Table 2 |
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|
Genes containing multiple probes that are affected by SNPs that also affect other probes in the same gene, but with opposite allelic directions |
|||||||
|
Source |
SNP |
HUGO |
Spearman |
Probe |
Unique Illumina Identifier* |
Probe Sequence |
Number of dbSNP polymorphisms known within probe region |
|
|
|||||||
|
Celiac |
rs1131383 |
POLR2J |
-0.48 |
GI_62422568 |
ILMN_1657317 |
0 |
|
|
HapMap |
rs1131383 |
POLR2J |
0.57 |
GI_21704275 |
4210731 |
0 |
|
|
Celiac |
rs1901198 |
IRF5 |
-0.6 |
GI_38683857 |
ILMN_1670576 |
0 |
|
|
HapMap |
rs1901198 |
IRF5 |
0.5 |
GI_38683858 |
1770358 |
0 |
|
|
Celiac |
rs6565724 |
LOC400566 |
0.67 |
GI_62177143 |
ILMN_1713803 |
0 |
|
|
HapMap |
rs6565724 |
LOC400566 |
-0.72 |
GI_37544593 |
6040008 |
0 |
|
|
HapMap |
rs6565724 |
LOC400566 |
-0.74 |
GI_42661283 |
103170403 |
0 |
|
|
Celiac |
rs2863095 |
MRPL43 |
0.45 |
GI_28872731 |
ILMN_1652147 |
0 |
|
|
Celiac |
rs2863095 |
MRPL43 |
-0.49 |
GI_28872733 |
ILMN_1700477 |
0 |
|
|
HapMap |
rs2863095 |
MRPL43 |
0.58 |
GI_28872731 |
3940465 |
0 |
|
|
HapMap |
rs2863095 |
MRPL43 |
-0.61 |
GI_28872733 |
5900487 |
0 |
|
|
HapMap |
rs4768933 |
DIP2B |
0.42 |
GI_17457388 |
101780735 |
0 |
|
|
HapMap |
rs4768933 |
DIP2B |
-0.44 |
GI_39930390 |
3940278 |
0 |
|
|
Celiac |
rs10774679 |
OAS1 |
-0.54 |
GI_74229010 |
ILMN_1658247 |
0 |
|
|
Celiac |
rs10774679 |
OAS1 |
0.51 |
GI_74229012 |
ILMN_1672606 |
0 |
|
|
HapMap |
rs3177979 |
OAS1 |
0.63 |
GI_8051620 |
2100154 |
0 |
|
|
HapMap |
rs3177979 |
OAS1 |
-0.72 |
GI_8051622 |
2100048 |
0 |
|
|
Celiac |
rs1040404 |
TIPRL |
-0.47 |
GI_73088904 |
ILMN_1779432 |
0 |
|
|
Celiac |
rs1040404 |
TIPRL |
0.5 |
GI_73088933 |
ILMN_1781457 |
0 |
|
|
HapMap |
rs222851 |
C17orf81 |
-0.72 |
GI_44662825 |
6380129 |
0 |
|
|
HapMap |
rs222851 |
C17orf81 |
0.64 |
GI_44662829 |
2760301 |
0 |
|
|
Celiac |
rs34374 |
PAM |
0.43 |
GI_21070979 |
ILMN_1788631 |
GGCTACAGTCGAAAAGGGTTTGACCGGCTTAGCACTGAGGGCAGTGACCA |
0 |
|
HapMap |
rs34374 |
PAM |
-0.41 |
GI_21070979 |
60056 |
GCCAGTGTCTTTCTTTGGTGCCTTTCCTGTTCAGCATTCTTAGCCTGTGG |
0 |
|
HapMap |
rs2838859 |
POFUT2 |
-0.48 |
GI_34147486 |
5900341 |
1 |
|
|
HapMap |
rs2838859 |
POFUT2 |
0.45 |
Hs.300736 |
106110059 |
0 |
|
|
Celiac |
rs7084722 |
PTER |
-0.43 |
GI_47933342 |
ILMN_1795336 |
0 |
|
|
HapMap |
rs7084722 |
PTER |
0.48 |
GI_20070185 |
5570040 |
1 |
|
|
Celiac |
rs10503170 |
MYOM2 |
0.43 |
GI_4505314 |
ILMN_1716733 |
ATTTTCACGGGTGTGGGCACATGGGTGTGGCACCTGGACGTGTGCAGCAT |
1 |
|
HapMap |
rs10503170 |
MYOM2 |
-0.42 |
GI_4505314 |
6620154 |
TTTACACGAGGGTAGACGGCAGATGCCTGACAGAGAGTGGGTTGGCAGAC |
1 |
|
Celiac |
rs11680305 |
ADI1 |
-0.42 |
GI_8922761 |
ILMN_1795671 |
CCGGTGGTGTGATGATGCCATATACCGCAGGGCTTGCTTCTGTCAAGTGT |
1 |
|
HapMap |
rs11680305 |
ADI1 |
0.41 |
GI_8922761 |
4730070 |
GAGCTCCCACCCTAAGGGGCACACACTGAGTTGCTTATGCCACTTCCTTG |
0 |
|
Celiac |
rs2395185 |
HLA-DRB5 |
-0.41 |
GI_26665892 |
ILMN_1697499 |
GGCTCTTATTCTTCCACAAGAGAGGACTTTCTCAGGCCCTGGTTGCTACC |
3 |
|
HapMap |
rs2395185 |
HLA-DRB5 |
0.47 |
GI_26665892 |
450332 |
ACGGCCTCCCATGCATCTGTACTCCCCCTGTGTGCCACAAATGCACTACG |
8 |
|
|
|||||||
|
Meta-analysis of different significant but opposite allelic effects of SNPs (FDR = 0.05, SNP-probe midpoint distance < 250 kb) in the celiac peripheral blood dataset and HapMap B cell line data set. Shown are 14 genes that contain probes for either of the two platforms but that show opposite allelic directions. If probes have identical identifiers on the two platforms, but different oligonucleotide sequences, the oligonucleotide sequences are indicated. *As provided by Illumina platform record. |
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|
Heap et al. BMC Medical Genomics 2009 2:1 doi:10.1186/1755-8794-2-1 |
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