Table 1.
Genetic variations associated with gastric cancer identified by GWAS.
|
Type |
-log10(P) |
Genomic position |
Locus including or closest to the SNP |
Gene name |
Description |
Function |
Variant associated with gastric cancer |
Position in the gene |
Amino acid change |
Corresponding locus in the strain 26 695 |
|---|---|---|---|---|---|---|---|---|---|---|
|
SNP |
5.5 |
533 482 |
91 bp upstream of HPF57_0521 [532 255–533391] (-) |
kch, trkA |
potassium channel |
potassium conductance regulator |
G |
|
HP0490 |
|
|
SNP |
5.5 |
256 111 |
HPF57_0250 [255 679–256476] (+) |
dsbG/K |
thiol:disulfide interchange protein |
disulfide bond formation for secretion |
A |
433 |
K145E |
HP0231 |
|
SNP |
5.2 |
155 782 |
HPF57_0151 [155 438–156307] (+) |
triH |
BIR, Dps/NapA, RAD21 similarity |
host interference? |
A |
345 |
K115K,X |
HP0130 |
|
SNP |
5.1 |
96 796 |
HPF57_0094 [95 423–96958] (-) |
tlpC |
chemotaxis sensor |
chemotaxis |
A |
163 |
K55E,Q |
HP0082 |
|
SNP |
5.0 |
1 459 449 |
HPF57_1382 [1 459 397–1460092] (+) |
ompA101 |
outer membrane protein of OmpA family |
uptake and outer membrane structure |
T |
53 |
V53A |
HP1467 |
|
SNP |
4.7 |
96 807 |
HPF57_0094 [95 423–96958] (-) |
tlpC |
methyl-accepting chemotaxis sensor |
chemotaxis |
C |
152 |
N51S |
HP0082 |
|
SNP |
4.6 |
1 434 839 |
HPF57_1355 [1 434 577–1435371] (-) |
isp |
inactive Ser protease |
inhibitor of proteases/chaperones? |
G |
533 |
G178E |
HP1440 |
|
SNP |
4.3 |
904 207 |
14 bp downstream of HPF57_0865 |
thiE |
thiamine-phosphate synthase |
supplying vitamin B1 |
A |
|
HP0776 |
|
|
SNP |
4.2 |
1 296 088 |
HPF57_1209 [1 295 855–1296457] (-) |
csd5 |
cell shape determinant |
helical cell shape |
A |
370 |
N124H,Y,D |
HP1250 |
|
SNP |
4.2 |
871 135 |
HPF57_0829 [870 769–873144] (-) |
fecA-2 |
iron importer in outer membrane |
iron uptake |
C |
2010 |
S670X,S |
HP0807 |
|
SNP |
4.2 |
839 132 |
29 bp upstream of HPF57_0798 [838 879–839103] (-) |
rpoZ |
RNA polymerase subunit omega |
prophage silencing? stringenet control? |
A |
|
HP0915 |
|
|
motif |
6.9 |
498631–498661 |
HPF57_0490 [497 344–498975] (-) |
hsdM |
Type I restriction enzyme M protein |
DNA methyltransferase |
not TAACGATAAC GATTTACACCT AAAGCTAGAC |
315–345 |
multiple e.g. D115D,X |
HP0463 |
|
motif |
5.6 |
1522425–1522455 |
HPF57_1436 [1 522 369–1524234] (-) |
recG |
DNA recombinase |
|
not ATTGACTTAG CCAAAGATGA AAACATTATCG |
1780–1810 |
multiple |
HP1523 |
|
motif |
5.5 |
978037–978077 |
HPF57_0925 [978 055–980244] (-) |
frpB-2 |
iron importer in outer membrane |
|
TTGAAATTTC TTATAAGTTT TAATAATGGA TCTAAAAATGA |
2168- C terminus-18bp downstream |
multiple |
HP_0915 |
position in F57 reference genome.
∗designated in this work.
isp, inactive serine protease; triH, triple halves.