Base frequencies and haplotypes of HERV-K106 3'LTR with haplotype frequencies in various ethnic groups within the United States.

Table 2 Notes
1Alleles at all three SNP sites in HERV-K106 3′ LTR consisted of two alternate nucleotide bases with one being predominant than the other (133: C>T, 403: G>A, and 835: C>T). Using these SNP four haplotypes of HERV-K106 could be constructed.
2The most common haplotype was C-G-C (f = 0.90) followed by T-A-C (f = 0.05), C-G-T (f = 0.02) and T-G-C (f = 0.02).
377% of African American and 91% European Americans in our study had CGC haplotype of HERV-K106 LTR. CGC was also the most prevalent in a heterogeneous sample labeled as ‘others’ that consisted of a few (n<5 from each group) individuals of Hispanic, Asian, and East Indian origins. Haplotypes TGC and TAC were present in 8% and 5% of African Americans and European Americans respectively whereas haplotype CGT was present in 5% of African Americans but was absent in European Americans. African Americans, although in lower numbers in our study, demonstrated greater haplotype diversity than European Americans which is consistent with the “out of Africa” hypothesis that HERV-K106 originated in Africa and migrated out of Africa with human migration.