These SNPs showed high linkage disequilibrium in the same block (r2 ≥ 0.99; Supplementary Fig. 2).
To assess the presence of genes which could have been targeted by selection in this locus, we identified the boundaries of high linkage disequilibrium with TdHMA3-B1 (squared correlation coefficient r2 ≥ 0.5) in both DWL and DWC.
We found that a large fraction of L1s were in high linkage disequilibrium with their surrounding genomic regions and that they were well tagged by SNPs.
The six novel SNPs in PRPF6 were in high linkage disequilibrium and associated with PRPF6 mRNA expression in lymphoblastoid cells from 373 Europeans in the 1000 Genomes Project.
However, long stretches of high linkage disequilibrium within the genome prevent us from differentiating between causal variants and perfect surrogates, thus limiting our ability to identify causal variants.
One of the 12 SNPs with high linkage disequilibrium (LD) at 11.6 Mb region (1 11608731) is 26Kb away from the right marker of qK1.11.
After removal of high linkage disequilibrium single-nucleotide polymorphism, we obtained a maximum nonparametric linkage score (NPL) of 3.39 (P = 0.0005) at 17q12-21.32 and the Z-score of 4.20 (P = 0.000007).
These tag SNPs are in high linkage disequilibrium with 2 functional variants in the ITPA gene, rs1127354 and rs7270101, that cause ITPase deficiency and protect against ribavirin (RBV -induced hemolytic anemia (HA).
This means a small land tax could raise more money than even a high linkage fee.
Obviously, small P-values indicate high linkage disequilibrium.
