In the clinical genotyping analysis of 1182 β-thalassemia subjects, we identified a group of additional variants that can be used for accurate diagnosis.
Furthermore, we identify eight additional variants that explain most of the SNP heritability of red hair, including variants at ASIP, where an eQTL shows epistatic interactions with the poorly penetrant MC1R variants.
"It raises the question: In the entire population, are there additional variants that might be useful?
However, GWAS not only has made it possible to predict risk factors that are associated with diseases, but also has discovered additional variants that are associated with many diseases [34], [35].
Under these less stringent conditions we found three additional variants that were active (1 2, 1 6 and 1 12).
These types of studies will lead to the identification of additional variants that can then be used for functional studies to elucidate the molecular mechanisms operating in lupus.
Additional variants that are known to be associated with diseases, or affect protein functionality and/or stability were also identified for each protein structure.
The most difficult challenge for HTS projects aiming to discover pathogenic variants is the correct identification of the disease-causing mutations among thousands of additional variants that could be either contributing to unrecognized phenotypes or neutral [ 3].
Note that it is challenging to determine the origin of additional variants that are not present in the sequences of the input strains but which may appear at high confidence in the data.
Further studies identified three additional variants that are strongly associated with LP in some African and Middle Eastern populations and/or have evidence of function, all are upstream of the LCT gene in the 13th intron of the MCM6 gene: -13,907*G, -13,915*G and -14,010*C [ 11, 12, 23, 24].
SNP selection in the present study considers the full set of SNPs reported in Brandstätter et al. [6] (with the exception of SNP A14552G which is replace here by C3936T; both leading to haplogroup H12) plus a selection of additional variants that define further sub-branches of R0 within Europe; see e.g. [4].
