mdecode

APOA1: apolipoprotein A-I

COMMON MDECODE SNP DATA

Chromosomal Location: 11q23-q24
Gene-Specific Links:      LocusLink (NCBI)     |     GoldenPath (UCSC Genome Browser);     |    PubMed
Individual Genotypes Genotypes for each individual sample at each polymorphic site.
Line format:  <Ref. Sequence Position>  <Sample ID>  <Allele1>  <Allele2>
Jackson Genotypes    Rochester Genotypes
SNP Sequence Context A multi-entry FASTA file containing each polymorphic site and 50 bp of flanking sequence both 5' and 3'. Each polymorphic position is listed according to the IUPAC ambiguity codes or the insertion allele at that site.
SNP Allele Frequency Frequency of each allele at each polymorphic site. Allele frequencies are listed for each sample population and the combined samples. The last three columns list the heterozygosity for each polymorphic site (hz).
Color FASTA Sequence The final reference sequence generated for this gene as a colored FASTA sequence in order to easily locate gene features. Variations are shown in red, exons are shown in blue, and protein translations are included in the coding regions.
SITE SPECIFIC DATA
SNP Locations Mapping of each SNP onto the gene structure. Each SNP can be listed as: --- (noncoding), 5UT (5'UTR), 3UT (3'UTR). If a SNP occurs in a coding region its effect on the amino acid translation is shown. All translations are done from the Locus Link RefSeq curated mRNA sequence (Acc. No.: NM* or XM*) for each gene.
SNP Alleles Alleles at each polymorphic site along with their respective counts. Allele counts are listed for each sample population and the combined samples.
SNP Hardy-Weinberg The genotype count at each polymorphic site. Genotype counts are listed for each sample population and the combined samples.  The last three columns list the Chi-squared values for the Hardy-Weinberg prediction.
IMAGES
Visual Genotype A graphical representation of the individual genotypes file data. Polymorphic sites are consecutively ordered (5' to 3') on the horizontal axis and individual samples on the vertical axis of the array. The genotype for each individual sample at each polymorphic site is color coded as   blue = homozygous (common allele),   yellow = homozygous (rare allele),   red = heterozygous (both alleles),   gray = genotype not determined.
Gene Structure GeneSNPs image of the gene, including an option to hide or show repeats (default = hide) and options to display selected variations by location. There is also a link to the color FASTA display.
   GeneSNPs Image.
RELATED INFORMATION
PCR Primers (FASTA) A FASTA formatted list of the PCR primers used to generate over-lapping amplicons (~800-1000 bp). A description of primers and the standard PCR conditions are available.
Human Reference Sequence A copy of or a link to the Genbank Record that contains the final reference sequence generated for the gene. This sequence is annotated with all polymorphic sites, repetitive sequence regions, and gene segments.
NOTE: The Genbank link will open a separate window to the Genbank website. Please see their disclaimer and copyright statement for data usage.