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Genomic structure of SLC2A4, substitutions found, inferred haplotypes and their frequencies.

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posted on 23.03.2010, 02:15 by Eduardo Tarazona-Santos, Cristina Fabbri, Meredith Yeager, Wagner C. Magalhaes, Laurie Burdett, Andrew Crenshaw, Davide Pettener, Stephen J. Chanock

Substitutions are represented by arrows and when no dbSNP name is available, named as in the SNP500Cancer database. A total of 29 polymorphisms (25 SNPs and 4 INDELs) were detected in the 204 worldwide re-sequenced chromosomes. Forty five percent of the substitutions were singletons and only 8 reached a MAF>0.05 in at least one studied population. Comparison with the homologous chimpanzee sequence suggests that for all SNPs the ancestral allele is modal in humans. In the human genome, there is a 27 bp fixed deletion 348 bp upstream of the transcription initiation site. Three non-coding SNPs are in evolutionarily conserved positions (UCSC Genome Browser, [33]): rs5415 (conservation score: 0.96), within the promoter region, as well as rs222847 and rs222849, both with conservation score of 0.99 and within the first intron. Only one of the 4 coding-SNPs is non-synonymous (rs8192702, Ala358Val, a conservative substitution in exon 9, in the ninth trans-membrane domain), observed in a European. Haplotypes are inferred using only the 8 common SNPs.