Population Research

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.