Sex difference of autosomal alleles in populations of European and African descent.

In the present study, we aimed to report the individual sex-different genetic markers across autosomes in European- and African-origin populations. A total of 8,400 females and 8,081 males in 19 independent cohorts were genotyped across genomes using Illumina or Affymetrix arrays. The allele frequencies were compared between females and males in 9 non-clean cohorts (with some human disease traits) using genome-wide logistic regression and then the nominally significant associations were replicated across 10 clean cohorts (without disease traits). Meta-analysis was performed to derive the combined p values across all cohorts. We found 13 markers that were genome-wide significant (p≤5×10-8) between females and males in the meta-analysis of all cohorts of European descent, including rs7740449 at SYNE1, rs7531151 at PLD5, rs697455 at PPP1R12B, rs6745746 at LOC100128413, rs17000079 at PARM1, rs11948070 at PDE4D, rs7801825 at INSIG1, rs9551642 at MTUS2, rs2932174 at TPTE2, rs1961597 at SALL3, rs4117529 at METTL4, rs6021473 at SALL4 and rs6092466 at RAE1, and one marker, i.e., rs10145208 at PCNX, that was genome-wide significant in the meta-analysis of all cohorts of African descent. The most robust finding was rs7740449 at SYNE1, next to ESR1. We conclude that there are many sex-different markers on autosomes. These markers may be informative in differentiating females and males.