Sequencing the IL4 locus in African Americans implicates rare noncoding variants in asthma susceptibility

Private SNP haplotypes in subjects with asthma and controls. A schematic of the IL4 gene is shown at the top of the figure, with relative SNP positions (with respect to ATG start site) marked. SNPs present only in asthma cases (CA) or only in asthma controls (CO; ie, private SNPs) are shown. SNPs present in asthma cases are connected to the gene figure by solid lines, and SNPs present in controls are connected by hatched lines. Individual haplotypes appear in rows, with nucleotides against a dark background representing the derived (private) allele.

Distribution of genomic European admixture in African American subjects with asthma (n = 54) and controls (n = 58) as estimated from the first principal component (PC) in EIGENSTRAT by using SNPs from the Illumina 1 M genotyping array.

Local ancestry in African American subjects with asthma (n = 54) and controls (n = 58) at the IL4 locus. The proportion of African ancestry (red) and European ancestry (blue) was estimated using SNPs from the Illumina 1 M genotyping array with the program LAMP.

Accuracy in imputing the minor allele for SNPs identified from sequencing studies of 112 African American individuals (54 subjects with asthma, 58 controls) as it relates to the MAF in the sample. Accuracy, Number of correctly inferred minor alleles/number of observed minor alleles; Private, SNPs that are unique to either subjects with asthma or controls; Shared, SNPs present in both subjects with asthma and controls; Tagged, IL4 SNPs that are tagged by a SNP on the Illumina 1 M genotyping array with an r² > 0.5.