From: Functional intronic polymorphisms: Buried treasure awaiting discovery within our genes
Gene | Disease/phenotype | Chromosomal location | Polymorphism, intronic location and dbSNP number | Consequences for gene expression or mRNA splicing | Reference |
---|---|---|---|---|---|
AGTR2 | Predisposition to congenital anomalies of the kidney and urinary tract | Xq22-q23 | IVS1, AS, A > G, -29 (rs1403543) | SNP occurs within branchpoint motif and alters splicing efficiency | Nishimura et al. (1999)a |
BANK1 | Susceptibility to systemic lupus erythematosus | 4q23 | IVS1, AS, T > C, -43 (rs17266594) | SNP occurs within branchpoint motif and risk allele alters expression of alternative transcripts | Kozyrev et al. (2008)b |
CD244 | Susceptibility to rheumatoid arthritis | 1q23.1 | IVS3, AS, T > C, -164 (rs6682654) | Risk allele associated with increased transcriptional activity | Suzuki et al. (2008)c |
CD244 | Susceptibility to rheumatoid arthritis | 1q23.1 | IVS5, DS, G > A, +526 (rs3766379) | Risk allele associated with increased transcriptional activity | Suzuki et al. (2008)c |
COL1A1 | Reduced bone density/osteoporosis | 17q21.33 | IVS1, AS, G > T, -440 (rs1800012) | SNP occurs within Sp1-binding site; risk allele alters Sp1 binding and transcriptional activity | Mann et al. (2001)d |
CXCR3 | Variation in immune cell response to chemokine-cytokine signals | Xq13 | IVS1, DS, G > A, +234 (rs2280964) | Risk allele associated with reduced CXCR3 gene expression | Choi et al. (2008)e |
CYP2D6 | Intermediate metaboliser (reduced expression of CYP2D6) | 22q13.1 | IVS6, DS, G > A, +39 (rs28371725) | Increased level (7.3-fold) of non-functional splice variant transcript lacking exon 6 and reduced level (2.9-fold) of functional transcript | Toscano et al. (2006)f |
DRD2 | Reduced DRD2 expression | 11q22-q23 | IVS1, DS, A > G, +3850 (rs2734836) | Risk allele associated with increased binding of transcriptional repressor (Freud-1) leading to reduced DRD2 expression | Rogaeva et al. (2007)g |
DRD2 | Reduced DRD2 expression | 11q23 | IVS6, AS, C > A, -83 (rs 1076560) | Risk allele alters expression of alternative transcripts | Zhang et al. (2007)h |
F2 | Elevated prothrombin level/thrombosis | 11p11-q12 | IVS13, AS, A > G, -59 | Risk allele influences splicing efficiency | von Ahsen & Oellerich (2004)i |
FGFR2 | Susceptibility to breast cancer | 10q26 | IVS2, DS, T > C,+ 12912 (rs2981578) | Risk allele alters binding affinity for transcription factors Oct-1/Runx2, leading to increased FGFR2 expression | Meyer et al. (2008)j |
FOXP3 | Susceptibility to psoriasis | Xp11.23 | IVS1, DS, A > C, +2882 (rs3761548) | Risk allele causes loss of binding of E47 and c-Myb, leading to reduced FOXP3 transcription | Shen et al. (2010)k |
GFPT1 | Reduced GFPT1 expression | 2p13 | IVS1, DS, T > C, +36 (rs6720415) | SNP occurs within GC box and risk allele decreases transcriptional activity | Kunika et al. (2006)[1] |
GSK3B | Risk of Parkinson's disease | 3q13.3 | IVS5, AS, T > C, -157 (rs6438552) | Risk allele associated with increased level of GSK3B transcripts lacking exons 9 and 11 | Kwok et al. (2005)m |
IRF4 | Risk of childhood acute lymphoblastic leukaemia in males | 6p25-p23 | IVS4, DS, C > T, +386 (rs12203592) | Risk allele increases IRF4 promoter activity/expression | Do et al. (2010)n |
LTA | Susceptibility to myocardial infarction | 6p21.3 | IVS1, AS, G > A, -198 (rs909253) | Risk allele associated with increased transcriptional activity | Ozaki et al. (2002)o |
NLRP3 | Susceptibility to food-induced anaphylaxis | 1q44 | IVS7, AS, C > T, -202 (rs4612666) | Risk allele increases enhancer activity by 20% | Hitomi et al. (2009)p |
SCG3 | Association with obesity | 15q21 | IVS1, DS, G > A, +190 (rs16964476) | Risk allele alters transcriptional activity | Tanabe et al. (2007)q |
TH | Risk of essential tension | 11p15.5 | IVS12, DS, T > C, +127 (rs2070762) | Risk allele associated with increased transcriptional activity | Wang et al. (2008)r |
USF1 | Association with familial combined hyperlipidaemia | 1q22-q23 | IVS7, AS, G > A, -100 (rs2073658) | SNP alleles exhibit differential binding to nuclear proteins. USF1-regulated genes are differentially regulated, depending on the identity of the rs2073658 allele | Naukkarinen et al. (2005)s Naukkarinen et al. (2009)t |