The function report on a SNP contains seven sections on the SNP's functional effects, namely (i) genomic information, presents the nearby sequence, the alleles and the allele frequency among different ethnic groups; (ii) functional effects summary, presents the risk assessment; (iii) transcription regulatory, shows the predicted transcription factor binding sites generated or disrupted by the different SNP alleles; (iv) alternative splicing regulatory, reports exonic splicing enhancer/silencer motifs changed by the SNP alleles leading to exon skipping or inclusion; (v) mRNA/protein domain effects, presents all spliced forms of mRNAs and protein variants extracted from GenBank (14). The protein domains that the SNP locates in are highlighted; (vi) protein structure effects, reports whether the SNP may cause a significant structural change in a protein; and (vii) SwissProt (15) feature table, provides information regarding other known mutations or variations of the translated protein of mRNAs related to the SNP. Some of these sections are specific to coding or non-coding SNPs and they will appear or not appear in the function report accordingly.
