refUCSC | G | blob | values |
observed | A/G | varchar(255) | values |
molType | genomic | enum('unknown', 'genomic', 'cDNA', 'mito') | values |
class | single | enum('single', 'in-del', 'microsatellite', 'named', 'mnp', 'insertion', 'deletion') | values |
valid | by-cluster | set('unknown', 'by-cluster', 'by-frequency', 'by-submitter', 'by-2hit-2allele', 'by-hapmap', 'by-1000genomes') | values |
avHet | 0 | float | range |
avHetSE | 0 | float | range |
func | coding-synon | set('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 |
locType | exact | enum('range', 'exact', 'between', 'rangeInsertion', 'rangeSubstitution', 'rangeDeletion', 'fuzzy') | values |
weight | 1 | int(10) unsigned | range |
exceptions | | set('RefAlleleMismatch', 'DuplicateObserved', 'MixedObserved', 'FlankMismatchGenomeLonger', 'FlankMismatchGenomeEqual', 'FlankMismatchGenomeShorter', 'NamedDeletionZeroSpan', 'NamedInsertionNonzeroSpan', 'SingleClassLongerSpan', 'SingleClassZeroSpan', 'SingleClassTriAllelic', 'SingleClassQuadAllelic', 'ObservedWrongFormat', 'ObservedTooLong', 'ObservedContainsIupac', 'ObservedMismatch', 'MultipleAlignments', 'NonIntegerChromCount', 'AlleleFreqSumNot1', 'SingleAlleleFreq', 'InconsistentAlleles') | values |
submitterCount | 1 | smallint(5) unsigned | range |
submitters | YSAMUELS, | longblob | |
alleleFreqCount | 0 | smallint(5) unsigned | range |
alleles | | longblob | |
alleleNs | | longblob | |
alleleFreqs | | longblob | |
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 |
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Connected Tables and Joining Fields
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Sample Rows
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bin | chrom | chromStart | chromEnd | name | score | strand | refNCBI | refUCSC | observed | molType | class | valid | avHet | avHetSE | func | locType | weight | exceptions | submitterCount | submitters | alleleFreqCount | alleles | alleleNs | alleleFreqs | bitfields |
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592 | chr1 | 948135 | 948136 | rs267598747 | 0 | + | G | G | A/G | genomic | single | by-cluster | 0 | 0 | coding-synon | exact | 1 | | 1 | YSAMUELS, | 0 | | | | clinically-assoc,submitted-by-lsdb |
592 | chr1 | 955963 | 955964 | rs267598748 | 0 | + | G | G | A/C/G | genomic | single | by-cluster,by-frequency | 0.000033 | 0.004069 | coding-synon | exact | 1 | SingleClassTriAllelic,InconsistentAlleles | 2 | EVA_EXAC,YSAMUELS, | 2 | C,G, | 2.000000,120776.000000, | 0.000017,0.999983, | clinically-assoc,submitted-by-lsdb |
592 | chr1 | 970787 | 970788 | rs267598759 | 0 | + | G | G | A/G | genomic | single | by-cluster | 0 | 0 | intron,ncRNA,missense | exact | 1 | | 1 | YSAMUELS, | 0 | | | | clinically-assoc,submitted-by-lsdb |
592 | chr1 | 1014142 | 1014143 | rs786201005 | 0 | + | C | C | C/T | genomic | single | unknown | 0 | 0 | nonsense | exact | 1 | | 1 | CLINVAR, | 0 | | | | clinically-assoc,has-omim-omia,submitted-by-lsdb |
592 | chr1 | 1014319 | 1014319 | rs672601345 | 0 | + | - | - | -/G | genomic | insertion | unknown | 0 | 0 | frameshift | between | 1 | | 1 | CLINVAR, | 0 | | | | clinically-assoc,has-omim-omia,submitted-by-lsdb |
592 | chr1 | 1014358 | 1014359 | rs672601312 | 0 | + | G | G | G/T | genomic | single | by-cluster | 0.000017 | 0.002892 | nonsense | exact | 1 | | 2 | CLINVAR,EVA_EXAC, | 2 | G,T, | 119543.000000,1.000000, | 0.999992,0.000008, | clinically-assoc,has-omim-omia,submitted-by-lsdb |
592 | chr1 | 1022312 | 1022313 | rs879253787 | 0 | + | A | A | A/T | genomic | single | unknown | 0 | 0 | ncRNA,missense | exact | 1 | | 1 | CLINVAR, | 0 | | | | clinically-assoc,submitted-by-lsdb |
592 | chr1 | 1041581 | 1041582 | rs587777299 | 0 | + | C | C | C/T | genomic | single | by-cluster | 0 | 0 | ncRNA,nonsense | exact | 1 | | 2 | ILLUMINA,OMIM-CURATED-RECORDS, | 0 | | | | clinically-assoc,has-omim-omia,submitted-by-lsdb |
592 | chr1 | 1041582 | 1041583 | rs150359724 | 0 | + | A | A | A/G | genomic | single | by-cluster,by-frequency,by-1000genomes | 0.009183 | 0.067134 | ncRNA,missense | exact | 1 | | 11 | 1000GENOMES,CLINVAR,EVA-GONL,EVA_DECODE,EVA_EXAC,EXOME_CHIP,ILLUMINA,JJLAB,NHLBI-ESP,TOPMED,WEILL_CORNELL_DGM, | 2 | A,G, | 111119.000000,555.000000, | 0.995030,0.004970, | clinically-assoc,submitted-by-lsdb |
592 | chr1 | 1042140 | 1042140 | rs879253788 | 0 | + | - | - | -/C | genomic | insertion | unknown | 0 | 0 | ncRNA,frameshift | between | 1 | MixedObserved | 1 | CLINVAR, | 0 | | | | clinically-assoc,submitted-by-lsdb |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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