The table containing genomic annotations has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
ID: Genomic Position ID <chromosome/contig/clone id,":",position,":","allele",":",strand>
dbSNP: link to dbSNP, if known
Chromosome: Variant mapped chromosome location
Position: Variant start position on chromosome
REF Allele: Reference allele
ALT Allele (IUPAC): Observed allele
Minor Allele: Minor allele observed in global population, if known
Minor Allele Frequency: Minor allele frequency observed in global population, if known
Contig: Variant mapped contig location
contigPosition: Variant start position on contig
Band: SNP cytogenetic location

The table containing information on overlapped or nearest genes has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Variant mapped chromosome location
Position: Variant start position on chromosome
Overlapped Gene: Name of the gene (HGNC system) to which the variant is overlapped
Type: Gene type, e.g., protein coding, miRNA, non coding, Pseudogene, snoRNA, lincRNA etc.
Annotation: Summary of whether the variant overlapped with the coding, intronic or untranslated regions of the various transcript isoforms of the gene, as annotated from Ensembl gene system.
Nearest Upstream Gene: If variant is not overlapped with any gene, then the gene whose end position is nearest to the variant on the left (considering the alignment of genes on the positive strand as left-to-right)
Type of Nearest Upstream Gene: Gene type, e.g., protein coding, miRNA, non coding, Pseudogene, snoRNA, lincRNA etc.
Distance to Nearest Upstream Gene: distance from the end position of the nearest upstream gene.
Nearest Downstream Gene: If variant is not overlapped with any gene, then the gene whose start position is nearest to the variant on the right (considering the alignment of genes on the positive strand as left-to-right)
Type of Nearest Downstream Gene: Gene type, e.g., protein coding, miRNA, non coding, Pseudogene, snoRNA, lincRNA etc.
Distance to Nearest Downstream Gene: distance from the start position of the nearest downstream gene.

The result table containing gene/protein consequences on a particular gene annotation system may have following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Variant: Examined alleles <reference allele,"|", observed allele(s) >. For Insertion, reference allele is "-". For other cases, reference allele is the allele found in reference genome sequence. Observed allele(s) can be multi-allelic separated by "|" depending on the input Allele2. If input Allele1 does not match with reference allele, then Allele1 becomes the first observed allele.
Strand: On which strand the variant is observed (1 or -1)
Symbol: Gene symbol
Gene: Gene name in the corresponding annotation system
Transcript: Transcript name in the corresponding annotation system
Entrez Gene: Entrez gene id
Predicted Function: Predicted function of the SNP/InDel/block substitution based on its location on the transcript. The result is based on the first nucleotide position of the variation. Possible categories: coding, intronic, intronic (splice_site), 5utr, 3utr, 5upstream, 3downstream, non-coding, non-coding intronic, non-coding intronic (splice_site). More detailed information on the predicted function is available on the "Note" column.
CDNA Position: SNP position on cdna, if the predicted function is coding, 3'UTR or 5'UTR
CDS Position: SNP position on cds, if the predicted function is coding
AA Position: Position of the first amino acid (possibly) effected in the resultant peptide chain, if the predicted function is coding
AA Change: Peptide <reference amino acid(s),">", observed amino acid(s)_1 [,"|", observed amino acid(s)_2, ... ] >
Detail (previously Note column): Detailed functional type for the variation. If the variation occurs over a single coding exon of a transcript, the type of the consequences on the corresponding protein is given. Possible values: syn (synonymous), nonsyn (non-synonymous) [stop-gain or stop-loss], frameshift [stop-gain or stop-loss], pepshift (peptide shift, block substitution). Preceded by "*", if the reference protein is found incomplete (missing stop-codon).
However, if the variation occurs over more than one functional regions on the transcript, the corresponding regions are given separated by "-".
Splice Distance: Distance to splice junction, if the predicted function is intronic
Proteins: Reference and observed peptide sequences separated by "|", if the predicted function is coding. Available only in the downloadable text files.

The SIFT result table containing the predicted effect on protein has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
SNP: SNP name
Variant: <reference allele,"/",observed allele>
Transcript: Transcript name in the Ensembl gene annotation system
Gene: Gene name
AA Position: Position of the amino acid affected in the resultant peptide chain
Wild AA: Reference amino acid
Mutant AA: Observed amino acid
Score: SIFT prediction score for non-synonymous substitution of reference amino acid with observed amino acid. Possible real values: 0 to 1.
Prediction: SIFT predicted effect on protein based on the score and SIFT median. Possible values: Deleterious (score <= 0.5 and median > 3.25); Deleterious - Low Confidence (score <= 0.5 and median <= 3.25); Tolerated (score > 0.5 and median > 3.25); Tolerated - Low Confidence (score > 0.5 and median <= 3.25).

The PolyPhen result table containing the predicted effect on protein has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
SNP: SNP name
Variant: <reference allele,"/",observed allele>
Transcript: Transcript name in the Ensembl gene annotation system
Gene: Protein name in the Ensembl gene annotation system
AA Position: Position of the amino acid affected in the resultant peptide chain
Wild AA: Reference amino acid
Mutant AA: Observed amino acid
Score: PolyPhen prediction score for non-synonymous substitution of reference amino acid with observed amino acid. Possible real values: 0 to 1.
Prediction: PolyPhen predicted effect on protein based on the score. Possible values: Probably Damaging (score > 0.908), Possibly Damaging (0.446 < score <= 0.908), Benign (score <= 0.446).

The result table containing the specific Hapmap population data has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Variant mapped chromosome location
Position: Variant start position on chromosome
REF Allele: Reference allele
ALT Allele: Observed allele
ASW Frequency: Percentage of observed samples with the allele in population with African Ancestry in SouthWestern US
CEU Frequency: Percentage of observed samples with the allele in population with Northern and Western Europe Ancenstry from Utah residents
CHB Frequency: Percentage of observed samples with the allele in the Han Chinese in Beijing, China from HapMap phase 3 population
CHD Frequency: Percentage of observed samples with the allele in population with Chinese Ancestry in Metropolitan Denver, US
GIH Frequency: Percentage of observed samples with the allele in the Gujarati Indians in Houston, Texas population
HCB Frequency: Percentage of observed samples with the allele in population from Unrelated Han Chinese in Beijing, China from the International HapMap project
JPT Frequency: Percentage of observed samples with the allele in the Japanese in Tokyo, Japan population
LWK Frequency: Percentage of observed samples with the allele in the Luhya in Webuye, Kenya population
MEX Frequency: Percentage of observed samples with the allele in population with Mexican Ancestery in Los Angeles, US
MKK Frequency: Percentage of observed samples with the allele in the Masai in Kinyawa, Kenya (MKK) population
TSI Frequency: Percentage of observed samples with the allele in the Toscani in Italia population
YRI Frequency: Percentage of observed samples with the allele in the Yoruba in Ibadan, Nigeria population

The result table containing the specific 1000 Genomes Super Population data has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Variant mapped chromosome location
Position: Variant start position on chromosome
REF Allele: Reference allele
ALT Allele: Observed allele
Minor Allele: Allele with the Minor Frequency observed
AFR Frequency: Percentage of observed samples with the allele in the African super population
AMR Frequency: Percentage of observed samples with the allele in the Ad Mixed American super population
EAS Frequency: Percentage of observed samples with the allele in the East Asian super population
EUR Frequency: Percentage of observed samples with the allele in the European super population
SAS Frequency: Percentage of observed samples with the allele in the South Asian super population

The result table containing the specific exome gnomAD Population data has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Variant mapped chromosome location
Position: Variant start position on chromosome
REF Allele: Reference allele
ALT Allele: Observed allele
Minor Allele: Allele with the Minor Frequency observed
AFR Frequency: Percentage of observed samples with the allele in the African/African American population
AMR Frequency: Percentage of observed samples with the allele in the Latino population
EAS Frequency: Percentage of observed samples with the allele in the East Asian population
FIN Frequency: Percentage of observed samples with the allele in the Finnish population
NFE Frequency: Percentage of observed samples with the allele in the Non-Finnish European population
SAS Frequency: Percentage of observed samples with the allele in the South Asian population
OTH Frequency: Percentage of observed samples with the allele in the Other populations

The result table containing the specific genome gnomAD Population data has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Variant mapped chromosome location
Position: Variant start position on chromosome
REF Allele: Reference allele
ALT Allele: Observed allele
Minor Allele: Allele with the Minor Frequency observed
AFR Frequency: Percentage of observed samples with the allele in the African/African American population
AMR Frequency: Percentage of observed samples with the allele in the Latino population
EAS Frequency: Percentage of observed samples with the allele in the East Asian population
FIN Frequency: Percentage of observed samples with the allele in the Finnish population
NFE Frequency: Percentage of observed samples with the allele in the Non-Finnish European population
OTH Frequency: Percentage of observed samples with the allele in the Other populations

The Transcription Factor Binding Sites (TFBS) result table has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
TFBS Name: Transcription factor name
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
TFBS Accession: TFBS accession number. Note that, browsing the link provided in the html and excel file requires free registration with TRANSFAC website.
Species: Transcription factor species
SwissProt Accession: SwissProt accession number

The miRBASE result table has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
TFBS ID: TFBS id
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
Name: microRNA name
Accession: miRBASE accession number
Strand: + or -
Type / Description: miRNA type. Possible values: mature miRNA, miRNA_primary_transcript

The Vista Enhancer prediction result table has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
Vista Item: Name of the Vista element
Score: Prediction score. Possible values: 900 (Positive-enhancer), 200 (Negative-enhancer)

The CpG Island prediction result table has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
CpG Island: Name of the CpG Island
Length: Island Length
Cpg%: Percentage of island that is CpG
C/G%: Percentage of island that is C or G
Ratio: Ratio of observed to expected CpG in island

The TargetScan miRNA regulatory sites result table has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
Item_Name: Name of the predicted target site
Score: Prediction scores by TargetScanS. Possible values: 0 to 1000
Strand: + or -

The TargetBase (TarBase) miRNA target sites result table has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
Strand: + or -
miRNA: miRNA targeting the site
Accession: miRBASE accession number
Gene: Gene name

The miRNAs/snoRNAs/scaRNAs result table has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
Name: Name of the miRNA/snoRNA/scaRNa
Score: Prediction scores. Possible values: 0 to 1000
Strand: + or -
Type: Type of RNA

The ENCODE and Roadmap Epigenomics result tables has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
Feature Type Class: Regulatory feature class
Feature Type: Regulatory feature name
Epigenome: Epigenome or cell name

The Ensembl Regulatory Build result table has following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
Feature Type Class: Regulatory feature class
Epigenome: Epigenome or cell name
Activity: State of activity (hg38)

The Vertebrate Alignment and Conservation (Phast) result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
Id: Name of the aligned element
Score: Estimated probability score for conservation as determined from PHAST package. Possible values: 0 to 1000

The Genomic Evolutionary Rate Profiling (GERP++) result table contains the following information:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the TFBS site in the chromosome
Region End: End position of the TFBS site in the chromosome
Element RS Score: Rejected Substitutions score for the conserved element as determined from GERP++ package.
Base RS Score: Rejected Substitutions score calculated per base as determined from GERP++ package.

The Genetic Association Database (GAD) result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
GAD ID: GAD id
Association: Confirmed association
Phenotype: Phenotype description
Disease_Class: Type of disease
Gene: Gene name
Reference: Reference of publication of the study
PubMed: Pubmed id of publication of the study
Associated SNPs: SNPs associated with the disease as reported in the study
p-Value: Statistical significance of the association study
Population: Sample population
Entrez gene: Entrez gene id

The COSMIC result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Mutation Id: Cosmic mutation id
Sample: Cosmic sample id
Site: Primary Effected site
Histology: Primary Histology
Histology Subtype : Subtype of primary histology
Symbol: Gene symbol
Pubmed: Pubmed id of publication of the study

The GWAS catalogue result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Catalogue ID: ID of SNP associated with trait
Region: Chromosome band/region of SNP
Genes: Reported Gene(s)
Allele_frequency: Risk Allele Frequency
Trait: Disease or trait assessed in study
Population: Initial sample population for the study
Platform: Platform and [SNPs passing Quality Control]
Pubmed: Pubmed id of publication of the study

The ClinVar result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Variant mapped chromosome location
Position: Variant start position on chromosome
Variation: Reference to Observed Allele
Type: Type of Variant
Clinical Significance: Whether identified as Pathogenic or Benign or uncertain
Phenotypes: List of phenotypes associated with the variant

The structural variations result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Chrom Start: Start position of the structural variation in the chromosome
Chrom End: End position of the structural variation in the chromosome
Type: Type of structural variation
Reference: Literature reference for the study that included this variant
PubMed: Pubmed id of publication of the study
Method: Brief description of method/platform
Sample: Description of sample population for the study
Gain: Copy number gains
Loss: Copy number losses

The CADD result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Position: Variant start position on chromosome
Variant: <reference allele,"/",observed allele> as reported in the tool's genome-wide score
Raw Score: "Raw" unaltered CADD-score for the variation. It has relative meaning, with higher values indicating that a variant is more likely to be simulated (or "not observed") and therefore more likely to have deleterious effects. <
PHRED: PHRED-like (-10*log₁₀(rank/total)) scaled CADD-score ranking a variant relative to all possible substitutions of the human genome. A score≥10 indicates that it is predicted to be in the 10% most deleterious substitutions that you can do to the human genome, a score≥20 indicates the 1% most deleterious and so on.

The FitCons result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Region Start: Start position of the non-coding region
Region End: End position of the non-coding region
Fitness Score: In the range [0-1]. Relative indicator of the potential for interesting genomic function, with higher scores indicating more potential. The range .05 to .35 may be most appealing as nearly all non-coding classes have scores in this range, while nearly all coding classes have scores>.40
P-val: P-val indicating the statistical significance of the Fitness Score.

The EIGEN result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Position: Variant start position in the chromosome
Variant: <reference allele,"/",observed allele> as reported in the tool's genome-wide score
Score: Aggregate functional score for variants of interest (Eigen Score). With genome-wide median score of ~0, higher score indicates more likelihood of the variant to be functional.
PC Score: An alternative score which is more sensitive than Eigen score, particularly useful for the noncoding variants. With genome-wide median score of ~0, higher score indicates more likelihood of the variant to be functional.

The FATHMM result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Chromosome: Chromosome name
Position: Variant start position in the chromosome
Variant: <reference allele,"/",observed allele> as reported in the tool's genome-wide score
Non-coding Score: Given as p-values in the range [0, 1]. Scores above 0.5 are predicted to be deleterious, while those below 0.5 are predicted to be neutral or benign. Scores close to the extremes (0 or 1) are the highest-confidence predictions that yield the highest accuracy.
Non-coding Groups: Annotation features used for the prediction score. Maximum 4 features are used labelled between A and D. See publication for more details.
Coding Score: Same as non-coding score.
Coding Groups: Annotation features used for the prediction score. Maximum 10 features are used labelled between A and J. See publication for more details.

The GWAVA result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Position: Variant start position in the chromosome
Known SNP: Known SNP description as reported in the tool's genome-wide score
Region Score, TSS Score, Unmatched Score: prediction scores from 3 different versions of the classifier, which are all in the range [0-1] with higher scores indicating variants predicted as more likely to be functional. See publication for more details.

The DeepSEA result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Position: Variant start position in the chromosome
Variant: <reference allele,"/",observed allele> as reported in the tool's genome-wide score
eQTL Probability: The probability of the variant being a eQTL variant given by functional variant prioritization classifier.
GWAS Probability: The probability of the variant being a trait-associated (GWAS) variant given by functional variant prioritization classifier.
HGMD Probability: The probability of the variant being a inherited disease-associated (HGMD) variant given by functional variant prioritization classifier.
Functional Significance Score: A measure in the range [0-1] depicting the significance of magnitude of predicted chromatin effect and evolutionary conservation. Lower score indicates higher likelihood of functional significance of the variant.

The funSeq2 result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Position: Variant start position in the chromosome
Variant: <reference allele,"/",observed allele> as reported in the tool's genome-wide score. "." as observed allele indicates any other nucleotide other than reference allele.
Non-coding Score: Given as p-values in the range [0, 1], with higher scores indicating variants predicted as more likely to be functional.

The ReMM result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Position: Variant start position in the chromosome
ReMM Score: Potential of the chromosome position in the non-coding region to cause a Mendelian disease if mutated. Given as p-values in the range [0, 1], with higher scores indicating variants predicted as more likely to be deleterious.

The Reactome Pathways result table contains the following columns:

Pathway ID: Link to Reactome Pathway
Description: Pathway description
Parent(s): Immediate parents of the Pathway
p-Value: Statistical significance of the Pathway calculated using the Fisher's Exact Test for all the genes involved in the original queryset
Genes Involved: Genes from the original queryset involved in the Pathway
Variation IDs: Variation in the original query affecting the genes involved in the Pathway. Available only in the downloadable text file.

The Cancer Genome Interpreter result table contains the following columns:

Variation ID: <dbsnp rs#> or <chromosome/contig/clone id,":",position,":","allele",":",strand>
Chromosome: Chromosome name
Gene: Gene name
Transcript: Transcript name in the Ensembl annotation system
Protein Change: Protein alteration in the format "Wild AA" "AA Position" "Mutant AA"
Consequence: Consequence type
Domain: Domain where the mutation is located (Pfam)
Oncogenic classification: Oncogenic potential of the mutation
Location: Location of the mutation in relation to the last exon of the gene
Tumour Driver: The gene has been identified as a driver of cancer
Role: Mechanism of Action of the driver gene
In cluster: Mutation falls in a cluster of somatic mutations of the gene (oncodriveCLUST)
Delicate Domain: The domain where the mutation is located is depleted for variants in the general population
Deleterious (CADD Score): Deleteriousness score using CADD

The Cancer Genome Interpreter - Biomarkers result table contains the following columns:

Gene: Gene name
Observed alteration: Alterations observed in genes described to affect the response to a drug
Biomarker: Genetic alteration described as a biomarker of response to a drug
Drug: Drugs influenced by the biomarker
Effect: How the presence of the biomarker affects the response to the drug
Tumour type: The tumour type in which the biomarker has been described
Evidence level: The level of evidence that supports the described biomarker
Biomarker match: Match between the observed alteration and the biomarker
Source: Source supporting the biomarker

The Cancer Genome Interpreter - Bioactivities result table contains the following columns:

Gene: Gene name
Observed alteration: Alterations observed in genes described to affect the response to a drug
Compound: Compounds interacting with the gene bearing driver alterations
Binding potential: Potency of binding between the compound and the altered gene label
MOA: Compound mechanism of action
Match: True if the mechanism of action of the drug is coherent with the role of the gene in cancer