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Figure 2 | BMC Genomics

Figure 2

From: Mouse SNP Miner: an annotated database of mouse functional single nucleotide polymorphisms

Figure 2

Web-based access to Mouse SNP Miner database. (not shown) 'SNP Query' mode allows selection of strain or strain group for comparison. Searching can be constrained by chromosomal interval, gene name, SNP accession number, and presence of human ortholog in OMIM database. QTL from the MGI database can be searched by name or keyword and associated chromosome intervals imported for convenient screening. (shown) 'SNP View' mode presents results from the search in a graphical format for convenient run-time scanning. SNPs in the interval are listed by functional consequence and PolyPhen/PANTHER prediction in the upper left and can be rapidly added or removed by clicking on the associated box. Boxes indicating transcripts and lines indicating SNPs are color and symbol coded by functional consequence in the graphical display. The placement of marks above and below the bar indicates transcripts in the forward and reverse strand, respectively. Clicking on a SNP causes detailed SNP information to be displayed in the 'Details' window above. The 'Associations' window displays GO, OMIM, and PolyPhen/PANTHER information and links for the selected SNP. Movement across the chromosome and between SNPs is facilitated by buttons at the bottom of the graphical display. In the example shown, a search has been performed for putative functional SNPs differing between C57BL/6J and all 129 strains (129% allows global searching of 129 strains) for the interval 153,482,802–154,678,264 bp on chromosome 4. A deleterious mutation (Ile706Thr) in the fourth transmembrane domain of Tas1r3 is highlighted.

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