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Interestingly, association to the same SNP and a second, independently associated polymorphism in the region (rs10499194) was detected in a GWAS in a US population, confirming the locus as important in RA causation (5).
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To narrow the confidence interval of Eae23 [20], and confirm the locus in a new strain combination, we investigated the region in the (DAxPVG.1AV1 G10 AIL [26] [29].
Pair-wise comparisons were conducted to further explore group differences and confirm the locus of effects.
This study confirmed the locus of LDI gene and detected a DArT marker, bpb-0068, associated with LDI activity.
The current results confirmed the locus of the gene controlling LDI activity and identified a new DArT markers associated with LDI activity.
Further fine mapping with an extended pedigree, with additional 10 markers, confirmed the locus at 9p21.2-p22.3 with a multipoint LOD = 4.21 within the interval between D9S1870 and D9S161 (Supplementary Fig. 1).
In addition, three significant SNPs for colour a* of LM were identified in a region around 58.13 Mb on SSC12, which confirms the locus reported by Luo et al. [ 39] for a Large White × Minzhu F2 intercross population.
More recently, a functional variant in DNASE1L3 was implicated in a familial form of SLE [ 33], and a pan-meta-analysis of SLE and SSc also confirmed the locus near PXK, but in particular for ACA-positive SSc (rs2176082 [ 7]; P = 1.4 × 10−4 in our data) strengthening the evidence that this locus plays a role in both diseases.
A follow up validation was also performed confirming the exact loci and alleles of the consensus set indels in two individuals.
A second validation was also performed confirming the exact loci and alleles of the consensus set INDELs using the Illumina HiSeq and MiSeq platforms at high depth coverage on two individuals.
This study confirmed the FTO locus but no new loci were identified for BMI [ 37].
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