Genome-wide association with transcript abundance(a)Manhattan plot of all 1,636 genome-wide associations at P < 10−8(NLP > 8) for model 3, which includes control for genotype-determined ethnicity, location, relatedness, and gender. Each chromosome is indicated by a different color. The horizontal red line indicates the genome-wide significance threshold (NLP > 11.4) for trans associations. Note the excess of peaks at the MHC complex on chromosome 6 due to multiple cis-eSNPs. (b) Cis-Trans plot showing target transcript location against eSNP location indicating that most eSNPs are in cis to the regulated transcript, while just 13 trans associations at NLP > 11.4are visible. (c) High correlation of significance measures for all eSNPs detected by simple correlation of genotype with expression (model 1) or robust control for ethnicity, gender and location (model 3). (d) Absence of genome-wide significance for the Genotype-by-Location interaction effect, which is not correlated with the Genotype effect.
