1.1 software (http://hydra.usc.edu/gxe) using minor allele frequency data from HapMap
It has been reported that the Leu34 allele is present in approximately 25% of Europeans, much less frequent in Africans and it is missed in Asians (International HapMap
project, www.hapmap.org) (30).
Four common single-nucleotide polymorphisms (SNPs) (rs1205, rs1130864, rs1800947, and rs1417938) on this gene were selected from the International HapMap
Project collection of Han Chinese data and because they were reported to be significantly related to CRP levels in a Chinese population. Genomic DNA was extracted from the peripheral blood using the salt fractionation method.
According to HapMap
genotype data (HapMap
#27, on NCBI B36 assembly), rs6759298 is not included within the LD blocks of its neighboring genes.
Whenever rs4988235 was not genotyped directly, we used either (a) the HapMap
II CEU (European) reference panel-imputed genetic information from genome-wide association studies (http://hapmap.ncbi.nlm.nih.gov/downloads/genotypes/200810_phaseII/) for rs4988235 or (b) genotype information from a predefined list of proxies that are in high linkage disequilibrium with rs4988235 (n = 5, [r.sup.2] > 0.9).
Pickrell et al., "DNA methylation patterns associate with genetic and gene expression variation in HapMap
cell lines," Genome Biology, vol.
In total, 33 haplotype-tagging single nucleotide polymorphisms (SNPs) were identified at the GLP-1R locus in the CHB (Han Chinese from Beijing) population from the HapMap
Phase II database (http://www.hapmap.org) (R#27, [r.sup.2] < 0.8, MAF [greater than or equal to] 0.05).
We selected 8 potential functional SNPs of UCP2 and 7 potential functional SNPs of PPAR[gamma], including promoter, exon, 5 untranslated region and 3 untranslated region based on the screening standards (the minor allele frequencies (MAF) are more than 20% in Han Chinese according to the HapMap
Han Chinese in Beijing (CHB) group).
Authors screened the data for the Tag SNPs on the International HapMap
Project website (http://www.hapmap.org/ index.html.ja), using a cutoff level of r2 > 0.5, and for the minor allele frequency, we used a cutoff level of >0.1.
Tag single-nucleotide polymorphisms (tag SNPs) in the IL23/Th17 axis genes were selected according to their susceptibility to other AIDs and to the genotyping data from the CEU available from the International HapMap
GTEx, gnomAD, GWAS, HapMap
, genome browser, SNPs, all acronyms and concepts that were not technically possible during my research time in the field.