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Table 1 - Genetic Variants Available, by Gene

View Table 2 - Genes Available, By Pathway[PDF 101KB]

Gene symbol Gene name Chromosomal position of gene Variant (dbSNP ID)* Nucleotide change† Amino acid change† Cellular or physiological pathway(s)‡
ABCB1
ATP-binding cassette, sub-family B (MDR/TAP), member 1
7q21.1
rs1045642
Ex27-55T>C T3435C
Ile1145Ile
Xenobiotic metabolism
ACE
Angiotensin I converting enzyme (peptidyl-dipeptidase A) 1
17q23.3
rs4646994
289-bp Alu insertion/deletion in intron 16
  Blood pressure regulation; Nutrient metabolism§
ADH1B
Alcohol dehydrogenase IB (class I), beta polypeptide
4q21-q23
rs1229984
Ex3+23G>A
Arg48His
Nutrient metabolism; Xenobiotic metabolism
rs17033
Ex9+77A>G
rs2066702
Ex9+5C>T
Arg370Cys
ADH1C
Alcohol dehydrogenase 1C (class I), gamma polypeptide
4q21-q23
rs1693482
Ex6-14G>A
Arg272Gln
Nutrient metabolism; Xenobiotic metabolism
rs698
Ex8-56A>G
Ile350Val
ADRB1
Adrenergic, beta-1-, receptor
10q24-q26
rs1801252
Ex1+231A>G
Ser49Gly
Blood pressure regulation, Cardiac function; Nutrient metabolism
ADRB2
Adrenergic, beta-2-, receptor, surface
5q31-q32
rs1042713
Ex1+265G>A
Gly16Arg
Blood pressure regulation, Cardiac function; Nutrient metabolism
rs1042714
Ex1+298G>C
Glu27Gln
ADRB3
Adrenergic, beta-3-, receptor
8p12-p11.2
rs4994
Ex1+387T>C
Trp64Arg
Nutrient metabolism
ALAD
Aminolevulinate, delta-, dehydratase
9q33.1
rs1800435
Ex4+13G>C G177C
 
Lys68Asn Lys88Asn
Nutrient metabolism; Xenobiotic metabolism
B9D2
B9 protein domain 2
19q13.2
rs1800468
Ex4-262G>A
-800G>A of TGFB1
Unknown
rs1800469
308bp 3' of STP C>T  
-509C>T of TGFB1
CAPN10
Calpain 10
2q37.3
rs3792267
IVS3-176G>A
Apoptosis; Nutrient metabolism
CAT
Catalase
11p13
rs769214
-843A>G 
Metabolism of free radicals/Oxidative stress; Nutrient metabolism
CBS
Cystathionine-beta-synthase
21q22.3
no rs number
844ins68 (68-bp insertion in exon 8)
Nutrient metabolism
CCL5
Chemokine (C-C motif) ligand 5
17q11.2-q12
rs2280788
-95C>G
Cell migration/motility; Immunity and inflammation
CCR2
Chemokine (C-C motif) receptor 2
3p21.31
rs1799864
Ex2+241G>A
Val64Ile
Cell migration/motility; Immunity and inflammation
CXCL12
Chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1)
10q11.1
rs169097
Ex5+709C>T
Cell migration/motility; Immunity and inflammation
CYP1A1
Cytochrome P450, family 1, subfamily A, polypeptide 1
15q22-q24
rs2472299
-17961C>T
Nutrient metabolism; Xenobiotic metabolism
rs2606345
IVS1+606G>T
CYP1A2
Cytochrome P450, family 1, subfamily A, polypeptide 2
15q24
rs11854147
5341bp 3' of STP C>T
Nutrient metabolism; Xenobiotic metabolism
rs2069514
-3859G>A
rs4886406
9773bp 3' of STP T>G
CYP1B1
Cytochrome P450, family 1, subfamily B, polypeptide 1
2p21
rs1056836
Ex3+251G>C
Val432Leu
Nutrient metabolism; Xenobiotic metabolism
rs1056837
Ex3+304T>C
Asp449Asp
rs162557
-2919C>T
CYP2A6
Cytochrome P450, family 2, subfamily A, polypeptide 6
19q13.2
rs1801272
Ex3-15T>A
Leu160His
Nutrient metabolism; Xenobiotic metabolism
CYP2C19
Cytochrome P450, family 2, subfamily C, polypeptide 19
10q24.1-q24.3
rs4986893
Ex4-7G>A
Trp212Stp
Nutrient metabolism; Xenobiotic metabolism
rs4986894
-97T>C
CYP2C9
Cytochrome P450, family 2, subfamily C, polypeptide 9
10q24
rs1057910
Ex7-75A>C
Ile359Leu
Nutrient metabolism; Xenobiotic metabolism
CYP2E1
Cytochrome P450, family 2, subfamily E, polypeptide 1
10q24.3-qter
rs2031920
-1054C>T
-1053C>T
Nutrient metabolism; Xenobiotic metabolism
CYP3A4
Cytochrome P450, family 3, subfamily A, polypeptide 4
7q21.1
rs2740574
-391A>G
Nutrient metabolism; Xenobiotic metabolism
F2
Coagulation factor II (thrombin)
11p11-q12
rs1799963
Ex14-1G>A
Cell migration/motility; Hemostasis
F5
Coagulation factor V (proaccelerin, labile factor)
1q23
rs6025
Ex10-11G>A
Arg534Gln
Hemostasis
FAM82A**
Family with sequence similarity 82, member A
2p22.2
rs163086
IVS10-1363C>T
Unknown
FCGR2A
Fc fragment of IgG, low affinity IIa, receptor (CD32)
1q23
rs1801274
Ex4-120A>G
His166Arg His167Arg
Immunity and inflammation
FGB
Fibrinogen beta chain
4q28
rs1800790
-462G>A
Cellular adhesion; Hemostasis
IL10
Interleukin 10
1q31-q32
rs1800871
-853C>T
-819C>T
Apoptosis, Cell cycle, Cellular growth and differentiation; Immunity and inflammation
rs1800872
-626C>A
-592C>A
rs1800896
-1116A>G
-1082A>G
IL1B
Interleukin 1, beta
2q14
rs1143623
-2022G>C
Apoptosis, Cellular growth and differentiation; Immunity and inflammation
IL4
Interleukin 4
5q31.1
rs2243248
-1098T>G
Apoptosis, Cellular growth and differentiation; Immunity and inflammation
rs2243250
-588C>T
-524C>T
-590C>T
rs2243270
IVS2-1297A>G
IL4R
Interleukin 4 receptor
16p11.2-12.1
rs1801275
Ex12+828A>G
Gln576Arg
Apoptosis, Cellular growth and differentiation; Immunity and inflammation
rs1805015
Ex12+608T>C
Ser503Pro
ITGA2
Integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)
5q23-q31
rs1126643
Ex7-21C>T
Phe253Phe
Cellular adhesion, Cell migration/motility; Hemostasis
ITGB3
Integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)
17q21.32
rs5918
Ex3+11T>C
Leu59Pro
Apoptosis; Cellular adhesion, Cell migration/motility; Hemostasis
MBL2
Mannose-binding lectin (protein C) 2, soluble (opsonic defect)
10q11.2-q21
rs11003125
-618G>C
-550G>C
Immunity and inflammation
rs1800450
Ex1-27G>A
Gly54Asp
rs1800451
Ex1-18G>A
Gly57Glu
rs5030737
Ex1-34C>T
Arg52Cys
rs7096206
-289G<C
-221G>C
MTHFR
5,10-methylenetetrahydrofolate reductase (NADPH)
1p36.3
rs1801131
Ex8-62A>C 1298A>C
Glu429Ala
Nutrient metabolism
rs1801133
Ex5+79C>T 677C>T
Ala222Val
rs2066470
Ex2-120C>T
Pro39Pro
MTRR
5-methyltetrahydrofolate-homocysteine methyltransferase reductase
5p15.3-p15.2
rs1801394
Ex2-64A>G
Ile22Met Ile49Met
Nutrient metabolism
NAT2
N-acetyltransferase 2 (arylamine N-acetyltransferase)
8p22
rs1041983
Ex2+288C>T
Tyr94Tyr
Xenobiotic metabolism
rs1208
Ex2-367A>G
Lys268Arg
rs1799930
Ex2-580G>A
Arg197Gln
rs1801279
Ex2+197G>A
Arg64Gln
rs1801280
Ex2+347T>C
Ile114Thr
NOS2A
Nitric oxide synthase 2A (inducible, hepatocytes)
17q11.2-q12
rs1800482
G>C in promoter
Blood pressure regulation; Immunity and inflammation; Metabolism of free radicals/Oxidative stress; Nutrient metabolism
rs9282799
-2892C>T
-1173C>T
NOS3
Nitric oxide synthase 3 (endothelial cell)
7q36
rs1799983
Ex8-63G>T
Glu298Asp
Blood pressure regulation, Cardiac function; Hemostasis; Metabolism of free radicals/Oxidative stress; Nutrient metabolism
rs2070744
IVS1-762T>C  
-786T>C
NQO1
NAD(P)H dehydrogenase, quinone 1
16q22.1
rs10517
Ex6-457C>T
Nutrient metabolism; Xenobiotic metabolism
rs1800566
Ex6+40C>T 609C>T
Pro187Ser Pro149Ser Pro153Ser
rs34755915
IVS3+20G>A
rs689452
IVS1-27C>G
rs689453
Ex2+65G>A
Glu24Glu
OGG1
8-oxoguanine DNA glycosylase
3p26.2
rs1052133
Ex6-315C>G
Ser326Cys Pro332Ala
DNA Repair
PON1
Paraoxonase 1
7q21.3
rs662
Ex6+78A>G
Gln192Arg
Metabolism of free radicals/Oxidative stress; Xenobiotic metabolism
rs854560
Ex3+18T>A
Leu55Met
PPARG
Peroxisome proliferator-activated receptor gamma
3p25
rs1801282
Ex4-49C>G
Pro12Ala
Cellular growth and differentiation; Immunity and inflammation; Nutrient metabolism
SERPINE1
Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1
7q21.3-q22
rs1799762 rs1799768 rs1799889
4G/5G insertion/deletion in promoter
Cellular adhesion, Cell migration/motility; Hemostasis; Nutrient metabolism
TGFB1
Transforming growth factor, beta 1
19q13.1
rs1982073
Ex1-327C>T
Pro10Leu
Apoptosis, Cell cycle, Cellular growth and differentiation; Immunity and inflammation
TLR4
Toll-like receptor 4
9q32-q33
rs4986790
Ex4+636A>G
Asp299Gly
Immunity and inflammation
TNF
Tumor necrosis factor (TNF superfamily, member 2)
6p21.3
rs1800629
-487G>A
-308G>A
Apoptosis, Cell cycle, Cellular growth and differentiation; Immunity and inflammation; Nutrient metabolism
rs1800750
-555G>A
rs361525
-417G>A  
-238G>A
VDR
Vitamin D (1,25- dihydroxyvitamin D3) receptor
12q13.11
rs2239185
IVS8-3968C>T
Cellular growth and differentiation; Immunity and inflammation; Nutrient metabolism
rs731236
Ex11+32T>C
Ile352Ile
(TaqI variant)
XRCC1
X-ray repair complementing defective repair in Chinese hamster cells 1
19q13.2
rs1001581
IVS2-216G>A
DNA Repair
rs1799782
Ex6-22C>T
Arg194Trp
rs25486
IVS9-59A>G
rs25487
Ex10-4G>A
Arg399Gln
rs25489
Ex9+16G>A
Arg280His

Official gene symbols and names are from the HUGO Gene Nomenclature Committee. All chromosomal positions are from Entrez Gene.

* Unique identifier in the Entrez SNP (single nucleotide polymorphisim) database at NCBI.            
† Nucleotide and amino acid change information are from the SNP500 Cancer database and dbSNP. Alternate designations and additional locus information are given, if available. 
‡ Inclusion of genes in pathways is based on information gathered from the GeneCards database, the KEGG GENES database, and selected publications for ACE (1, 2), CAPN10 (3), and SERPINE1 (4-6).
§ Nutrient metabolism encompasses the intracellular and physiological metabolism of nucleotides, amino acids and proteins, carbohydrates (e.g., glucose), lipids, cofactors, vitamins, and hormones (e.g., estrogen).
B9D2 is a protein that lies partially within the TGFB1 promoter. Although within B9D2, these two SNPs are believed to be promoter polymorphisms of TGFB1.
** FAM82A is a hypothetical protein that lies immediately 5' of CYP1B1. This variant may be an intronic polymorphism of FAM82A or a CYP1B1 variant that lies 3’ of the gene


References

  1. Hu J, Igarashi A, Kamata M, et al. Angiotensin-converting enzyme degrades Alzheimer amyloid beta-peptide (A beta); retards A beta aggregation, deposition, fibril formation; and inhibits cytotoxicity. J Biol Chem 2001;276:47863-8.
  2. Sayed-Tabatabaei FA, Oostra BA, Isaacs A, et al. ACE polymorphisms. Circ Res 2006;98:1123-33.
  3. Turner MD, Cassell PG, Hitman GA. Calpain-10: from genome search to function. Diabetes Metab Res Rev 2005;21:505-14.
  4. Durand MK, Bodker JS, Christensen A, et al. Plasminogen activator inhibitor-I and tumour growth, invasion, and metastasis. Thromb Haemost 2004;91:438-49.
  5. Lijnen HR. Pleiotropic functions of plasminogen activator inhibitor-1. J Thromb Haemost 2005;3:35-45.
  6. Alessi MC, Juhan-Vague I. PAI-1 and the metabolic syndrome: links, causes, and consequences. Arterioscler Thromb Vasc Biol 2006;26:2200-7.
 
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