Hi,
my Question is how to find the genes related to given SNPs the part of Snps data I have as follows:
> rs987435 C G 1 1 1 0 2
> rs345783 C G 0 0 1 0 0
> rs955894 G T 1 1 2 2 1
> rs6088791 A G 1 2 0 0 1
> rs11180435 C T 1 0 1 1 1
> rs17571465 A T 1 2 2 2 2
> rs17011450 C T 2 2 2 2 2
> rs6919430 A C 2 1 2 2 2
> rs2342723 C T 0 2 0 0 0
> rs11992567 C T 2 2 2 2 2
While the data for the gene annotation was downloaded from UCSC website
> DDX11L1 NR_046018 chr1 + 11873 14409 14409 14409
> WASH7P NR_024540 chr1 - 14361 29370 29370 29370
> LINC01204 NR_104644 chrX + 45364632 45386484 45386484 45386484
> LOC392232 NR_033867 chr8 - 73114986 73163869 73163869 73163869
> FBXL22 NM_203373 chr15 + 63889551 63894620 63889591 63893885
> LOC729737 NR_039983 chr1 - 134772 140566 140566 140566
> LOC100132287 NR_028322 chr1 + 323891 328581 328581 328581
> LOC100132062 NR_028325 chr1 + 323891 328581 328581 328581
> >
> > where the columns names are as follows table refFlat "A gene
> > prediction with additional geneName field."
> > (
> > string geneName; "Name of gene as it appears in Genome Browser."
> > string name; "Name of gene"
> > string chrom; "Chromosome name"
> > char[1] strand; "+ or - for strand"
> > uint txStart; "Transcription start position"
> > uint txEnd; "Transcription end position"
> > uint cdsStart; "Coding region start"
> > uint cdsEnd; "Coding region end"
> > uint exonCount; "Number of exons"
> > uint[exonCount] exonStarts; "Exon start positions"
> > uint[exonCount] exonEnds; "Exon end positions"
> > )
how can I use this data to find the gene related to which SNPs
Thank you