On the other hand, T2DM was found to be associated with mitochondrial haplogroups J and T and with polymorphisms T4216C and A4917G (in linkage with J and T), in Caucasian-Brazilian patients [36].
Proteasome Modulator 9 (PSMD9) lies in the 12q24 locus and is in linkage with MODY3, type 2 diabetes (T2D), microvascular and macrovascular pathology, carpal tunnel syndrome, and hypercholesterolemia in Italian families.
Notably, this SNP is highly expressed in human Amerindian populations, up to 45% in the Paez, and is in linkage with Amerindian HLA haplotypes [19], suggesting that it is a marker for a cassette of genes that are positively selected in humans.
Finally, Medtr7g085120.1 is an apyrase-like protein and is in linkage with two genes (Medtr7g084910.1, Medtr7g084940.1) involved in flavonoid synthesis.
They reported a statistical significant association only for one SNP, rs4420638, that is located near APOC1 and is in linkage with APOE [ 26].
The presence of different morphologies for the ASGR-carrier chromosome in different species and variation in linkage with rDNA infers that the ASGR can be translocated within the genome and those genomes can support gross chromosomal aberrations as a consequence.
In the lamprey, the genome region GL476611 contained two potential PTH/PTHrP-like genes that shared similarity with the vertebrate homologues and were in linkage with the BTBD10 gene, which is present in the vertebrate PTH gene environment [ 2] (Additional file 3).
Our study shows that the PSMD9 SNPs IVS3+nt460, IVS3+nt437, and 197G are in linkage with overweight condition and waist circumference in Italians.
These SNP calls are unreliable and often not in linkage with their surrounding SNPs, and could either be SNPs within regions that are repetitive in one but not in the other parent, or result from misaligned reads.
Nonetheless, it is worth noting that the allele with opposite risk profile (rs10484565) has a low MAF (frequency of minor allele < 0.10) in all populations and our data suggest that it is not (and is not in linkage with) the balancing selection target.
Ergo, haplogroups may be regarded as broadly representative of genomic ancestry but are neither the sole nor definitive ancestral tags and may exist in linkage with other nuclear DNA markers [ 16, 17].
