FoxA2 SNPs identified by resequencing the genomic DNA from 127 whites
| Position in Ref Seqa | Position wrt ATGb Position in cDNA GenBank Accession Number NM_153675 | Position wrt TSS0.2c (22514102) | Position wrt TSS0.1c (22513101) GenBank Accession Number NM_021784 | rs Number | Site in Gene | Strd | Change in Amino Acid | SNP and Flanking Sequence | Minor Allele | MAFe |
|---|---|---|---|---|---|---|---|---|---|---|
| 22515614 | −2716 | −1512 | −2513 | Prom. | (−) | ccgagtcccc(C>G)cgaaggcgtt | G | 0.004 | ||
| 22515608 | −2710 | −1506 | −2507 | rs1337918 | Prom. | (−) | ccccccgaag(G>T)cgttttcgga | T | 0.054 | |
| 22515585 | −2687 | −1483 | −2484 | Prom. | (−) | gactgggag▵G>A)cgggggagaa | A | 0.008 | ||
| 22514586 | −1688 | −484 | −1485 | Prom. | (+) | aaattggggg(C>A)gatggtggca | A | 0.004 | ||
| 22514124 | −1226 | −22 | −1023 | rs2277764 | Prom. | (−) | aatatcagag(A>G)caaatctcag | G | 0.048 | |
| 22513313 | −415 | 789 | −212 | Intron 1 | (−) | gcggtccac▵CCT>−/−)cctcctcctc | (CCT)13 | 0.083 | ||
| 22513313 | −415 | 789 | −212 | Intron 1 | (−) | gcggtccac▵CCT>−/−)cctcctcctc | (CCT)15 | 0.038 | ||
| 22513313 | −415 | 789 | −212 | Intron 1 | (−) | gcggtccac▵CCT>−/−)cctcctcctc | (CCT)17 | 0.033 | ||
| 22513313 | −415 | 789 | −212 | Intron 1 | (−) | gcggtccac▵CCT>−/−)cctcctcctc | (CCT)19 | 0.008 | ||
| 22513312 | −414 | 790 | −211 | Intron 1 | (+) | ggtggaggag(G>A)aggaggagga | A | 0.038 | ||
| 22513307 | −409 | 795 | −206 | Intron 1 | (+) | gtggtggtgg(A>T)ggaggaggag | T | 0.169 | ||
| 22512479 | 420 | Intron 2 | (−) | gaggagaag(T>C)gggtaggagt | C | 0.012 | ||||
| 22511603 | 1296 (450) | Exon3 | (−) | M87V | cgcgggcgcc(A>G)tggcgggcat | G | 0.004 | |||
| 22511571 | 1328 (482) | rs1800847 | Exon3 | (−) | A97A | ccggggcggc(C>T)ggcgtggcgg | T | 0.044 | ||
| 22511501 | 1398 (552) | Exon3 | (−) | M121V | ggccggggcc(A>G)tgggcggcct | G | 0.004 | |||
| 22511052 | 1848 (1001) | Exon3 | (+) | A270A | tgccgctgcc(G>A)gcggcgcctg | A | 0.004 | |||
| 22511025 | 1874 (1028) | rs1203910 | Exon3 | (+) | G279G | aggcctgggc(T>C)ccggcggccg | C | 0.056 | ||
| 22510674 | 2225 (1379) | rs1212275 | Exon3 | (+) | Q396Q | ttttgtgggg(C>T)tggtggtggt | T | 0.160 | ||
| 22510438 | 2461 | rs1055080 | UTR | (−) | ggatcgagg(C>T)aagtgagaga | A | 0.070 | |||
| 22510311 | 2588 | rs1974 | UTR | (−) | ccgctgcagc(C>T)gttccgtccc | G | 0.054 | |||
| 22509981 | 2918 | UTR | (+) | cttttttttt(T>C)ctttttcttg | C | 0.045 | ||||
| 22509960 | 2939 | UTR | (+) | accgtgtca(G>T)attgggaatg | T | 0.008 | ||||
| 22509953 | 2946 | UTR | (+) | ggatttcacc(G>A)tgtcaagatt | A | 0.020 | ||||
| 22509865 | 3034 | UTR | (+) | tggaactctg(G>A)cccttgcagc | A | 0.004 |
wrt, with respect to; prom., promoter.
↵a NC_000020 (FoxA2: 22509823 … 0.22514102) from the human genome assembly build 36.2.
↵b Complement; ATG = 22512898-96; with the nucleotide 22512898 being +1, the base immediately 5′ is −1.
↵c Position of the FoxA2 transcription start site (TSS) in NC_000020 (build 36.2): for isoform 1 (TSS0.1) = 22513101; for isoform 2 (TSS0.2) = 22514102; with the base immediately 5′ to the TSS being −1.
↵d Strand orientation with respect to GenBank sequence.
↵e Minor allele frequency; polymorphisms significantly associated with FoxA2 or target gene expression are in bold.