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Since rs12901499 is not in linkage disequilibrium with a non-synonymous polymorphism, it is likely the association is operating by influencing expression of SMAD3.
The T allele of SNP606/RsaI of MNTR1A gene was associated with a greater percentage of oestrous cyclic ewes in the Rasa Aragonesa breed, indicating that this SNP may be in linkage disequilibrium with a mutation responsible for this trait close to MTNR1A, or in regulatory sequences of the gene.
This SNP is in linkage disequilibrium with a functional variant (rs4149056) that results in decreased OATP1B1 transporter activity.
On the other hand, growth at a high degree of disequilibrium with a limited number of nuclei may result in a porphyroblastic texture.
Given that variant alleles are located on an intronic site, it is possible that these polymorphisms affect transcriptional efficiency of REL gene or these variants may be in strong linkage disequilibrium with a variant inside a neighbor gene.
Alternatively, the rs2297630 SNP might be a functionally neutral marker that is in linkage disequilibrium with a functional polymorphism located elsewhere at the SDF1 locus.
Another possibility is that these 2 SNPs might have very high linkage disequilibrium with a mutation of a nearby SNP in exons.
Further work is necessary to determine whether these two haplotypes capture ancestrally distinct causative mutations or are in linkage disequilibrium with a single disease-causing mutation.
Since rs3864180 is a non-coding SNP, the possibility exists that it is either in linkage disequilibrium with a coding SNP or has a regulatory function.
This polymorphism may nevertheless be in linkage disequilibrium with a functional sequence change as recently demonstrated with the identification of the rs10490924 polymorphism in the ARMS2 gene which results in instability of the transcript [62].
It can also be argued that the significant SNPs actually are not functional variants of the IL-12RB1 protein, but instead it is presumably in linkage disequilibrium with a potential functional variant(s) in other loci of the gene.
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