Natural variation in cone ratios is associated with RA signaling regulation.

(A) Histogram of the ratios of % L from 738 human males with normal color vision. (B) L cone ratios for SNP rs372754794 genotypes. Original data sets are in S4 Data. (C) SNP rs372754794 genotype frequencies for L cone ratio deciles. Original data sets are in S4 Data. (D) Manhattan plot of the genetic variant p-values. Dots represent genetic variants in genes. Genetic variants above the gray line (Bonferroni corrected threshold) are significant (p < 0.05). The dots for each gene locus are presented in the same color (ex: DIO1 = dark blue; PIAS3 = orange). Along the X axis, the dots are spaced to scale as they occur in the genome. As OPN1LW and OPN1MW are nearby each other in the genome, the variants are represented together at the OPN1LW/MW locus in the same dark blue color. Due to the highly similar sequences of OPN1LW and OPN1MW, many reads could not be mapped, resulting in the gap in the variants at the OPN1LW/MW locus. Original data sets are in S4 Data. (E) Location of SNP rs372754794 upstream at the NR2F2 gene locus. NR2F2 gene (blue); NR2F2 antisense RNA (pink). Yellow arrow denotes the location of the SNP. (F) Local LD plot for rs37275494 based on data from an African American (ASW) population from the 1000 Genomes Project. Top indicates variants. Bottom indicates gene predictions. (G) Minor (G) allele ratio at rs37275494 by ancestry. Original data sets are in S4 Data. (H) Association of L:M ratio and rs372754794 stratified by self-reported ancestry. Original data sets are in S4 Data.