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One additional table links variants to samples and holds quality information from GATK.
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Linkage was found in 8 (18.6%), with linked variants constituting 25 50% of the sequences evaluated for each linked pair.
New mutations can remain associated with physically linked variants for hundreds of generations.
These sweeps are caused when an advantageous allele and neighboring linked variants increase their frequency in a population.
Rs2900180 in C5-TRAF1 and linked variants in a 66Kb region were associated with radiographic progression in ACPA-negative RA.
We investigated the associated and linked variants to be eQTL using the eQTL browser eqtl.uchicago.edu/Home.html.html
Such information is invaluable both as a screening system for variants and as an aid in the study of phenotypically linked variants.
Because loci linked to drive alleles also benefit from the transmission advantage, linked variants that enhance drive will also be selected (Crow, 1991).
More detailed exploration is required to determine whether rs1943779 alters expression of MMP7, how this affects tumour invasiveness and whether other closely linked variants are involved.
If this is not observed, one possibility other than a false positive is that the QTL is caused by a combination of linked variants.
They could therefore be employed to systematically link variants with individual expression profiles, much like eQTLs but with the power to identify long-distance and trans interactions.
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