MINOR ALLELE FREQUENCY
For each SNP this feature consider the MAF score (from HapMap data).
Available populations are CEU, CHB, YRI and JPT.
This feature returns a real number [0, 0.5].
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

SNP LOCALIZATION
This feature computes the score for the localization of the SNP within the DNA.
The user can choose and set a weight for each single localization type.
If the user is interested to multiple locations, the localization score represents the sum of all the relative weights.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

ESSENTIAL GENES
If the gene is considered essential for human life this feature returns 1, else 0.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

CONSERVED REGIONS
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu): the field lowerLimit represents the score of the feature. Each SNP obtains a score related to the conservetion value assigned to the region it belongs to.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

LAMINA ASSOCIATED DOMAINS
Description of the function and values.
Based on the SNP position, this feature checks for entries in the SNP region. Returns 1 if elements exist, 0 otherwise.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

OPEN CHROMATIN

This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature and is internally normalized for each cell line (range 0-1). Each SNP obtains a score according to its genomic position. If a single cell line is selected the single score value is considered. If multiple cell lines are chosenthe finel value is computed as the SUM of each cell line score in the related genomic position.

CHROMATIN STRUCTURE
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature and is internally normalized for each cell line (range 0-1). Each SNP obtains a score according to its genomic position. If a single cell line is selected the single score value is considered. If multiple cell lines are chosenthe finel value is computed as the SUM of each cell line score in the related genomic position.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

METHYLATION SEQ REGIONS
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature and is internally normalized for each cell line (range 0-1). Each SNP obtains a score according to its genomic position. If a single cell line is selected the single score value is considered. If multiple cell lines are chosenthe finel value is computed as the SUM of each cell line score in the related genomic position.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

METHYLATION
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature and is internally normalized for each cell line (range 0-1). Each SNP obtains a score according to its genomic position. If a single cell line is selected the single score value is considered. If multiple cell lines are chosenthe finel value is computed as the SUM of each cell line score in the related genomic position.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

CPG ISLAND
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu) and evaluates promoting regions: the field obsExp represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

DNAse
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu) and evaluates promoting and regulating regions: the field score represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

TSS
Description of the function and values. Trascriptinoal Start Sites from Eponime.
This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

CPG ISLAND, PROMOTERS AND FIRST EXONS
Description of the function and values. CPG Island, promoters and first exons, predicted in silico.
This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

FOX2
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

TAF1 BINDING SITES
Description of the function and values. Taf1 binding sites, from ChIP-chip.
This value comes from UCSC database(http://genome.ucsc.edu). Based on the SNP position, this feature checks for values that wrap the region and returns 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

INTERGENIC REGULATORY ELEMENTS
Description of the function and values: literature-curated regulatory regions, transcription factor binding sites, and regulatory polymorphisms from ORegAnno (Open Regulatory Annotation).
This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

TSS SWITCH GEAR
Description of the function and values. Transcriptional start sites, from empirical experiments (SG).
This value comes from UCSC database(http://genome.ucsc.edu): the field confScore represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

REGULATORY REGIONS
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu). Based on the SNP position, this feature checks for values and returns 1 if the position of the SNP is included in at least one element.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

TRANSFAC TFBS
Description of the function and values.
This value comes from TRANSFAC database: the field score represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

TXN FACTOR
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu): the field expScore represents the score of the feature. Based on the SNP position, this feature checks for values and returns the SUM of all entries CSV in this field.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

ENHANCERS
Description of the function and values. Regulatory regions, in silico predicted and empirically validated.
This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

KNOWN ALTERNATIVE
Description of the function and values.
Alternate Promoter (altPromoter) - Transcription starts at multiple places. The altPromoter extends from 100 bases before to 50 bases after transcription start.
Alternate Finish Site (altFinish) - Transcription ends at multiple places.
Cassette Exon (cassetteExon) - Exon is present in some transcripts but not others. These are found by looking for exons that overlap an intron in the same transcript.
Retained Intron (retainedIntron) - Introns are spliced out in some transcripts but not others. In some cases, particularly when the intron is near the 3' end, this can reflect an incompletely processed transcript rather than a true alt-splicing event.
Overlapping Exon (bleedingExon) - Initial or terminal exons overlap in an intron in another transcript. These often are associated with incompletely processed transcripts.
Alternate 3' End (altThreePrime) - Variations on the 3' end of an intron.
Alternate 5' End (altFivePrime) - Variations on the 5' end of an intron.
Intron Ends have AT/AC (atacIntron) - An intron with AT/AC ends rather than the usual GT/AG. These are associated with the minor spliceosome.
Strange Intron Ends (strangeSplice) - An intron with ends that are not GT/AG, GC/AG, or AT/AC. These are usually artifacts of some sort due to sequencing error or polymorphism.

MIRNA BINDING REGIONS
Description of the function and values.
This value comes from UCSC database(http://genome.ucsc.edu): the field score represents the score of the feature. Based on the SNP position, this feature checks for values and returns the maximum one.
Final value is normalized in the range of the field bundaries, obtaining a real number between 0 and 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

HUB PROTEIN
If the gene codes for a hub protein this features returns 1, else 0.
The number of interactions represents the parameter to evaluate if a protein acts as hub protein or not. The distinctive threshold can be modified by the user.
It is expressed as a positive integer number.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

PROTEIN DOMAIN
If the gene codes for a protein domain this features returns 1, else 0.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

POLYPHEN
If the SNP is in the databse PolyPhen returns 1, else 0.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

SNPS 3D
If the SNPs is included in the database SNPS3D this features returns 1, else 0. 3D features are related to protein and amminoacid alteration.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

LS-SNP
If the SNP is included in the LS-SNP this features returns 1, else 0.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

PROTEIN INTERACTIONS
Description of the function and values.
This value comes from STRING database: if the SNP is included in a protein with an interacting level greater than 400, then the feature returns a value of 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

POST TRANSLATIONAL MODIFICATIONS
Description of the function and values.
If the SNP involves a nucleotide that codifies for an aminoacid which is a recognized site for PTM, than the feature returns value 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.

OMIM
Description of the function and values.
This value comes from OMIM database(www.ncbi.nlm.nih.gov/Omim/): if the SNP is described as disease-causative, then the feature returns a value of 1.
The feature weight balances how much this feature affects the final score. Real numbers between 0 and 1 are allowed.