| ID |
Type |
Default annotation |
Description |
Histogram |
Range |
| RS |
int |
dbSNP_RS
|
dbSNP ID (i.e. rs number)
|
 |
[3.000, 1491589548.000] |
| RSPOS |
int |
None
|
Chr position reported in dbSNP
|
 |
[10002.000, 248946420.000] |
| RV |
bool |
None
|
RS orientation is reversed
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| VP |
str |
None
|
Variation Property. Documentation is at ftp://ftp.ncbi.nlm.nih.gov/snp/specs/dbSNP_BitField_latest.pdf
|
No histogram: Empty histogram for VP in a region: Too many unique values 101 for categorical histogram. |
NO DOMAIN |
| GENEINFO |
str |
None
|
Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)
|
No histogram: Empty histogram for GENEINFO in a region: Too many unique values 101 for categorical histogram. |
NO DOMAIN |
| dbSNPBuildID |
int |
None
|
First dbSNP Build for RS
|
 |
[36.000, 151.000] |
| SAO |
int |
None
|
Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both
|
 |
[0.000, 3.000] |
| SSR |
int |
None
|
Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other
|
 |
[0.000, 16.000] |
| WGT |
int |
None
|
Weight, 00 - unmapped, 1 - weight 1, 2 - weight 2, 3 - weight 3 or more
|
No histogram: Failed to create empty histogram from config: division by zero |
NO DOMAIN |
| VC |
str |
None
|
Variation Class
|
 |
SNV, DIV, MNV, 0 |
| PM |
bool |
None
|
Variant is Precious(Clinical,Pubmed Cited)
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| TPA |
bool |
None
|
Provisional Third Party Annotation(TPA) (currently rs from PHARMGKB who will give phenotype data)
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| PMC |
bool |
None
|
Links exist to PubMed Central article
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| S3D |
bool |
None
|
Has 3D structure - SNP3D table
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| SLO |
bool |
None
|
Has SubmitterLinkOut - From SNP->SubSNP->Batch.link_out
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| NSF |
bool |
None
|
Has non-synonymous frameshift A coding region variation where one allele in the set changes all downstream amino acids. FxnClass = 44
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| NSM |
bool |
None
|
Has non-synonymous missense A coding region variation where one allele in the set changes protein peptide. FxnClass = 42
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| NSN |
bool |
None
|
Has non-synonymous nonsense A coding region variation where one allele in the set changes to STOP codon (TER). FxnClass = 41
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| REF |
bool |
None
|
Has reference A coding region variation where one allele in the set is identical to the reference sequence. FxnCode = 8
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| SYN |
bool |
None
|
Has synonymous A coding region variation where one allele in the set does not change the encoded amino acid. FxnCode = 3
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| U3 |
bool |
None
|
In 3' UTR Location is in an untranslated region (UTR). FxnCode = 53
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| U5 |
bool |
None
|
In 5' UTR Location is in an untranslated region (UTR). FxnCode = 55
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| ASS |
bool |
None
|
In acceptor splice site FxnCode = 73
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| DSS |
bool |
None
|
In donor splice-site FxnCode = 75
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| INT |
bool |
None
|
In Intron FxnCode = 6
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| R3 |
bool |
None
|
In 3' gene region FxnCode = 13
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| R5 |
bool |
None
|
In 5' gene region FxnCode = 15
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| OTH |
bool |
None
|
Has other variant with exactly the same set of mapped positions on NCBI refernce assembly.
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| CFL |
bool |
None
|
Has Assembly conflict. This is for weight 1 and 2 variant that maps to different chromosomes on different assemblies.
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| ASP |
bool |
None
|
Is Assembly specific. This is set if the variant only maps to one assembly
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| MUT |
bool |
None
|
Is mutation (journal citation, explicit fact): a low frequency variation that is cited in journal and other reputable sources
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| VLD |
bool |
None
|
Is Validated. This bit is set if the variant has 2+ minor allele count based on frequency or genotype data.
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| G5A |
bool |
None
|
>5% minor allele frequency in each and all populations
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| G5 |
bool |
None
|
>5% minor allele frequency in 1+ populations
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| HD |
bool |
None
|
Marker is on high density genotyping kit (50K density or greater). The variant may have phenotype associations present in dbGaP.
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| GNO |
bool |
None
|
Genotypes available. The variant has individual genotype (in SubInd table).
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| KGPhase1 |
bool |
None
|
1000 Genome phase 1 (incl. June Interim phase 1)
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| KGPhase3 |
bool |
None
|
1000 Genome phase 3
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| CDA |
bool |
None
|
Variation is interrogated in a clinical diagnostic assay
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| LSD |
bool |
None
|
Submitted from a locus-specific database
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| MTP |
bool |
None
|
Microattribution/third-party annotation(TPA:GWAS,PAGE)
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| OM |
bool |
None
|
Has OMIM/OMIA
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| NOC |
bool |
None
|
Contig allele not present in variant allele list. The reference sequence allele at the mapped position is not present in the variant allele list, adjusted for orientation.
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| WTD |
bool |
None
|
Is Withdrawn by submitter If one member ss is withdrawn by submitter, then this bit is set. If all member ss' are withdrawn, then the rs is deleted to SNPHistory
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| NOV |
bool |
None
|
Rs cluster has non-overlapping allele sets. True when rs set has more than 2 alleles from different submissions and these sets share no alleles in common.
|
No histogram: No histogram configured and no default config available for typebool |
NO DOMAIN |
| CAF |
str |
None
|
An ordered, comma delimited list of allele frequencies based on 1000Genomes, starting with the reference allele followed by alternate alleles as ordered in the ALT column. Where a 1000Genomes alternate allele is not in the dbSNPs alternate allele set, the allele is added to the ALT column. The minor allele is the second largest value in the list, and was previuosly reported in VCF as the GMAF. This is the GMAF reported on the RefSNP and EntrezSNP pages and VariationReporter
|
No histogram: Empty histogram for CAF in a region: Too many unique values 101 for categorical histogram. |
NO DOMAIN |
| COMMON |
int |
None
|
RS is a common SNP. A common SNP is one that has at least one 1000Genomes population with a minor allele of frequency >= 1% and for which 2 or more founders contribute to that minor allele frequency.
|
 |
[0.000, 1.000] |
| TOPMED |
str |
None
|
An ordered, comma delimited list of allele frequencies based on TOPMed, starting with the reference allele followed by alternate alleles as ordered in the ALT column. The TOPMed minor allele is the second largest value in the list.
|
No histogram: Empty histogram for TOPMED in a region: Too many unique values 101 for categorical histogram. |
NO DOMAIN |
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