Comprehensive Functional Annotation of Seventy-One Breast Cancer Risk Loci
Figure 2
21 High LD SNPs in exon and effect of each variant to the respective protein.
(A) The list of high LD SNPs (r2≥0.5) in exons. The risk region number was derived from Table S1 and ordered by chromosome number. Index SNP of each corrSNP and the value of r2 between these SNPs were listed. The distance from the index SNP to each corrSNP was shown along with the name of the nearest gene. The type of each exon variant was also annotated. (B) A genomic browser view of two high LD SNPs, rs8100241 and rs8108174. The first track showed FunciSNP results for the exons. The name of the correlated SNP (rsnumber – r2 value) was shown in blue. The index SNP was shown in black. The bottom tracks were biofeature tracks, RefSeq genes/mRNA/Pseudogene tracks from UCSC Genes, common SNPs (version 137), and Linkage Disequilibrium (LD) blocks. LD block, which was measured by r2 value in phased CEU is shown. Allele frequencies of each SNP (in all populations) and zoomed in view of the genome browser for each SNP were shown, including the amino acid changes by missense variants. (C) The effect of amino acid changes by missense variants of the respective protein was predicted by SIFT and PolyPhen [34], [35].