Significant conditional and joint analysis SNPs with rare allele frequency in European populations.

In the GWAS of HCHS/SoL, we found 29 independent associations between SNPs and 4 lipid traits in the joint analysis, including 2 SNPs with minor allele frequency < 0.01 in Europeans. bJ indicates the effect size and pJ represents the p-value, both from a joint analysis of all the SNPs at the significant loci. The SNPs included in this table have pJ < 5×10−8 and EUR MAF < 0.01. Neither of these SNPs were present in our genotype data for MESA. Full results for all conditional and joint analyses are in S1 Table.