Annotating SNPs in the Human Genome
According to dbSNP (build 124) there are over 10 million SNPs in the human genome, more than half of which have been validated. Although this amounts to
roughly one SNP every 1,000 bp, research has shown that SNPs tend to be clustered near one another rather than evenly spaced throughout the genome.
We obtained repeat-masked FASTA files for the human genome from the FTP server of UCSC's Golden Path
(build hg18; Karolchik et al, 2003; International Human Genome Sequencing Consortium, 2001).
Using information from public databases, we marked the position of each non-indel SNP in public databases using IUPAC ambiguity codes.
With repetitive and polymorphic elements annotated, these files are ideal for primer design.
This work was presented as a poster at the AAAS meeting in February 2006.
| SNP-masked Genomic Sequence |
| region |
snps |
|
| Chromosome 1 | 671,783 | chr1.ambigs.fasta.gz |
| Chromosome 2 | 651,716 | chr2.ambigs.fasta.gz |
| Chromosome 3 | 522,952 | chr3.ambigs.fasta.gz |
| Chromosome 4 | 521,207 | chr4.ambigs.fasta.gz |
| Chromosome 5 | 485,152 | chr5.ambigs.fasta.gz |
| Chromosome 6 | 551,388 | chr6.ambigs.fasta.gz |
| Chromosome 7 | 452,712 | chr7.ambigs.fasta.gz |
| Chromosome 8 | 404,562 | chr8.ambigs.fasta.gz |
| Chromosome 9 | 394,448 | chr9.ambigs.fasta.gz |
| Chromosome 10 | 438,671 | chr10.ambigs.fasta.gz |
| Chromosome 11 | 432,671 | chr11.ambigs.fasta.gz |
| Chromosome 12 | 402,692 | chr12.ambigs.fasta.gz |
| Chromosome 13 | 315,940 | chr13.ambigs.fasta.gz |
| Chromosome 14 | 238,882 | chr14.ambigs.fasta.gz |
| Chromosome 15 | 221,678 | chr15.ambigs.fasta.gz |
| Chromosome 16 | 256,474 | chr16.ambigs.fasta.gz |
| Chromosome 17 | 216,458 | chr17.ambigs.fasta.gz |
| Chromosome 18 | 222,368 | chr18.ambigs.fasta.gz |
| Chromosome 19 | 172,776 | chr19.ambigs.fasta.gz |
| Chromosome 20 | 244,331 | chr20.ambigs.fasta.gz |
| Chromosome 21 | 119,681 | chr21.ambigs.fasta.gz |
| Chromosome 22 | 145,223 | chr22.ambigs.fasta.gz |
| Chromosome X | 285,722 | chrX.ambigs.fasta.gz |
| Chromosome Y | 34,748 | chrY.ambigs.fasta.gz |
|
