[Genome] Non-matching of SNP flanking sequence to its stated position

[John Darlow]

Exon 1 of TEMEM12 (recently renamed CLRN3) is stated to run from
Chr10:129,566,104-129,566,495 and to have the sequence
 
129,566,104
|   110       120       130       140       150
|     |         |         |         |         |    
AATGTCCATTAGCATAACCCTTCCTCAGGAAGAGTGAGATTTTATATTTG
 
    160
      |
ACAATAAAGTGTTAGACTCCATTTCTAAATACCAGACTTCAAAAGATAAG
     |
129,566,159

GTTCAAAAGTGTTATAAGAAGATATTCCTTTTTTTGTCCTAGAGAACTTA

TTTTCCTGTGAAAATGCCTACCACAAAGAAGACATTGATGTTCTTATCAA      

GCTTTTTCACCAGCCTTGGGTCCTTCATTGTAATTTGCTCTATTCTTGGG

ACACAAGCATGGATCACCAGTACAATTGCTGTTAGAGACTCTGCTTCAAA

TGGGAGCATTTTCATCACTTACGGACTTTTTCGTGGGGAGAGTAGTGAAG

AATTGAGTCACGGACTTGCAGAACCAAAGAAAAAGTTTGCAG
 
The SNP rs2296785 is supposed to be within this exon, at 129,566,159 but
it is supposed to C or T in the context:
 
AGCACTTGGTCCTGGAAAGGTGAGTTCTGAAACCCTCTGTTCCCAGAAGTCTTCATGCATAGAGTAGAATAA
AAATACCCAGTCCCTCCTGAGGGGAATG
AGATCATAGGCACTGAAGTGCTTTGAGATACTCAAAGAAAAGAAACATGACACAGCCTTTTATTATTTCAGA
TCGTGAGACCAGGTCAGAAGGGTCGTTA
Y
GCTCATCATGATACTACTGCTTTGAATACCACACAGACCAGCGACATTTCCCATTCATTTCCCCAACCTTGT
GGGAAAAATTTTCAGGAGTACAGCATCA
ATGAAGAACACAGTGTCATGAAACACAAATGCTGTCACAGATGACAGTCACGTTACCATGCTGAATTGTCCA
GAGAAGCTAACCAGTTACTACTCAGGGC
 
but I can find no match between these sequences. I tried the next SNP
along, rs34656572, which is supposed to be in the first intron at
129,566,510 but I likewise found no match for its context.
 
Can you please explain this and tell me how I can discover the true
relationship of SNPs to genes. I'm trying to relate genes to the maximum
linkage positions of a genome scan and work out what to do next.
 
John Darlow
 
Dr. John M. Darlow
National Centre for Medical Genetics
Our Lady's Children's Hospital
Crumlin
Dublin 12
Ireland