Figure - PMC

Skip to main content

View full-text article in PMC

. Author manuscript; available in PMC: 2009 Jul 31.

Published in final edited form as: Nature. 2007 Jun 7;447(7145):661–678. doi: 10.1038/nature05911

Characteristics of genomic regions 1.25 Mb to either side of ‘hit SNPs’—SNPs with lowest P values. Region boundaries (vertical dotted lines) were chosen to coincide with locations where test statistics returned to background levels and, where possible, recombination hotspots. Upper panel, -log₁₀(P values) for the test (trend or genotypic) with the smallest P value at the hit SNP. Black points represent SNPs tyred in the study, and grey points represent SNPs whose genotypes were imputed. SNPs imputed with higher confidence are shown in darker grey. Middle panel, fine-scale recombination rate (centimorgans per Mb) estimated from Phase II HapMap. The purple line shows the cumulative genetic distance (in cM) from the hit SNP. Lower panel, known genes, and sequence conservation in 17 vertebrates. Known genes (orange) in the hit region are listed in the upper right part of each plot in chromosomal order, starting at the left edge of the region. The top track shows plus-strand genes and the middle track shows minus-strand genes. Sequence conservation (bottom track) scores are based on the phylogenetic hidden Markov model phastCons. Highly conserved regions (phastCons score≥600) are shown in blue. Information in middle and lower panels is taken from the USCS Genome Browser. Positions are in NCBI build-35 coordinates. See Supplementary Information on ‘signal plots.’

Characteristics of genomic regions 1.25 Mb to either side of ‘hit SNPs’—SNPs with lowest P values. Region boundaries (vertical dotted lines) were chosen to coincide with locations where test statistics returned to background levels and, where possible, recombination hotspots. Upper panel, -log₁₀(P values) for the test (trend or genotypic) with the smallest P value at the hit SNP. Black points represent SNPs tyred in the study, and grey points represent SNPs whose genotypes were imputed. SNPs imputed with higher confidence are shown in darker grey. Middle panel, fine-scale recombination rate (centimorgans per Mb) estimated from Phase II HapMap. The purple line shows the cumulative genetic distance (in cM) from the hit SNP. Lower panel, known genes, and sequence conservation in 17 vertebrates. Known genes (orange) in the hit region are listed in the upper right part of each plot in chromosomal order, starting at the left edge of the region. The top track shows plus-strand genes and the middle track shows minus-strand genes. Sequence conservation (bottom track) scores are based on the phylogenetic hidden Markov model phastCons. Highly conserved regions (phastCons score≥600) are shown in blue. Information in middle and lower panels is taken from the USCS Genome Browser. Positions are in NCBI build-35 coordinates. See Supplementary Information on ‘signal plots.’