Typing of SNPs around the SHOX gene of the Xp/Yp pseudoautosomal region

The location of each SNP used in the linkage disequilibrium and sperm recombination studies is given in basepairs relative to Genbank entry U82668. [Markers shown in green were independently identified and submitted to dbSNP subsequent to this work]. Allele frequencies were determined from genotypes of 99 unrelated UK Caucasian semen donors (UK), 40 Saami samples (S) and 35 Vlax Roma (VR), established by hybridisation of appropriate 1 to 3kb genomic PCR products with each of the indicated allele-specific oligonucleotides (ASOs). The SNP or indel site in each ASO is indicated in red. Alu repeat sequences are shown in blue. "-" = not determined.

 

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SNP       location   allele       freq                    ASO
                               UK   S    VR
+6/597     4557      C        0.87   -    0.74    5' GAAACATCGCTTGGGTAT 3'
                     T        0.13   -    0.26    5' GAAACATCGCTTGGGTAT 3'
+6/1323    5880      C        0.03   -    0.06    5' GGGAAAGCTTTCCTTCGT 3'
                     G        0.97   -    0.94    5' GGGAAAGGTTTCCTTCGT 3'
+4/165    36312      A        0.64   -    0.74    5' CAGGACGCATGGCTGCCC 3'
                     G        0.36   -    0.26    5' CAGGACGCGTGGCTGCCC 3'
+4/223    36370      C        0.44   -    0.60    5' CCAAGCGCAAGCCTCCAG 3'
                     G        0.56   -    0.40    5' CCAAGCGGAAGCCTCCAG 3'
+4/375    36522      C        0.85   -    0.80    5' GGCCAGCCCCGGCCTCCC 3'
                     T        0.15   -    0.20    5' GGCCAGCCCCAGCCTCCC 3'
+4/500L   36649      3        0.71   -    0.44    5' CTGCAGAGGGTCCCGGAG 3'
                     4        0.29   -    0.56    5' TGCAGAGGGTCCCCGGAG 3'
+4/1063   37210      C        0.28   -    0.14    5' TGCGGGACGTGGTGACCG 3'
                     G        0.72   -    0.86    5' TGCGGGAGGTGGTGACCG 3'
+701      42851      C        0.83  0.83  0.76    5' CGGCCTCCGCCGCCGCCG 3'
                     T        0.17  0.17  0.24    5' CGGCCTCTGCCGCCGCCG 3'
+876      43026      A        0.25  0.28  0.38    5' GGCGCCCGGATCCCCCCC 3'
                     G        0.75  0.72  0.62    5' GGCGCCCGGGTCCCCCCC 3'
+1096     43246      A        0.17  0.23  0.24    5' GGGGGACTCGGGCGCCTG 3'
                     G        0.83  0.77  0.76    5' GGGGGGCTCGGGCGCCTG 3'
+2190     44340      C        0.77  0.78  0.66    5' CAACCTCCGCCTCCTGGG 3'
                     T        0.23  0.22  0.34    5' CAACCTCTGCCTCCTGGG 3'
+2378     44528      C        0.28  0.37  0.16    5' GTGCTGGGACGACAGGCG 3'
                     T        0.72  0.63  0.84    5' GTGCTGGGATGACAGGCG 3'
+2784     44933      A        0.08  0.19  0.19    5' CAAGGTTATCAGAGCGCA 3'
                     G        0.92  0.81  0.81    5' CAAGGTTGTCAGAGCGCA 3'
+2900     45050      A        0.20  0.18  0.34    5' AGAGAGAGGGGCTGGCCC 3'
                     G        0.80  0.82  0.66    5' AGAGAGAAGGGCTGGCCC 3'
+3571     45721      C        0.64  0.66  0.71    5' GACCTTTCGAAAGTGAGA 3'
                     T        0.36  0.34  0.29    5' GACCTTTTGAAAGTGAGA 3'
+3837     45987      C        0.95  0.96  1.00    5' AAGCCTGCGGGTGTTTGA 3'
                     T        0.05  0.04  0.00    5' AAGCCTGTGGGTGTTTGA 3'
+3955     46105      A        0.58  0.55  0.73    5' CTTGGGGAGAAGGAATGG 3'
                     G        0.42  0.45  0.27    5' CTTGGGGGGAAGGAATGG 3'
+3983     46133      A        0.36  0.45  0.30    5' CTTGCAGGCACATGTCTG 3'
                     G        0.64  0.55  0.70    5' CTTGCAGGCACGTGTCTG 3'
+3990     46140      A        0.63  0.55  0.74    5' TGTCTGATAGGAGGTGAA 3'
                     T        0.37  0.45  0.26    5' TGTCTGTTAGGAGGTGAA 3'
+5053     47203      C        0.76  0.81  0.71    5' GCTTTTGCCTTATGGACC 3'
                     G        0.24  0.19  0.29    5' GCTTTTGCGTTATGGACC 3'
+5683     47833      C        0.43  0.55  0.56    5' ATGGGTATATCGTATATA 3'
                     T        0.57  0.45  0.44    5' ATGGGTATATTGTATATA 3'
+6085     48235      C        0.75  0.61  0.39    5' ACCACCCCCTCCTCCCTC 3'
                     T        0.25  0.39  0.61    5' ACCACCCTCTCCTCCCTC 3'
+6139     48289      A        0.41  0.42  0.61    5' GATGAGCAGAGACTATTA 3'
                     G        0.59  0.58  0.39    5' GATGAGCGGAGACTATTA 3'
+6195     48345      C        0.84  0.93  0.99    5' CGCTGCCCCATGAGACCA 3'
                     T        0.16  0.07  0.01    5' CGCTGCCTCATGAGACCA 3'
+6211     48361      C        0.93  0.99  0.94    5' CAGGCACCGGGGGGCGGA 3'
                     T        0.07  0.01  0.06    5' CAGGCACTGGGGGGCGGA 3'
+6236     48386      C        0.76  0.95  0.84    5' TGGGTGTCCGCAGAGGGA 3'
                     G        0.24  0.05  0.16    5' TGGGTGTGCGCAGAGGGA 3'
+6260     48410      A        0.13   -    0.11    5' GGCAGAGCCTTCCTCCGC 3'
                     C        0.87   -    0.89    5' GGCAGAGACTTCCTCCGC 3'
+6485     48635      A        0.23  0.68  0.14    5' CTGGGGAACCCGTCAAAA 3'
                     C        0.77  0.32  0.86    5' CTGGGGACCCCGTCAAAA 3'
+6630     48770      G        0.11   -     -      5' CTTGCTCGGGATTTTGCT 3'
                     T        0.89   -     -      5' CTTGCTCTGGATTTTGCT 3'
+7445     49585      C        0.90  0.98  0.84    5' ATCGTTACGATTAAATCA 3'
                     G        0.10  0.02  0.16    5' ATCGTTAGGATTAAATCA 3'
+7982     50132      A        0.86  0.95  0.91    5' AATAAAAACAAACATGGG 3'
                     C        0.14  0.05  0.09    5' AATAACAACAAACATGGG 3'
+8965     51115      C        0.26  0.29  0.39    5' CTTTGCTCGGAAACAGGA 3'
                     G        0.74  0.71  0.61    5' CTTTGCTGGGAAACAGGA 3'
+9177     51327      C        0.93  0.98  0.93    5' CACAGTGCGTAAGGGTGG 3'
                     T        0.07  0.02  0.07    5' CACAGTGTGTAAGGGTGG 3'
+9595     51745      C        0.67  0.85  0.66    5' TCCCCTGCGCTATTGCAC 3'
                     T        0.33  0.15  0.34    5' TCCCCTGTGCTATTGCAC 3'
+9697     51847      G        0.63  0.71  0.56    5' GTCCTCAGGACCCTTGGT 3'
                     T        0.37  0.29  0.44    5' GTCCTCATGACCCTTGGT 3'
+3/341    61494      A        0.31   -    0.47    5' TGTTCCGTTGTAACGCCG 3'
                     T        0.69   -    0.53    5' TGTTCCGATGTAACGCCG 3'
+3/663    61817      C        0.65   -    0.56    5' GATGTTGCTATTAGATTT 3'
                     G        0.35   -    0.44    5' GATGTTGGTATTAGATTT 3'
+3/849    62003      C        0.06   -    0.04    5' AAAGAGACGGGACAGATT 3'
                     T        0.94   -    0.96    5' AAAGAGATGGGACAGATT 3'
+3/1035   62189      A        0.23   -    0.20    5' CAGCCAGACCCCCGAAAT 3'
                     G        0.77   -    0.80    5' CAGCCAGGCCCCCGAAAT 3'
+3/1239   62393      C        0.37   -    0.37    5' GAGGACACAGGACTCTGG 3'
                     G        0.63   -    0.63    5' GAGGACAGAGGACTCTGG 3'
+3/1248   62401      A        0.49   -    0.56    5' TGTCCTCACCTCTGGGTT 3'
                     G        0.51   -    0.44    5' TGTCCTCGCCTCTGGGTT 3'
+35/1652  62931      C        0.53   -     -      5' GtATGtGCATTTGTTATT 3'
                     G        0.47   -     -      5' GtATGtGGATTTGTTATT 3'
+35/2287  63568      A        0.24   -     -      5' GGTACCCAGTGTTGCCCC 3'
                     G        0.76   -     -      5' GGTACCCGGTGTTGCCCC 3'
+35/2637  63918      A        0.43   -     -      5' CACCACCACGCCCGGCTC 3'
                     G        0.57   -     -      5' CACCACCGCGCCCGGCTC 3'
+35/3390  64671      C        0.16   -     -      5' TTTTTGCCTGTTAGCAGA 3'
                     G        0.85   -     -      5' TTTTTGCGTGTTAGCAGA 3'
+35/4673  65954      A        0.56   -     -      5' AACAATAATGGCCAAAAC 3'
                     G        0.44   -     -      5' AACAATAGTGGCCAAAAC 3'
+35/6219  67500      C        0.38   -     -      5' ACCAGCTCATCTACTGGT 3'
                     T        0.62   -     -      5' ACCAGCTTATCTACTGGT 3'
+35/6445  67725      C        0.17   -     -      5' TAGCTCACGCTTGTTGTA 3'
                     T        0.83   -     -      5' TAGCTCATGCTTGTTGTA 3'
+35/6978  68259      A        0.83   -     -      5' CTGGCTGATGCCTGTAAT 3'
                     G        0.17   -     -      5' CTGGCTGGTGCCTGTAAT 3'
+5/507    69507      A        0.20   -    0.35    5' AGCACAGATTTGTTTCCT 3'
                     G        0.80   -    0.65    5' AGCACAGGTTTGTTTCCT 3'
+5/772    69772      G        0.80   -    0.62    5' GTGGAAGGGGCAGATGGA 3'
                     T        0.20   -    0.38    5' GTGGAAGTGGCAGATGGA 3'
+5/934    69935      A        0.59   -    0.68    5' TGGCGTGATCTCGGCTCA 3'
                     C        0.41   -    0.32    5' TGGCGTGCTCTCGGCTCA 3'
+35/375   71375      A        0.17   -     -      5' CGTGTGCGCAcGTGTGTG 3'
                     G        0.83   -     -      5' CGTGTGCGCGCGTGTGTG 3'
+35/520   71520*     C        0.17   -     -      5' TGTATTTCTGAGACAGAG 3'
                     T        0.83   -     -      5' TGTATTTTTGAGGCAGAG 3'
+35/801   71801      C        0.90   -     -      5' GCCCACCGCCACACCTGG 3'
                     T        0.10   -     -      5' GCCCACTGCCACACCTGG 3'
+35/939   71939      A        0.37   -     -      5' GGCCACCACGTCCaGCCT 3'
                     G        0.63   -     -      5' GGCCACCGCGTCCaGCCT 3'
+35/151   72151      A        0.10   -     -      5' TAGAGACAGGGCTTCACC 3'
                     G        0.90   -     -      5' TAGAGACGGGGCTTCACC 3'
+35/329   72329      A        0.20   -     -      5' GACGTCCAGCGAAGAGAA 3'
                     G        0.80   -     -      5' GACGTCCGGCGAAGAGAA 3'
+7/1400   78440      C        0.45   -     -      5' ATTCCTGCGGCATGCATC 3'
                     T        0.55   -     -      5' ATTCCTGTGGCATGCATC 3'
+7/1593   78633      C        0.99   -     -      5' CTGCAGCCGGAAGACGCA 3'
                     T        0.01   -     -      5' CTGCAGCTGGAAGACGCA 3'
+7/1985   79025      A        0.13   -     -      5' TTCGAAGATCTCCAGTGC 3'
                     G        0.87   -     -      5' TTCGAAGGTCTCCAGTGC 3'

*  actually detecting 2 SNPS which are in complete disequilibrium at positions 71517 & 71522
   (CG & TA primers did not hybridise to the semen donor panel).

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Last updated: 8 September, 2005
Celia A. May
The views expressed in this document are those of the document owner, Celia A. May.