This track contains information about single nucleotide polymorphisms
and small insertions and deletions (indels) — collectively Simple
Nucleotide Polymorphisms — from
a provisional release of
dbSNP
build 130, available from
ftp.ncbi.nih.gov/snp.
dbSNP build 130 was officially released with genomic coordinates for the NCBI build 36
human genome; dbSNP provided a provisional release of genomic coordinates mapped from
NCBI build 36 to GRCh37 (see
ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/misc/exchange/README.txt).
Interpreting and Configuring the Graphical Display
Variants are shown as single tick marks at most zoom levels.
When viewing the track at or near base-level resolution, the displayed
width of the SNP corresponds to the width of the variant in the reference
sequence. Insertions are indicated by a single tick mark displayed between
two nucleotides, single nucleotide polymorphisms are displayed as the width
of a single base, and multiple nucleotide variants are represented by a
block that spans two or more bases.
The configuration categories reflect the following definitions (not all categories apply
to this assembly):
Class: Describes the observed alleles
Single - single nucleotide variation: all observed alleles are single nucleotides
(can have 2, 3 or 4 alleles)
Microsatellite - the observed allele from dbSNP is variation in counts of short tandem repeats
Named - the observed allele from dbSNP is given as a text name
No Variation - no variation asserted for sequence
Mixed - the cluster contains submissions from multiple classes
Multiple Nucleotide Polymorphism - alleles of the same length, length > 1, and from set of {A,T,C,G}
Insertion - the polymorphism is an insertion relative to the reference assembly
Deletion - the polymorphism is a deletion relative to the reference assembly
Unknown - no classification provided by data contributor
Validation: Method used to validate
the variant (each variant may be validated by more than one method)
By Frequency - at least one submitted SNP in cluster has frequency data submitted
By Cluster - cluster has at least 2 submissions, with at least one submission assayed with a non-computational method
By Submitter - at least one submitter SNP in cluster was validated by independent assay
By 2 Hit/2 Allele - all alleles have been observed in at least 2 chromosomes
By HapMap - validated by HapMap project
Unknown - no validation has been reported for this variant
Function: Predicted functional role
(each variant may have more than one functional role)
Locus Region - variation within 2000 bases of gene, but not
in transcript (near-gene-3, near-gene-5)
Coding - Synonymous - no change in peptide for allele with
respect to reference assembly (coding-synon)
Coding - Non-Synonymous - change in peptide for allele with
respect to reference assembly (nonsense, missense,
frameshift)
Untranslated - variation in transcript, but not in coding
region interval (untranslated-3, untranslated-5)
Intron - variation in intron, but not in first two or last two bases of intron
Splice Site - variation in first two or last two bases of
intron (splice-3, splice-5)
Unknown - no known functional classification
Molecule Type: Sample used to find this variant
Genomic - variant discovered using a genomic template
cDNA - variant discovered using a cDNA template
Unknown - sample type not known
Average heterozygosity: Calculated by dbSNP as described
here
Average heterozygosity should not exceed 0.5 for bi-allelic
single-base substitutions.
Weight: Alignment quality assigned by dbSNP
Weight can be 0, 1, 2, 3 or 10.
Weight = 1 are the highest quality alignments.
Weight = 0 and weight = 10 are excluded from the data set.
A filter on maximum weight value is supported, which defaults to 3.
You can configure this track such that the details page displays
the function and coding differences relative to
particular gene sets. Choose the gene sets from the list on the SNP
configuration page displayed beneath this heading: On details page,
show function and coding differences relative to.
When one or more gene tracks are selected, the SNP details page
lists all genes that the SNP hits (or is close to), with the same keywords
used in the function category. The function usually
agrees with NCBI's function, but can sometimes give a bit more detail
(e.g. more detail about how close a near-gene SNP is to a nearby gene).
Insertions/Deletions
dbSNP uses a class called 'in-del'. We compare the length of the
reference allele to the length(s) of observed alleles; if the
reference allele is shorter than all other observed alleles, we change
'in-del' to 'insertion'. Likewise, if the reference allele is longer
than all other observed alleles, we change 'in-del' to 'deletion'.
UCSC Annotations
UCSC checks for several unusual conditions that may indicate a problem
with the mapping, and reports them in the Annotations section if found:
The dbSNP reference allele is not the same as the UCSC reference
allele, i.e. the bases in the mapped position range.
Class is single, in-del, mnp or mixed and the UCSC reference
allele does not match any observed allele.
In NCBI's alignment of flanking sequences to the genome, part
of the flanking sequence around the SNP does not align to
the genome.
Class is single, but the size of the mapped SNP is not one base.
Class is named and indicates an insertion or deletion, but the size
of the mapped SNP implies otherwise.
Class is single and the format of observed alleles is unexpected.
The length of the observed allele(s) is not available because it is
too long.
Multiple distinct insertion SNPs have been mapped to this location.
At least one observed allele contains an ambiguous
IUPAC base (e.g. R, Y, N).
Another condition, which does not necessarily imply any problem, is noted:
Class is single and SNP is tri-allelic or quad-allelic.
UCSC Re-alignment of flanking sequences
dbSNP determines the genomic locations of SNPs by aligning their flanking
sequences to the genome.
UCSC displays SNPs in the locations determined by dbSNP, but does not
have access to the alignments on which dbSNP based its mappings.
Instead, UCSC re-aligns the flanking sequences
to the neighboring genomic sequence for display on SNP details pages.
While the recomputed alignments may differ from dbSNP's alignments,
they often are informative when UCSC has annotated an unusual condition.
Non-repetitive genomic sequence is shown in upper case like the flanking
sequence, and a "|" indicates each match between genomic and flanking bases.
Repetitive genomic sequence (annotated by RepeatMasker and/or the
Tandem Repeats Finder with period <= 12) is shown in lower case, and matching
bases are indicated by a "+".
Data Sources
The data that comprise this track were extracted from database dump files
and headers of fasta files downloaded from NCBI.
The database dump files were downloaded from
ftp://ftp.ncbi.nih.gov/snp/organisms/organism_tax_id/database/
(e.g. for Human, organism_tax_id = human_9606).
The fasta files were downloaded from
ftp://ftp.ncbi.nih.gov/snp/organisms/organism_tax_id/rs_fasta/
NCBI build 36 coordinates, orientation, location type and dbSNP reference allele data
were obtained from b130_SNPContigLoc_36_3.bcp.gz and
b130_SNPContigInfo_36_3.bcp.gz.
b130_SNPMapInfo_36_3.bcp.gz provided the alignment weights.
Functional classification was obtained from
b130_SNPContigLocusId_36_3.bcp.gz.
Validation status and heterozygosity were obtained from SNP.bcp.gz.
The header lines in the rs_fasta files were used for molecule type,
class and observed polymorphism.
Beginning with the March 2006 human assembly, we provide a related table that
contains orthologous alleles in the chimpanzee and rhesus macaque assemblies.
Beginning with dbSNP build 129, the orangutan assembly is also included.
We use our liftOver utility to identify the orthologous alleles. The candidate human SNPs are
a filtered list that meet the criteria:
class = 'single'
chromEnd = chromStart + 1
align to just one location
are not aligned to a chrN_random chrom
are biallelic (not tri or quad allelic)
In some cases the orthologous allele is unknown; these are set to 'N'.
If a lift was not possible, we set the orthologous allele to '?' and the
orthologous start and end position to 0 (zero).
Masked FASTA Files (human assemblies only)
FASTA files that have been modified to use
IUPAC
ambiguous nucleotide characters at
each base covered by a single-base substitution are available for download
here.
Note that only single-base substitutions (no insertions or deletions) were used
to mask the sequence, and these were filtered to exlcude problematic SNPs.