Table 4 Pleiotropic SNPs selected by our different approaches. For each method, we reported if the SNP effect was find in the same direction between the two studies (+), the opposite direction (-) or not selected (ns)
From: Leveraging pleiotropic association using sparse group variable selection in genomics data
SNP | Chr | Pos (kbp) | EA | BA | DE | SGMT | ||
|---|---|---|---|---|---|---|---|---|
BC | TC | Gene | Pathway | |||||
rs1342862 * | 1 | 72,657 | G | A | − | − | NEGR1 | F _obesity |
rs17483835 * | 1 | 183,297 | A | G | − | − | F _tobacco_hsa00760 | |
rs17332991 * | 5 | 60,179 | A | C | − | − | ERCC8 | F _DNA |
rs6151640 * | 5 | 79,967 | G | C | − | − | F _DNA | |
rs249634 * | 5 | 80,164 | G | A | + | − | F _DNA | |
rs4978820 * | 9 | 110,057 | A | G | − | − | F _DNA | |
rs4255624 | 12 | 24,960 | G | A | − | − | F _pub_he2010_4 | |
rs878156 * | 14 | 20,824 | G | A | − | + | PARP2 | F _DNA |
rs1482057 * | 15 | 61,064 | A | C | − | + | RORA ** | F _circadian |
rs12150110 | 17 | 11,962 | A | G | + | + | F _cell_cycle | |
rs3087592 | 22 | 41,079 | A | G | + | − | F _obesity | |