Serotonin transporter gene SLC6A4

SNP
Single nucleotide polymorphisms, frequently called SNPs (pronounced 'snips'), are the most common type of genetic variation among people. Each SNP represents a difference in a single DNA building block, called a nucleotide. For example, a SNP may replace the nucleotide cytosine (C) with the nucleotide thymine (T) in a certain stretch of DNA.
Learn more about SNPs

RefSNP Alleles
RefSNP alleles are the alleles submitted to the SNP database (dbSNP) by genetic researchers. For example the SNP CBS C699T has RefSNPs A/G. This means that a genetic researcher found allele A on one DNA strand and G on the other DNA strand at the gene location for CBS C699T.

Ambigous RefSNP Alleles
SNPs and RefSNP Alleles for a particular gene location in a genome build, are submitted to dbSNP by multiple genetic researchers. Each SNP will usually only have two RefSNP alleles. When different researchers submit conflicting information about RefSNP alleles, then it is possible for more than 2 alleles to be listed for one SNP, making it more difficult to determine the correct minor allele.
Learn more about ambigous RefSNP alleles

More definitions

RSID
The rs number is an accession number used by researchers and databases to refer to specific SNPs. It stands for Reference SNP cluster ID.
Learn more about RSID

Minor alleles

• Minor alleles or Minor Allele Frequency is value representing the percentage of people in the default global population, who carry a variant allele.
• Minor alleles used in computing phenotype will vary based on DNA strand orientation. SNP Sandbox will automatically flip alleles to match the DNA strand used in your raw data.
• You can edit the minor allele as needed using A, T, C or G.
• A risk allele and a minor allele are not always the same. A minor allele is the one (of 2 alleles) that occurs with less frequency in the default general population. The allele that occurs more frequently is thought to represent a normal phenotype, while the other one represents an abnormal phenotype. This is usually accurate, but not in all cases. The appropriate risk allele can only be determined by genome-wide studies. See: PMID

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