Background
Methods
Study subjects
SNP genotyping
Statistical analyses
Bioinformatics prediction and expression quantitative trait loci (eQTL) analysis
Results
Population characteristics
SNPs and the risk of CRC
SNP_ID | Gene | Chromosome | Position | Allele | Minor allele frequency | HWE p value | OR (95% CI) |
p
a
| |
---|---|---|---|---|---|---|---|---|---|
Case | Control | ||||||||
rs3783550 | IL1A | 2q13 | 113,532,885 | T/G | 0.358 | 0.326 | 0.399 | 1.15 (0.91–1.45) | 0.222 |
rs3783546 | IL1A | 2q13 | 113,534,830 | C/G | 0.353 | 0.325 | 0.458 | 1.13 (0.90–1.42) | 0.296 |
rs2856838 | IL1A | 2q13 | 113,539,972 | A/G | 0.256 | 0.247 | 0.319 | 1.04 (0.81–1.35) | 0.716 |
rs1609682 | IL1A | 2q13 | 113,540,205 | T/G | 0.354 | 0.327 | 0.398 | 1.12 (0.90–1.42) | 0.298 |
rs3783521 | IL1A | 2q13 | 113,543,577 | G/A | 0.356 | 0.326 | 0.399 | 1.14 (0.91–1.44) | 0.252 |
SNP_ID | Genotypes | Controls, n (%) | Patients, n (%) | Without adjustment | With adjustment | ||
---|---|---|---|---|---|---|---|
OR (95% CI) |
p
a
| OR (95% CI) |
p
b
| ||||
rs3783550 | |||||||
G/G | 206 (44.5%) | 103 (41.7%) | 1.00 | 1.00 | |||
Codominant | G/T | 212 (45.8%) | 111 (44.9%) | 1.05 (0.75–1.46) | 0.330 | 1.01 (0.72–1.44) | 0.310 |
T/T | 45 (9.7%) | 33 (13.4%) | 1.47 (0.88–2.44) | 1.49 (0.88–2.52) | |||
Dominant (ref: G/G) | G/T-T/T | 257 (55.5%) | 144 (58.3%) | 1.12 (0.82–1.53) | 0.470 | 1.10 (0.79–1.52) | 0.580 |
Recessive (ref: G/G + G/T) | T/T | 45 (9.7%) | 33 (13.4%) | 1.43 (0.89–2.31) | 0.140 | 1.48 (0.90–2.43) | 0.130 |
rs3783546 | |||||||
G/G | 206 (44.7%) | 104 (41.9%) | 1.00 | 1.00 | |||
Codominant | G/C | 210 (45.5%) | 113 (45.6%) | 1.07 (0.77–1.48) | 0.500 | 1.02 (0.73–1.45) | 0.500 |
C/C | 45 (9.8%) | 31 (12.5%) | 1.36 (0.82–2.28) | 1.37 (0.80–2.34) | |||
Dominant (ref: G/G) | G/C-C/C | 255 (55.3%) | 144 (58.1%) | 1.12 (0.82–1.53) | 0.480 | 1.09 (0.78–1.51) | 0.620 |
Recessive (ref: G/G + G/C) | C/C | 45 (9.8%) | 31 (12.5%) | 1.32 (0.81–2.15) | 0.270 | 1.35 (0.82–2.24) | 0.240 |
rs2856838 | |||||||
G/G | 257 (55.8%) | 143 (57.7%) | 1.00 | 1.00 | |||
Codominant | G/A | 180 (39%) | 83 (33.5%) | 0.83 (0.60–1.15) | 0.096 | 0.83 (0.58–1.17) | 0.063 |
A/A | 24 (5.2%) | 22 (8.9%) | 1.65 (0.89–3.04) | 1.84 (0.96–3.50) | |||
Dominant (ref:G/G) | G/A-A/A | 204 (44.2%) | 105 (42.3%) | 0.93 (0.68–1.26) | 0.620 | 0.94 (0.68–1.31) | 0.720 |
Recessive (ref: G/G + G/A) | A/A | 24 (5.2%) | 22 (8.9%) | 1.77 (0.97–3.23) | 0.064 |
1.98 (1.05–3.72)
|
0.036
|
rs1609682 | |||||||
G/G | 205 (44.4%) | 105 (42.5%) | 1.00 | 1.00 | |||
Codominant | G/T | 212 (45.9%) | 109 (44.1%) | 1.00 (0.72–1.40) | 0.350 | 0.97 (0.68–1.37) | 0.310 |
T/T | 45 (9.7%) | 33 (13.4%) | 1.43 (0.86–2.38) | 1.45 (0.85–2.45) | |||
Dominant (ref: G/G) | G/T-T/T | 257 (55.6%) | 142 (57.5%) | 1.08 (0.79–1.47) | 0.630 | 1.05 (0.76–1.46) | 0.770 |
Recessive (ref: G/G + G/T) | T/T | 45 (9.7%) | 33 (13.4%) | 1.43 (0.89–2.31) | 0.150 | 1.47 (0.89–2.42) | 0.130 |
rs3783521 | |||||||
A/A | 206 (44.5%) | 103 (41.7%) | 1.00 | 1.00 | |||
Codominant | G/A | 212 (45.8%) | 112 (45.3%) | 1.06 (0.76–1.47) | 0.400 | 1.02 (0.72–1.44) | 0.410 |
G/G | 45 (9.7%) | 32 (13.0%) | 1.42 (0.85–2.37) | 1.42 (0.84–2.42) | |||
Dominant (ref: A/A) | G/A-G/G | 257 (55.5%) | 144 (58.3%) | 1.12 (0.82–1.53) | 0.470 | 1.09 (0.79–1.51) | 0.610 |
Recessive (ref: A/A + G/A) | G/G | 45 (9.7%) | 32 (13.0%) | 1.38 (0.85–2.24) | 0.190 | 1.41 (0.86–2.33) | 0.180 |
SNP_ID | Genotypes | Male | OR (95% CI) |
p
a
| Female | OR (95% CI) |
p
b
| ||
---|---|---|---|---|---|---|---|---|---|
Controls, n(%) | Patients, n(%) | Controls, n(%) | Patients, n(%) | ||||||
rs3783550 | |||||||||
G/G | 113 (42.6%) | 62 (43.7%) | 1.00 | 93 (47.0%) | 41 (39.0%) | 1.00 | |||
Codominant | G/T | 123 (46.4%) | 63 (44.4%) | 0.85 (0.53–1.38) | 0.800 | 89 (45.0%) | 48 (45.7%) | 1.22 (0.73–2.04) | 0.096 |
T/T | 29 (10.9%) | 17 (12.0%) | 0.96 (0.47–1.98) | 16 (8.1%) | 16 (15.2%) | 2.41 (1.09–5.34) | |||
Dominant (ref: G/G) | G/T-T/T | 152 (57.4%) | 80 (56.3%) | 0.88 (0.56–1.38) | 0.560 | 105 (53.0%) | 64 (61.0%) | 1.40 (0.86–2.27) | 0.180 |
Recessive (ref: G/G + G/T) | T/T | 29 (10.9%) | 17 (12.0%) | 1.05 (0.53–2.06) | 0.900 | 16 (8.1%) | 16 (15.2%) |
2.17 (1.03–4.60)
|
0.043
|
rs3783546 | |||||||||
G/G | 113 (42.8%) | 62 (43.4%) | 1.00 | 93 (47.2%) | 42 (40.0%) | 1.00 | |||
Codominant | G/C | 122 (46.2%) | 65 (45.5%) | 0.87 (0.54–1.40) | 0.850 | 88 (44.7%) | 48 (45.7%) | 1.21 (0.72–2.01) | 0.170 |
C/C | 29 (11.0%) | 16 (11.2%) | 0.92 (0.44–1.90) | 16 (8.1%) | 15 (14.3%) | 2.18 (0.97–4.85) | |||
Dominant (ref: G/G) | G/C-C/C | 151 (57.2%) | 81 (56.6%) | 0.88 (0.56–1.38) | 0.580 | 104 (52.8%) | 63 (60.0%) | 1.35 (0.83–2.20) | 0.220 |
Recessive (ref: G/G + G/C) | C/C | 29 (11.0%) | 16 (11.2%) | 0.98 (0.49–1.95) | 0.960 | 16 (8.1%) | 15 (14.3%) | 1.98 (0.93–4.21) | 0.080 |
rs2856838 | |||||||||
G/G | 142 (54.0%) | 88 (61.5%) | 1.00 | 115 (58.1%) | 55 (52.4%) | 1.00 | |||
Codominant | G/A | 109 (41.4%) | 47 (32.9%) | 0.68 (0.42–1.10) | 0.260 | 71 (35.9%) | 36 (34.3%) | 1.06 (0.63–1.77) | 0.078 |
A/A | 12 (4.6%) | 8 (5.6%) | 1.07 (0.39–2.94) | 12 (6.1%) | 14 (13.3%) | 2.63 (1.13–6.15) | |||
Dominant (ref: G/G) | G/A-A/A | 121 (46.0%) | 55 (38.5%) | 0.72 (0.46–1.14) | 0.160 | 83 (41.9%) | 50 (47.6%) | 1.27 (0.79–2.06) | 0.330 |
Recessive (ref: G/G + G/A) | A/A | 12 (4.6%) | 8 (5.6%) | 1.24 (0.46–3.36) | 0.670 | 12 (6.1%) | 14 (13.3%) |
2.58 (1.13–5.87)
|
0.024
|
rs1609682 | |||||||||
G/G | 113 (42.6%) | 64 (44.8%) | 1.00 | 92 (46.7%) | 41 (39.4%) | 1.00 | |||
Codominant | G/T | 123 (46.4%) | 62 (43.4%) | 0.81 (0.50–1.30) | 0.670 | 89 (45.2%) | 47 (45.2%) | 1.18 (0.70–1.98) | 0.100 |
T/T | 29 (10.9%) | 17 (11.9%) | 0.93 (0.45–1.90) | 16 (8.1%) | 16 (15.4%) | 2.39 (1.08–5.31) | |||
Dominant (ref: G/G) | G/T-T/T | 152 (57.4%) | 79 (55.2%) | 0.83 (0.53–1.31) | 0.420 | 105 (53.3%) | 63 (60.6%) | 1.36 (0.83–2.21) | 0.220 |
Recessive (ref: G/G + G/T) | T/T | 29 (10.9%) | 17 (11.9%) | 1.03 (0.53–2.04) | 0.920 | 16 (8.1%) | 16 (15.4%) |
2.20 (1.04–4.65)
|
0.040
|
rs3783521 | |||||||||
A/A | 113 (42.6%) | 62 (43.7%) | 1.00 | 93 (47.0%) | 41 (39.0%) | 1.00 | |||
Codominant | G/A | 123 (46.4%) | 64 (45.1%) | 0.86 (0.53–1.38) | 0.820 | 89 (45.0%) | 48 (45.7%) | 1.22 (0.73–2.04) | 0.110 |
G/G | 29 (10.9%) | 16 (11.3%) | 0.92 (0.44–1.90) | 16 (8.1%) | 16 (15.2%) | 2.36 (1.07–5.22) | |||
Dominant (ref: A/A) | G/A-G/G | 152 (57.4%) | 80 (56.3%) | 0.87 (0.55–1.37) | 0.540 | 105 (53.0%) | 64 (61.0%) | 1.39 (0.86–2.26) | 0.180 |
Recessive (ref: A/A + G/A) | G/G | 29 (10.9%) | 16 (11.3%) | 0.99 (0.50–1.97) | 0.980 | 16 (8.1%) | 16 (15.2%) |
2.13 (1.01–4.49)
|
0.048
|
CRC and haplotypes on chromosome 2q13
Block | Haplotype | Freq (case) | Freq (control) | OR (95% CI) |
p
a
|
---|---|---|---|---|---|
rs3783550/rs3783546/rs2856838 /rs1609682/rs3783521 | GGGGA | 0.640 | 0.674 | 1.00 | |
TCATG | 0.250 | 0.249 | 1.07 (0.83–1.39) | 0.600 | |
TCGTG | 0.100 | 0.077 | 1.33 (0.90–1.97) | 0.150 |