From Genome Analysis Wiki
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1. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables].
2. One can specify the regieon to be whole genome or any particular gene position (e.g. chr21:33031597-33041570).
Here is an example of input gene file headlines:
5'UTR=A26C2[-] means the SNP is in the 5'UTR region of gene A26C2 with a minus strand.
INTRONIC=POTEG[-] means the SNP is in the intronic region of gene POTEG with a minus strand.
SYNONYMOUS_CODING=GAB4:Ala15826157Ala[-] means that the SNP is synonymous coding at position
15826167 in gene GAB4 with a minus strand and it keeps amino-acid Ala unchaged.
NON_SYNONYMOUS_CODING=GAB4:Leu15830952Pro[-] means that the SNP is non_synonymous coding at position 15830925 in gene GAB4 with a minus strand and it changes amino-acid Leu to Pro.
SPLICE_SITE=NCAPH2[+] means that the SNP is in the SPLICE_SITE (5 bp within exon start or end positions in the coding reegion) of gene MCAPH2 with a plus strand.