Table 2 Differential RADseq SNPs causing amino acid changes with unidirectional allele effect on TSC, TY and TSY in QUEST case-control populations
SNP position (v2.1.11) | Amino acid change | Locus PGSC0003 | Locus position [Mbp] (v4.03) | Annotation | Function category |
|---|---|---|---|---|---|
chr01:37,823,297 | G/R | DMG400036984 | chr01: 42.92 | Gene of unknown function | Unknown |
chr01:63,201,542 | M/K | DMG400025974 | chr01: 70.21 | EF hand family protein | Calcium binding (IPR002048)a |
chr01:63,201,571 | K/N | DMG400025974 | chr01: 70.21 | EF hand family protein | dito |
chr01:63,201,582 | V/F | DMG400025974 | chr01: 70.21 | EF hand family protein | dito |
chr01:76,804,110 | G/R | DMG400025760 | chr01: 83.89 | Homeobox protein HAT3.1 | Transcription regulation (uniprot/Q04996)b |
chr01:78,272,215 | H/Y | DMG400025931 | chr01: 85.36 | GTP-binding protein alpha subunit, gna | Signalling [59] |
chr01:78,272,224 | Y/D | DMG400025931 | chr01: 85.36 | GTP-binding protein alpha subunit, gna | dito |
chr02:46,113,238 | R/G | DMG400012646 | chr02: 47.66 | Conserved gene of unknown function | Unknown |
chr05:4,555,061 | D/G | DMG400018440 | chr05: 4.78 | Conserved gene of unknown function | Unknown |
chr05:5,636,330 | S/F | DMG400017641 | chr05: 5.99 | Conserved gene of unknown function | Unknown |
chr06:47,805,636 | C/G | DMG402027033 | chr06: 53.48 | Zinc finger family protein | Multiple regulatory functions [60] |
chr07:872,052 | I/L | DMG400011219 | chr07: 1.53 | Tetratricopeptide repeat protein | Protein-protein interactions, complex assembly (IPR013026) |
chr07:872,053 | I/N | DMG400011219 | chr07: 1.53 | Tetratricopeptide repeat protein | dito |
chr08:5,319,820 | L/F | DMG400005778 | chr08: 4.84 | NADPH-dependent thioredoxin reductase B | Defense to stress [61] |
chr10:1,920,325 | A/S | DMG400025036 | chr10: 1.91 | Nucleic acid binding protein | Unknown |
chr11:3,818,033 | T/I | DMG400016135 | chr11: 2.31 | Tyrosine phosphatase | Posttranlational regulation [62] |
chr11:9,422,323 | V/L | DMG400044200 | chr11: 9.48 | Gene of unknown function | Unknown |
chr11:36,440,960 | I/L | DMG400000457 | chr11: 39.25 | Lethal leaf spot 1 | Chlorophyll catabolism, cell death [63] |
chr11:36,440,962 | S/N | DMG400000457 | chr11: 39.25 | Lethal leaf spot 1 | dito |
chr12:50,607,969 | M/V | DMG400041652 | chr12: 52.23 | Microsomal oleic acid desaturase | Lipid metabolism |
chr12:50,608,022 | Q/H | DMG400041652 | chr12: 52.23 | Microsomal oleic acid desaturase | dito |
chr12:50,526,275 | D/N | DMG400011613 | chr12: 52.32 | ABC transporter family protein | Transport [64] |
chr12:51,537,813 | E/G | DMG400004984 | chr12: 53.87 | Conserved gene of unknown function | Unknown |
chr12:58,658,881 | P/S | DMG400023861 | chr12: 60.72 | Extensin Ext1 | Cell wall [57] |
chr12:58,658,917 | E/K | DMG400023861 | chr12: 60.72 | Extensin Ext1 | dito |
chr12:58,658,927 | S/L | DMG400023861 | chr12: 60.72 | Extensin Ext1 | dito |