Table 3 Assay DNA sequences for the SNPs analyzed.
From: Physiogenomic comparison of human fat loss in response to diets restrictive of carbohydrate or fat
SNP | Gene | Chr | mac | min | maj | Freq | Sequence Context |
|---|---|---|---|---|---|---|---|
rs694066 | GAL | 11 | 20 | A | G | 0.09 | TTCTAAGTCCTCTGCCATGCC [A/G]GGAAAGCCTGGGTGCACCCA |
rs7602 | LEPR | 1 | 29 | A | G | 0.16 | CTTGGAGAGGCAGATAACGCT [A/G]AAGCAGGCCTCTCATGACCC |
rs1171276 | APOA4 | 1 | 23 | A | G | 0.13 | AGTTTCATGTACATTAAATAT [A/G]AATTTCTTTTGGCTGGAAAT |
rs8179183 | APOA4 | 1 | 31 | C | G | 0.18 | TAATGGAGATACTATGAAAAA [C/G]GAGAAAAATGTCACTTTACT |
rs6024725 | MC3R | 20 | 31 | T | C | 0.22 | CCTAGAGACATATCTCAGTTA [A/G]GTTTTAGCCTCACCAGTATT |
rs1468271 | NPY | 7 | 12 | A | G | 0.06 | GACCCTGTAATTTTCAGAAAC [A/G]CACATAGGAGTGGGTGTCTG |
rs11100494 | NPY5R | 4 | 10 | A | C | 0.05 | CAGAAAGATGTCATCATCCAG [A/C]ATTGCGTCCACACAGTCAAC |
rs6837793 | NPY5R | 4 | 18 | A | G | 0.10 | ATGAATTGTCACTCAGAAGAA [A/G]CTTAATAGGCATTAATACTA |
rs1801105 | HNMT | 2 | 14 | T | C | 0.08 | TTTACGTTCTCGAGGTTCGAT [A/G]TCTTGGCTACAAGCTCTAAA |
rs12691940 | HNMT | 2 | 66 | A | G | 0.00 | AATCAACCAAGTGGAAGAAAG [A/G]ATATCAGAGTCTGAAGACAA |
rs675 | APOA4 | 11 | 32 | T | A | 0.16 | GAGAAAGAGAGCCAGGACAAG [A/T]CTCTCTCCCTCCCTGAGCTG |
rs5092 | APOA4 | 11 | 30 | A | G | 0.16 | CAGTGCTGACCAGGTGGCCAC [A/G]GTGATGTGGGACTACTTCAG |
rs26312 | GHRL | 3 | 36 | A | G | 0.15 | GCTGTTGCTGCTCTGGCCTCT [A/G]TGAGCCCCGGGAGTCCGCAG |
rs814628 | LIPF | 10 | 26 | A | G | 0.14 | ATCGACTTCATTGTAAAGAAA [A/G]CTGGACAGAAGCAGCTACAC |
rs1058046 | PYY | 17 | 78 | C | G | 0.38 | GGAAAAGAGACGGCCCGGACA [C/G]GCTTCTTTCCAAAACGTTCT |
rs231460 | PYY | 17 | 43 | T | C | 0.23 | TGCTCACCCTAGGATGGAGGG [A/G]GCAGTGGGGGCTGGTTAGGA |
rs4688046 | GSK3B | 3 | 44 | T | C | 0.24 | TAGTAAACTATTTCTTCCCAT [A/G]GGAGAAGATGGATTCTTTTC |
rs334555 | GSK3B | 3 | 24 | C | G | 0.13 | AATTATATCTTATTATTAAAA [C/G]TCTACCAACTCAAAGCTTCC |
rs10934502 | GSK3B | 3 | 40 | T | C | 0.24 | GCTTCCTTATGTAAAATGTAG [A/G]TATTTCTAAAGTAACGCAAT |
rs2287754 | GYS1 | 19 | 25 | A | G | 0.15 | CGGGAAGCTTGCAAGACGCTC [A/G]GCTTCCTATTGCAAGACCGC |
rs1478290 | GYS2 | 12 | 59 | T | G | 0.26 | AATGTGGCTGAAGCCAAAAGC [A/C]TAATGAATGAGGGGAAGCCT |
rs2306179 | GYS2 | 12 | 52 | A | G | 0.27 | TTTCAGTAGGTTTGCAGGGAA [A/G]CCAACTCAAAGCTATATCTG |
rs10505873 | GYS2 | 12 | 67 | T | C | 0.49 | TGCTCAGCCTTCTTCAATGAC [A/G]GTGTTTTGCTATTGTCTCTA |
rs2838549 | PFKL | 21 | 15 | A | G | 0.09 | GGACACTGGTTCCACCTCCGC [A/G]TGGCTGTACAGTGCTGCCGA |
rs2269935 | PFKM | 12 | 53 | A | C | 0.26 | CGGCAATTAGACTGGCTAGAG [A/C]CACCTCAGTCAGGCTCTCCC |
rs3762272 | PKLR | 1 | 13 | A | G | 0.06 | AACAAAGATTCTCCTTTCCTC [A/G]TTCACCACTTTCTTGCTGTT |
rs2856929 | PKM2 | 15 | 39 | A | G | 0.24 | CAGGCTCAGGGTCTAAATTCC [A/G]TATCCTTTCTTCCATACCCT |
rs4890109 | RARA | 17 | 10 | T | G | 0.05 | GGCTGCTCAGGGCCTCGTCCA [A/C]CCCCAGCCTGACAGAGAGCT |
rs9904270 | RARA | 17 | 29 | T | C | 0.15 | GCCTTCCCCTTAGAGAAGAGC [A/G]CCTGCCAGACAAGGGAGAAG |
rs2033447 | RARB | 3 | 43 | T | C | 0.20 | ATGCCGGGTGCTAGAGATACA [A/G]CAGTGAACATGACAAAGTTC |
rs1290443 | RARB | 3 | 30 | A | G | 0.15 | AGAAGCTCTTTCATGTTGTCA [A/G]TTTTAGAAATCCAAATCATT |
rs322695 | RARB | 3 | 29 | A | G | 0.15 | CCTGTAGGATTGTGTTCCTCT [A/G]AAACTGTCCCCTAAATTATG |
rs2838549 | PFKL | 21 | 51 | A | G | 0.09 | GGACACTGGTTCCACCTCCGC [A/G]TGGCTGTACAGTGCTGCCGA |
rs157864 | RXRG | 1 | 17 | T | C | 0.10 | ATGATATTGAATTAAAGGAAA [A/G]TGAATGGTCTCAGTCAGAGA |
rs3118536 | RXRA | 9 | 31 | A | C | 0.14 | CTGCAGGTGCACGGTTTCCTG [A/C]TTGCCCAGGTGTCTCTGAGC |
rs4917348 | RXRA | 9 | 40 | A | G | 0.21 | GGTGGGGTTAGAGGGGATGGT [A/G]CCTGGCAGTGTGCAGCAGAC |
rs3750546 | RXRA | 9 | 43 | A | G | 0.20 | CCTGAGGATGAAGGGGCGTCC [A/G]TGGCCAGGCAGCAGTGAGAA |
rs157864 | PYY | 1 | 17 | T | C | 0.10 | ATGATATTGAATTAAAGGAAA [A/G]TGAATGGTCTCAGTCAGAGA |
rs2058112 | ADIPOR2 | 12 | 27 | T | C | 0.15 | TCTTCTTGCCCTACATACTTC [A/G]AAAGCCCTTGGAGAAATCCT |
rs7975375 | ADIPOR2 | 12 | 31 | T | C | 0.17 | CTTTTCACAGGAAAATTTCTT [A/G]GGAGTCTATTGTCACTGTCT |
rs12695902 | AGTR1 | 3 | 16 | A | G | 0.09 | CATCAGGATTATCAGCATTTA [A/G]GCCAGAGTTGCAAATTAAGT |
rs931490 | AGTR1 | 3 | 23 | A | G | 0.19 | GGCGCCCCCTGGACTTCTGCT [A/G]GAATTTAGATTTAAATAGAT |
rs5950584 | AGTR2 | X | 8 | T | G | 0.04 | CTATCCTCAAATGCTATATAA [A/C]CCAACTGGTGGAAAAAAATT |
rs3219177 | RETN | 19 | 31 | T | C | 0.15 | CCAGGGATCAGTGAGGTCTCT [A/G]AGACCCTTGGGGAGCTTGCC |
rs7412 | APOE | 19 | 18 | T | C | 0.08 | CGGCCTGGTACACTGCCAGGC [A/G]CTTCTGCAGGTCATCGGCAT |
rs429358 | APOE | 19 | 31 | T | C | 0.14 | GGTACTGCACCAGGCGGCCGC [A/G]CACGTCCTCCATGTCCGCGC |
rs405509 | APOE | 19 | 79 | A | C | 0.00 | GAGGACACCTCGCCCAGTAAT [A/C]CAGACACCCTCCTCCATTCT |
rs439401 | APOE | 19 | 59 | T | C | 0.34 | GAGAACTGAGGGGGTGGGAGG [A/G]GAAGAGAGTGCCGGCGGCTC |
rs446037 | APOE | 19 | 5 | A | C | 0.02 | AGACACAGGTGACCCAACTCC [A/C]ATGGCTGGCCTAGGCCCCTC |
rs5883 | CETP | 16 | 13 | T | C | 0.06 | AGCTACCTTGGCCAGCGAGTG [A/G]AAGACTCGCTCAGAGAACCA |
rs1532624 | CETP | 16 | 76 | T | G | 0.00 | TCTGCCCCTTTGGGCTGCAGC [A/C]TCACAAGCTGTGTGGCGTTG |
rs3764261 | CETP | 16 | 46 | T | G | 0.27 | AGTGAATGAGATAGCAGACAA [A/C]CCAGATGCCTACCGACAGGT |
rs5880 | CETP | 16 | 15 | C | G | 0.08 | GATATCGTGACTACCGTCCAG [C/G]CCTCCTATTCTAAGAAAAGC |