This track shows short genetic variants (up to approximately 50 base pairs) from dbSNP build 153: single-nucleotide variants (SNVs), small insertions, deletions, and complex deletion/insertions (indels), relative to the reference genome assembly. Most variants in dbSNP are rare, not true polymorphisms, and some variants are known to be pathogenic.
For hg38 (GRCh38), approximately 667 million distinct variants (RefSNP clusters with rs# ids) have been mapped to more than 702 million genomic locations including alternate haplotype and fix patch sequences. dbSNP remapped variants from hg38 to hg19 (GRCh37); approximately 658 million distinct variants were mapped to more than 683 million genomic locations including alternate haplotype and fix patch sequences (not all of which are included in UCSC's hg19).
This track includes four subtracks of variants:
A fifth subtrack highlights coordinate ranges to which dbSNP mapped a variant but with genomic coordinates that are not internally consistent, i.e. different coordinate ranges were provided when describing different alleles. This can occur due to a bug with mapping variants from one assembly sequence to another when there is an indel difference between the assembly sequences:
SNVs and pure deletions are displayed as boxes covering the affected base(s). Pure insertions are drawn as single-pixel tickmarks between the base before and the base after the insertion.
Insertions and/or deletions in repetitive regions may be represented by a half-height box showing uncertainty in placement, followed by a full-height box showing the number of deleted bases, or a full-height tickmark to indicate an insertion. When an insertion or deletion falls in a repetitive region, the placement may be ambiguous. For example, if the reference genome contains "TAAAG" but some individuals have "TAAG" at the same location, then the variant is a deletion of a single A relative to the reference genome. However, which A was deleted? There is no way to tell whether the first, second or third A was removed. Different variant mapping tools may place the deletion at different bases in the reference genome. To reduce errors in merging variant calls made with different left vs. right biases, dbSNP made a major change in its representation of deletion/insertion variants in build 152. Now, instead of assigning a single-base genomic location at one of the A's, dbSNP expands the coordinates to encompass the whole repetitive region, so the variant is represented as a deletion of 3 A's combined with an insertion of 2 A's. In the track display, there will be a half-height box covering the first two A's, followed by a full-height box covering the third A, to show a net loss of one base but an uncertain placement within the three A's.
Variants are colored according to functional effect on genes annotated by dbSNP:
Protein-altering variants and splice site variants are
red.
Synonymous codon variants are
green.
Non-coding transcript or Untranslated Region (UTR) variants are
blue.
On the track controls page, several variant properties can be included or excluded from the item labels: rs# identifier assigned by dbSNP, reference/alternate alleles, major/minor alleles (when available) and minor allele frequency (when available). Allele frequencies are reported independently by twelve projects (some of which may have overlapping sets of samples):
Using the track controls, variants can be filtered by
While processing the information downloaded from dbSNP, UCSC annotates some properties of interest. These are noted on the item details page, and may be useful to include or exclude affected variants.
Some are purely informational:
| keyword in data file (dbSnp153.bb) | # in hg19 | # in hg38 | description |
|---|---|---|---|
| clinvar | 454678 | 453996 | Variant is in ClinVar. |
| clinvarBenign | 143864 | 143736 | Variant is in ClinVar with clinical significance of benign and/or likely benign. |
| clinvarConflicting | 7932 | 7950 | Variant is in ClinVar with reports of both benign and pathogenic significance. |
| clinvarPathogenic | 96242 | 95262 | Variant is in ClinVar with clinical significance of pathogenic and/or likely pathogenic. |
| commonAll | 12184521 | 12438655 | Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in all projects reporting frequencies. |
| commonSome | 20541190 | 20902944 | Variant is "common", i.e. has a Minor Allele Frequency of at least 1% in some, but not all, projects reporting frequencies. |
| diffMajor | 1377831 | 1399109 | Different frequency sources have different major alleles. |
| overlapDiffClass | 107015341 | 110007682 | This variant overlaps another variant with a different type/class. |
| overlapSameClass | 16915239 | 17291289 | This variant overlaps another with the same type/class but different start/end. |
| rareAll | 662601770 | 681696398 | Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in all projects reporting frequencies, or has no frequency data. |
| rareSome | 670958439 | 690160687 | Variant is "rare", i.e. has a Minor Allele Frequency of less than 1% in some, but not all, projects reporting frequencies, or has no frequency data. |
| revStrand | 3813702 | 4532511 | Alleles are displayed on the + strand at the current position. dbSNP's alleles are displayed on the + strand of a different assembly sequence, so dbSNP's variant page shows alleles that are reverse-complemented with respect to the alleles displayed above. |
while others may indicate that the reference genome contains a rare variant or sequencing issue:
| keyword in data file (dbSnp153.bb) | # in hg19 | # in hg38 | description |
|---|---|---|---|
| refIsAmbiguous | 101 | 111 | The reference genome allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G', or 'N' for 'any base'). |
| refIsMinor | 3272116 | 3360435 | The reference genome allele is not the major allele in at least one project. |
| refIsRare | 136547 | 160827 | The reference genome allele is rare (i.e. allele frequency < 1%). |
| refIsSingleton | 37832 | 50927 | The reference genome allele has never been observed in a population sequencing project reporting frequencies. |
| refMismatch | 4 | 33 | The reference genome allele reported by dbSNP differs from the GenBank assembly sequence. This is very rare and in all cases observed so far, the GenBank assembly has an 'N' while the RefSeq assembly used by dbSNP has a less ambiguous character such as 'R'. |
and others may indicate an anomaly or problem with the variant data:
| keyword in data file (dbSnp153.bb) | # in hg19 | # in hg38 | description |
|---|---|---|---|
| altIsAmbiguous | 10755 | 10888 | At least one alternate allele contains an IUPAC ambiguous base (e.g. 'R' for 'A or G'). For alleles containing more than one ambiguous base, this may create a combinatoric explosion of possible alleles. |
| classMismatch | 5998 | 6216 | Variation class/type is inconsistent with alleles mapped to this genome assembly. |
| clusterError | 114826 | 128306 | This variant has the same start, end and class as another variant; they probably should have been merged into one variant. |
| freqIncomplete | 3922 | 4673 | At least one project reported counts for only one allele which implies that at least one allele is missing from the report; that project's frequency data are ignored. |
| freqIsAmbiguous | 7656 | 7756 | At least one allele reported by at least one project that reports frequencies contains an IUPAC ambiguous base. |
| freqNotMapped | 2685 | 6590 | At least one project reported allele frequencies relative to a different assembly; However, dbSNP does not include a mapping of this variant to that assembly, which implies a problem with mapping the variant across assemblies. The mapping on this assembly may have an issue; evaluate carefully vs. original submissions, which you can view by clicking through to dbSNP above. |
| freqNotRefAlt | 17694 | 32170 | At least one allele reported by at least one project that reports frequencies does not match any of the reference or alternate alleles listed by dbSNP. |
| multiMap | 562180 | 132123 | This variant has been mapped to more than one distinct genomic location. |
| otherMapErr | 114095 | 204219 | At least one other mapping of this variant has erroneous coordinates. The mapping(s) with erroneous coordinates are excluded from this track and are included in the Map Err subtrack. Sometimes despite this mapping having legal coordinates, there may still be an issue with this mapping's coordinates and alleles; you may want to click through to dbSNP to compare the initial submission's coordinates and alleles. In hg19, 55454 distinct rsIDs are affected; in hg38, 86636. |
dbSNP has collected genetic variant reports from researchers worldwide for more than 20 years. Since the advent of next-generation sequencing methods and the population sequencing efforts that they enable, dbSNP has grown exponentially, requiring a new data schema, computational pipeline, web infrastructure, and download files. (Holmes et al.) The same challenges of exponential growth affected UCSC's presentation of dbSNP variants, so we have taken the opportunity to change our internal representation and import pipeline. Most notably, flanking sequences are no longer provided by dbSNP, because most submissions have been genomic variant calls in VCF format as opposed to independent sequences.
We downloaded JSON files available from dbSNP at ftp://ftp.ncbi.nlm.nih.gov/snp/archive/b153/JSON/, extracted a subset of the information about each variant, and collated it into a bigBed file using the bigDbSnp.as schema with the information necessary for filtering and displaying the variants, as well as a separate file containing more detailed information to be displayed on each variant's details page (dbSnpDetails.as schema).
Note: It is not recommeneded to use LiftOver to convert SNPs between assemblies, and more information about how to convert SNPs between assemblies can be found on the following FAQ entry.
Since dbSNP has grown to include approximately 700 million variants, the size of the All dbSNP (153) subtrack can cause the Table Browser and Data Integrator to time out, leading to a blank page or truncated output, unless queries are restricted to a chromosomal region, to particular defined regions, to a specific set of rs# IDs (which can be pasted/uploaded into the Table Browser), or to one of the subset tracks such as Common (~15 million variants) or ClinVar (~0.5M variants).
For automated analysis, the track data files can be downloaded from the downloads server for hg19 and hg38.
| file | format | subtrack | ||
|---|---|---|---|---|
| dbSnp153.bb | hg19 | hg38 | bigDbSnp (bigBed4+13) | All dbSNP (153) |
| dbSnp153ClinVar.bb | hg19 | hg38 | bigDbSnp (bigBed4+13) | ClinVar dbSNP (153) |
| dbSnp153Common.bb | hg19 | hg38 | bigDbSnp (bigBed4+13) | Common dbSNP (153) |
| dbSnp153Mult.bb | hg19 | hg38 | bigDbSnp (bigBed4+13) | Mult. dbSNP (153) |
| dbSnp153BadCoords.bb | hg19 | hg38 | bigBed4 | Map Err (153) |
| dbSnp153Details.tab.gz | gzip-compressed tab-separated text | Detailed variant properties, independent of genome assembly version | ||
Several utilities for working with bigBed-formatted binary files can be downloaded here. Run a utility with no arguments to see a brief description of the utility and its options.
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/snp/dbSnp153.bb -chrom=chr1 -start=200000 -end=200400 stdout
bigBedNamedItems dbSnp153.bb rs6657048 stdout
bigBedNamedItems -nameFile dbSnp153.bb myIds.txt dbSnp153.myIds.bed
The columns in the bigDbSnp/bigBed files and dbSnp153Details.tab.gz file are described in bigDbSnp.as and dbSnpDetails.as respectively. For columns that contain lists of allele frequency data, the order of projects providing the data listed is as follows:
UCSC also has an API that can be used to retrieve values from a particular chromosome range.
A list of rs# IDs can be pasted/uploaded in the Variant Annotation Integrator tool to find out which genes (if any) the variants are located in, as well as functional effect such as intron, coding-synonymous, missense, frameshift, etc.
Please refer to our searchable mailing list archives for more questions and example queries, or our Data Access FAQ for more information.
Holmes JB, Moyer E, Phan L, Maglott D, Kattman B. SPDI: Data Model for Variants and Applications at NCBI. Bioinformatics. 2019 Nov 18;. PMID: 31738401
Sayers EW, Agarwala R, Bolton EE, Brister JR, Canese K, Clark K, Connor R, Fiorini N, Funk K, Hefferon T et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2019 Jan 8;47(D1):D23-D28. PMID: 30395293; PMC: PMC6323993
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PMID: 11125122; PMC: PMC29783