General considerations:

This data set includes information for over 1000 SNPs. 874 SNPs were discovered in genomic segments at 75 human genes. An additional 39 were discovered in 11 cDNAs. A survey of SNPs previously reported in the literature represent an additional 138 SNPs listed here. This data will be maintained and if information changes (paticularly for the confirmation status), the site will be updated. A general rule of thumb is if a SNP has not been confirmed, then a rank order for the chance the SNP is real is as follows: All "Certain" sites are likely real, sites found in "both" populations are highly likely to be real, SNPs with a high heterozygosity are likely to be real, and SNPs that are rare and found in a single population are the class least likely to be real. For any location where the information is unavailable, the term "N/A" (for Not Available) has been used. Additonal genomic information about each gene is available from the Hypertension Candidate Gene Information Web Site built as a compendum to this information by hyperlinking from the gene name for most pages.

Specific help for columns.

SNP ID

The SNP ID is an internal reference for the SNP. All SNPs found in this study have been submitted to dbSNP (http://www.ncbi.nlm.nih.gov/SNP/) and can be searched based on these values. SNPs detected from a literature search were not submitted to dbSNP.

Exon

The Exon most often represents the exon a SNP is contained in or adjacent to. Sequence within an "exon" can include flanking intronic segments or 5' and 3' UTR.

Position in exon

The Position in exon is the location of a SNP relative to the "exon" record. It does not refer to a specific location in the true exon relative to any standard naming convention.

Confirmation

The Confirmation is the current status of each SNP. All SNPs are "candidates" until proven as SNPs based on an independent method. Methods of confirmation include sequencing, identifying polymorphic individuals on a genotyping array, and comparision to previously reported sites. A SNP is either "Confirmed" or "Not Confirmed." Often SNPs, particularly rare SNPs, are not polymorphic in all populations, only in one or some.

Call Quality

The Call Quality is either "Certain" or "Likely" for each SNP as based on a determination using the program Ulysees version 1.0. "Certain" SNPs have been confirmed 100% of the time in this study. "Likely SNPs have been confirmed 71% of the time in this study. Polymorphisms that have been identified as false positives are often in the rare heterozygosity class of SNP.

Heterozygosity Class

The Heterozygosity Class is either "Rare," "Low," "Medium," or "High." These refer to SNPs whose heterozygosity (as calculated by 2pq) are between 0.01-0.10, 0.10-0.20, 0.20-0.40, and 0.40-0.50 respectively.

Sample Detected

The Sample Detected refers to the detection of a SNP in one or four sample collections. The "African" sample, of individuals from Harare, Zimbabwe, consisted of 80 chromosomes. The "U.S. White" sample, of individuals from Tecumseh, Michigan and 2 CEPH individuals (1331-01,-2) consisted of 68 individuals. "Both" represents the SNP was detected in both the African and U.S. White populations. "cDNA" refers to a set of 88 chromosomes obtained from cell lines.

Location

The Location refers to the position of a SNP relative to a gene. The positions are "Promoter," "5' UTR," "Coding," "Intron," and "3' UTR." "Coding" refers to SNPs in the traslated regions of genes and does not include any untranslated regions of exons.

Amino Acid 1

If the SNP is in a "Coding" location, amino acid information is provided. Amino Acid 1 represents the amino acid (in three letter form) from one of the two alleles.

Amino Acid 2

If the SNP is in a "Coding" location, amino acid information is provided. Amino Acid 2 represents the amino acid (in three letter form) from the second of the two alleles.

Type of Amino Acid Change

The Type of Amino Acid Change can be either a "Synonymous" (does not alter the amino acid) or "Nonsynonymous" (alters the amino acid) change.

Codon Position

The Codon Position refers to the position in the codon where a SNP was located. The value can be either "1," "2," "3," or "0" corresponding to the 1st codon position, the 2nd codon position, the 3rd codon position, and a SNP not occuring in a codon, respectively.

Codon 1

The Codon 1 refers to the three nucleotide code for an amino acid, at which a SNP was detected.

Codon 2

The Codon 2 refers to the alternative three nucleotide code for an amino acid, at which a SNP was detected.

GenBank Accession

The GenBank Accession value is a segment of DNA that the SNP is located within. Each GenBank Accession value is hyperlinked to the GenBank record for additional information.

Allele 1

The Allele 1 value refers to the "reference nucleotide allele" at a given position. This reference status is designated by it being the nucleotide found on the GenBank record. This "Allele 1" is not always the more common allele.

Allele 1 Frequency

The Allele 1 Frequency is the frequency of that allele in the samples used for its detection. If the only sample a SNP was detected in was the African sample, then this frequency is based upon 80 chromosomes. If it was detected in "Both" samples, then it's frequency was based on 148 chromosomes. This value was calculated as p/(p+q) and has been rounded to the nearest 0.05 frequency.

Allele 2

The Allele 2 value refers to the "alternative nucleotide allele" at a given position. This nucleotide was discovered in the SNP detection survey. It is not always the rare allele.

Allele 2 Frequency

The Allele 2 Frequency is the frequency of that allele in the samples used for its detection. If the only sample a SNP was detected in was the African sample, then this frequency is based upon 80 chromosomes. If it was detected in "Both" samples, then it's frequency was based on 148 chromosomes. This value was calculated as q/(p+q) and has been rounded to the nearest 0.05 frequency.

Sequence

The Sequence is a flanking segment of ~100 bp of DNA for each polymorphism. The site of the polymorphism is designated as "*" in each sequence record.



 SNPs Home Page | Hypertension Candidate Genes | GIST