Figure 1.
An overview of the methods and major results.
The 1000 Genomes Project genotypic data are mapped to the Affymetrix GeneChip Human Exon Array 1.0ST. CEU (Caucasians from Utah, USA) and YRI (Yoruba people from Ibadan, Nigeria) are lymphoblastoid cell lines from the International HapMap Project. Known SNPs are those recorded in the NCBI dbSNP v129 database. Common SNPs are those with minor allele frequencies greater than 5%. Within the exon array, probesets are exon-level and transcript clusters are gene-level.
Table 1.
Functional annotations of common SNPs in the exon array.
Figure 2.
Distribution of SNP locations with the 25-mer exon array probes.
Each bin is 5 nt. Left is 5′ and right is 3′. Common SNPs (MAF>0.05) are included. MAF: minor allele frequency.
Table 2.
Probesets containing common SNPs based on the 1000 Genomes Project data.
Table 3.
Comparison with the SNPinProbe database(dbSNP v129).
Figure 3.
A differentially spliced probeset that could be affected by novel SNPs.
The probeset 3017096 (chr7: 102526627–102527377) has a novel SNP (chr7: 102526628) in the CEU samples. The probeset was originally found to be differentially spliced between the CEU and YRI samples. UCSC Genome Browser (http://genome.ucsc.edu/) was used to plot the genomic positions (hg18, March, 2006) of the probeset in relation to the other probesets for the ARMC10 gene. This novel SNP lies within the probe chr7:102526627–102526651.