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1Department of Internal Medicine and Clinical Biochemistry Laboratory, King Abdulaziz Hospital, National Guard Health Affairs, Al-Ahsa, Saudi Arabia.
2Department of Medical Biochemistry, Arabian Gulf University College of Medicine and Medical Sciences, Manama, Bahrain.
3Clinical Biochemistry Laboratory, Salmaniya Medical Complex, Manama, Bahrain.
4Cell and Developmental Biology, Division of Biosciences, University College London, London, United Kingdom.
Copyright © 2017 Korean Endocrine Society
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
CONFLICTS OF INTEREST: No potential conflict of interest relevant to this article was reported.
Values are expressed as median (interquartile range).
HbA1c, hemoglobin A1c; SNP, single-nucleotide polymorphism.
aMann-Whitney rank sum test; bKruskal-Wallis 1-way analysis of variance on ranks; cThe numbers of carriers of rare homozygous, heterozygous, and common homozygous genotypes, respectively, for each SNP.
Values are expressed as median (interquartile range).
HOMA, homeostatic model assessment; SNP, single-nucleotide polymorphism.
aMann-Whitney rank sum test; bKruskal-Wallis 1-way analysis of variance on ranks; cThe numbers of carriers of the rare homozygous, heterozygous, and common homozygous genotypes, respectively, for each SNP.
SNP | CHR | Cytogenic band | CHR locus | Gene site | SNP type |
---|---|---|---|---|---|
rs2075356 CT (+3056 TC) | 3 | 3p25.3b | 10328809 | Intron | Transition substitution |
rs696217 GT (Leu72Met) | 3 | 3p25.3b | 10331457 | Intron | Transversion substitution |
rs27647 CT (–604 GA) | 3 | 3p25.3b | 10332468 | Intron | Transition substitution |
rs3755777 CG (–1500 CG) | 3 | 3p25.3b | 10333364 | Intron | Transversion substitution |
rs509030 GC | 3 | 3q26.31 | 6693674 | Unknown | Transversion substitution |
SNP | Subjects | ||||||
---|---|---|---|---|---|---|---|
HWE, X2 (all subjects) | MAF (chi-square test) | Rare genotype prevalence, % (no./total no.) | |||||
Healthy | T2DM | P value | Healthy | T2DM | P valuea | ||
rs2075356 CT | 0.56 | 0.096 (18/188) | 0.114 (21/184) | 0.682 | 0.00 (0/94) | 3.3 (3/92) | 0.237 |
rs696217 TG | 0.85 | 0.036 (7/192) | 0.054 (10/186) | 0.573 | 0 (0/96) | 1.08 (1/93) | 0.987 |
rs27647 CT | 1.48 | 0.355 (66/186) | 0.34 (62/182) | 0.860 | 14.0 (13/93) | 14.3 (13/91) | 0.879 |
rs3755777 GC | 3.72 | 0.181 (34/188) | 0.156 (29/186) | 0.613 | 6.4 (6/94) | 3.2 (3/93) | 0.505 |
rs509030 GC | 2.36 | 0.300 (51/170) | 0.317 (57/180) | 0.825 | 11.8 (10/85) | 12.2 (11/90) | 0.889 |
Haplotypes (relatively common ≥3%) | Haplotype prevalence | P valuea | |
---|---|---|---|
Non-diabetic (n=85) | T2DM (n=89) | ||
GG TT TT GC CG | 5.9 (5) | 0 | 0.062 |
GG TT TT GC CC | 3.5 (3) | 6.7 (6) | 0.539 |
GG TT TT CC CG | 7.1 (6) | 6.7 (6) | 0.828 |
GG TT TT CC CC | 9.4 (8) | 6.7 (6) | 0.712 |
GG TT CT CC CG | 4.7 (4) | 1.1 (1) | 0.337 |
GG CT TT GG CC | 4.7 (4) | 0 | 0.118 |
GG CT TT GC CC | 10.6 (9) | 6.7 (6) | 0.526 |
GG CT TT CC CG | 4.7 (4) | 9 (8) | 0.415 |
GG CT TT CC CC | 11.8 (10) | 14.6 (13) | 0.742 |
GG CT CT GC CC | 4.7 (4) | 0 | 0.118 |
GG CC TT GC CC | 3.5 (3) | 9 (8) | 0.243 |
Total | 11 haplotype | 8 haplotype | |
Rare haplotypes (<3%) | |||
Number | 16 | 20 | |
Carrier | 29.4 (25) | 39.3 (35) | |
Total no. of haplotypes | 27 (11+16) | 28 (8+20) | 0.905 |
SNP (all study subjects) | HbA1c, % | ||||||
---|---|---|---|---|---|---|---|
Allele carrier | Genotype carrier | ||||||
Minor | Non-minor | P valuea | Rare homozygous | Heterozygous | Common homozygous | P valueb | |
rs2075356 CT (3, 33, 150)c | 6.00 (5.50–7.00) | 6.05 (5.50–8.10) | 0.484 | 6.20 (6.05–7.78) | 5.80 (5.48–7.00) | 6.05 (5.50–8.10) | 0.539 |
rs696217 TG (1, 15, 173) | 5.7 (5.5–8.0) | 6.0 (5.5–8.0) | 0.941 | - | - | - | - |
rs27647 CT (26, 76, 82) | 6.15 (5.40–8.00) | 6.0 (5.5–7.9) | 0.853 | 6.25 (5.7–8.30) | 5.95 (5.40–7.95) | 6.0 (5.50–7.90) | 0.784 |
rs3755777 GC (9, 45, 133) | 5.90 (5.20–7.90) | 6.20 (5.60–8.03) | 0.207 | 5.40 (4.78–7.93) | 6.00 (5.43–7.80) | 6.20 (5.60–8.03) | 0.202 |
rs509030 GC (21, 66, 88) | 6.00 (5.5–7.75) | 6.20 (5.50–8.10) | 0.488 | 6.20 (5.58–8.80) | 6.00 (5.50–7.30) | 6.20 (5.50–8.10) | 0.431 |
SNP (all study subjects) | HOMA index | ||||||
---|---|---|---|---|---|---|---|
Minor allele | Genotype carriers | ||||||
Carriers | Non-carrier | P valuea | Rare homozygous | Heterozygous | Common homozygous | P valueb | |
rs2075356 CT (3, 33, 150)c | 1.70 (1.25–2.75) | 2.10 (1.50–3.50) | 0.132 | 1.40 (1.33–5.30) | 1.70 (1.18–2.73) | 2.1 (1.50–3.50) | 0.319 |
rs696217 TG (1, 15, 173) | 2.4 (1.6–4.2) | 2.0 (1.4–3.4) | 0.517 | - | - | - | - |
rs27647 CT (26, 76, 82) | 2.2 (1.50–3.60) | 1.80 (1.30–3.00) | 0.165 | 2.25 (1.6–3.1) | 2.15 (1.4–4.15) | 1.8 (1.3–3.0) | 0.369 |
rs3755777 GC (9, 45, 133) | 2.00 (1.20–3.10) | 2.10 (1.50–3.50) | 0.434 | 1.60 (1.10–2.50) | 2.20 (1.20–3.65) | 2.10 (1.50–3.50) | 0.345 |
rs509030 GC (21, 66, 88) | 2.00 (1.50–3.28) | 2.25 (1.40–3.60) | 0.519 | 1.60 (1.38–2.08) | 2.10 (1.50–3.40) | 2.25 (1.40–3.60) | 0.386 |
SNP (all study subjects) | Ghrelin levels, pmol/L | ||||||
---|---|---|---|---|---|---|---|
Minor allele | Genotype carrier | ||||||
Carrier | Non-carrier | P valuea | Rare homozygous | Heterozygous | Common homozygous | P valueb | |
rs2075356 CT (3, 27, 127)c | 16.0 (14.2–21.4) | 14.8 (10.2–21.4) | 0.192 | 15.7 (14.8–19.1) | 16.3 (14.0–22.5) | 14.8 (10.2–21.4) | 0.425 |
rs696217 TG (1, 13, 145) | 17.2 (14.2–22.0) | 15.13 (10.9–20.9) | 0.182 | - | - | - | - |
rs27647 CT (23, 60, 72) | 14.8 (10.7–22.0) | 15.7 (12.2–21.1) | 0.762 | 16.9 (9.9–23.6) | 14.8 (11.7–19.0) | 15.7 (12.2–21.1) | 0.640 |
rs3755777 GC (6, 41, 110) | 15.1 (10.8–19.3) | 15.3 (11.6–22.3) | 0.345 | 12.6 (8.0–19.3) | 15.1 (12.0–19.7) | 15.3 (11.6–22.3) | 0.477 |
rs509030 GC (17, 57, 78) | 15.1 (11.0–20.8) | 15.1 (11.6–21.4) | 0.808 | 14.2 (9.4–21.5) | 15.4 (12.1–20.1) | 15.1 (11.6–21.4) | 0.791 |
SNP, single-nucleotide polymorphism; CHR, chromosome.
MAF, minor allele frequency; SNP, single-nucleotide polymorphism; T2DM, type 2 diabetes mellitus; HWE, Hardy-Weinberg equilibrium. aChi-square test.
Values are expressed as percentage (number). Total number of shared haplotypes ( SNP, single-nucleotide polymorphism; T2DM, type 2 diabetes mellitus. aChi-square test.
Values are expressed as median (interquartile range). HbA1c, hemoglobin A1c; SNP, single-nucleotide polymorphism. aMann-Whitney rank sum test; bKruskal-Wallis 1-way analysis of variance on ranks; cThe numbers of carriers of rare homozygous, heterozygous, and common homozygous genotypes, respectively, for each SNP.
Values are expressed as median (interquartile range). HOMA, homeostatic model assessment; SNP, single-nucleotide polymorphism. aMann-Whitney rank sum test; bKruskal-Wallis 1-way analysis of variance on ranks; cThe numbers of carriers of the rare homozygous, heterozygous, and common homozygous genotypes, respectively, for each SNP.
Values are expressed as median (interquartile range). SNP, single-nucleotide polymorphism. aMann-Whitney rank sum test; bKruskal-Wallis 1-way analysis of variance on ranks; cThe numbers of carriers of the rare homozygous, heterozygous, and common homozygous genotypes, respectively, for each SNP.