APOE c.-24+69C>G (rs440446)

Other Names: rs440446, +113C/G, IE1, IVS1+69, +969


Clinical Phenotype: Alzheimer's Disease, Multiple Conditions
Reference Assembly: GRCh37/hg19
Position: Chr19:45409167 C>G
Transcript: NM_000041; ENSG00000130203
dbSNP ID: rs440446
Coding/Non-Coding: Non-Coding
DNA Change: Substitution
Expected RNA Consequence: Substitution
Reference Isoform: APOE Isoform 1
Genomic Region: Intron 1


This common intronic variant is strongly associated with Alzheimer’s disease (AD) risk, but the association appears to be primarily due to its genetic linkage to C130R (APOE4). It was first identified in a search for polymorphisms affecting AD risk that included portions of the APOE promoter, nearby enhancer elements, and the receptor binding domain (Mui et al., 1996). Located in the intron 1 enhancer element (IE1), the G allele of this polymorphism was reported as significantly associated with AD in a cohort of 94 Americans. The authors also found that when they adjusted their analyses for the presence of APOE4, the association was no longer statistically significant. They concluded that the apparent association of c.-24+69C>G with AD was a consequence of its linkage to APOE4.

Most subsequent studies, including cohorts of different ancestries, yielded results consistent with this conclusion (e.g., Rebeck et al., 1999; Cui et al., 2000; Yang et al., 2003Nicodemus et al., 2004; Belbin et al., 2007; Yu et al., 2007; Takei et al., 2009; Limon-Sztencel et al., 2016; Rantalainen et al., 2018). Moreover, more recent analyses of larger cohorts, including genome-wide association studies (GWAS) and meta-analyses, have been supportive of these findings, with association p-values that fall dramatically after APOE4 adjustment or stratification (see table below).

Nevertheless, located in a site thought to regulate transcription, this variant may do more than simply tag along with APOE4. Although based on observations in small cohorts, some studies suggest it may modulate the impact of APOE4 (Lambert et al., 1998), affect the rate of cognitive decline in AD without affecting risk (Belbin et al. 2007), modulate cognitive ability in elderly, nondemented APOE3 homozygotes (Rantalainen et al., 2016), and/or alter the risk for ischemic stroke independently of APOE4 (Abboud et al., 2008). 

Teasing out its effects has been complicated, not only because of its linkage to APOE4, but because of its linkage to other variants in APOE and nearby genes. Early reports, for example, found a tight linkage between c.-24+69C>G and the APOE promoter variant c.-286T>G (Lambert et al., 1998, Myllykangas et al., 2002, Belbin et al., 2007). Indeed, some studies suggest late-onset AD genetic risk can be better understood by studying the combined effects of multiple variants that tend to be inherited together, also known as haplotypes. In this context, a haplotype including c.-24+69C>G has been reported to modify the effect of the protective allele R176C (APOE2) (Kulminski et al., 2020). Data on the linkage between c.-24+69C>G and neighboring variants, across several populations, can be found in the GWAS catalog (click on “Linkage Disequilibrium” tab in the “Available data” section). 

Also of note, the frequencies of c.-24+69C>G vary across groups of different ancestries. Globally, the G allele is found at a frequency of 0.62, with a higher frequency in African Americans (0.88) than in Europeans (0.64) or East Asians (0.40) (gnomAD v2.1.1, Aug 2022). Interestingly, in a study of 19,398 East Asians, 15,836 individuals of European ancestry, and 4,985 African Americans, even larger differences were reported pertaining to the GG genotype (African=0.75, European=0.46, East Asian=0.18), but the differences were much smaller among APOE4 homozygotes (African=0.99, European=0.90, East Asian=0.71), consistent with these two variants being strongly linked to each other (Choi et al., 2019). 

Non-neurological effects

Multiple studies have examined the relationship of this variant with cardiovascular disease, but results have been mixed and most have not accounted for linkage with other APOE variants. A study of nearly 2,000 German patients found no association with death and myocardial infarction, nor with formation of new arterial blockages after treatment with a stent (Koch et al., 2004). Also, a study of young Finns failed to detect an association with markers of subclinical atherosclerosis (Viiri et al., 2006), and a study of a small cohort of Chinese individuals found no association with essential hypertension (Yang et al,, 2012). On the other hand, in two Finnish studies, the c.-24+69C allele was associated with an elevated risk for coronary heart disease (Silander et al., 2008), and with larger aortic atherosclerotic lesions in nonsmokers and smaller lesions in smokers (Viiri et al., 2008).

Studies of blood lipid profiles have also yielded mixed results. Possible explanations for these discrepancies include differences in cohorts, particularly ancestryand gender, as well as whether and how studies accounted for linkage with other APOE variants. For example, elevated levels of cholesterol and low density lipoprotein (LDL) were reported in Finnish and Chinese carriers of the C allele (Viiri et al., 2006; Andreotti et al., 2009), while lower cholesterol levels were associated with the C allele in an American cohort of non-Hispanic whites (Radwan et al., 2014Pirim et al., 2019). Of note, Radwan and colleagues adjusted for the presence of APOE2 and APOE4, and Viiri et al. included only APOE3 homozygotes. Also, the latter study examined the c.-24+69C>G variant in the context of APOE variant c.-286T>G, which resides in the APOE promoter and appears to modulate transcription. They found that male, but not female, carriers of the c.-286T/c.-24+69C/APOE3 haplotype had higher LDL-cholesterol and total cholesterol concentrations across a 21-year follow-up period compared with homozygous G allele carriers or noncarriers of c.-286T/c.-24+69C/APOE3.

In addition, carriers of c.-24+69C were reported to have higher levels of ApoB, a marker of cardiovascular disease risk, in African Blacks, and lower levels of triglycerides and very low-density lipoprotein (VLDL) in non-Hispanic whites (Pirim et al., 2019). Both the triglyceride and ApoB associations were also observed in a study of Finnish individuals, although this study did not adjust for the common APOE isoforms (Viiri et al., 2005). Some studies, on the other hand, have failed to find distinct patterns of blood lipid profiles associated with this variant. For example, a study of approximately 500 Spaniards reported no differences between individuals with a c.-24+69GG genotype versus heterozygotes or CC homozygotes (Gomez-Delgado et al., 2019).

The c.-24+69C>G variant has also been studied in the context of other phenotypes. A large GWAS including 440,000 Europeans, for example, found an association of the variant with eosinophil counts, although the effect allele was not noted (Kichaev et al., 2018). Studies of small cohorts of patients with diabetes and diabetes-related phenotypes (Geng et al., 2011; Komurcu-Bayrak et al., 2011; Araki et al., 2000), and patients with reduced bone density (Tolonen et al., 2011; Singh et al., 2010; Tong et al., 2010) have yielded inconsistent results. One study found an association of the c.-24+69G allele with risk for cancer and stones in the biliary tract (Andreotti et al., 2008).

Biological Effect

The c.-24+69C>G variant resides within the evolutionarily conserved IE1 intronic sequence which is thought to regulate transcriptional activity (Paik et al., 1998; Viiri et al., 2008). In a reporter assay, transcription of a construct carrying a C allele upstream of the luciferase gene was approximately 1.4-fold higher than that of a construct carrying the G allele (Viiri et al., 2008). Interestingly, an antisense C-allele construct placed downstream of the luciferase gene performed similarly, enhancing transcription roughly 1.6 times compared with the G allele.

Consistent with these findings, proteins in nuclear extracts from human hepatoma cells and Chinese hamster ovary cells showed affinity for IE1 (Paik et al., 1998). Overall, proteins from hepatoma extracts had a lower affinity for constructs carrying the C allele than the G allele. In addition, NFκB and RBP-Jκ were identified as transcription factors likely to interact with IE1, with NFκB having a fourfold higher affinity for the C allele (Viiri et al., 2008).

In addition, it has been noted that c.-24+69C>G contributes to determining the CG dinucleotide composition of this region, affecting methylation status, which may impact gene expression (Babenko et al., 2018).

Also of note, although c.-24+69C>G resides in an intron of the canonical APOE transcript, it localizes in an exon in an alternate APOE mRNA species that encodes a truncated protein (ENST_434152.1, Ensembl RNA database). In this case, the substitution of a cytosine for a guanine results in the substitution of an asparagine for a lysine at position 14 (see dbSNP; Lee et al., 2020). The transcript has not been described in the literature, and it remains unclear if it is of physiological significance or simply an artefact.

This variant's PHRED-scaled CADD score (5.86), which integrates diverse information in silico, did not reach 20, a commonly used threshold to predict deleteriousness (CADD v.1.6, Nov 2022).


Study Type Risk Allele(s) Allele Freq.
Cases | CTRL
Association Results


GWAS Meta-analysis C   71,8880a | 383,378 Z score=-25.41
Effect size = -0.056
Jansen et al., 2019
GWAS Meta-analysis C   21,982 | 41,944 p=2.28x10-112 European
(IGAP Rare Variants: Stage 1)
Kunkle et al., 2019b
GWAS C   21,392 | 38,164 p=9.5x10-70 Mixed
(ADGC: Transethnic LOAD: All Samples)
Jun et al., 2017b
GWAS C   21,392 | 38,164


(Adjusted for APOE4)

(ADGC: Transethnic LOAD: All Samples)
Jun et al., 2017b
GWAS Meta-analysis C   17,008 | 37,154 p=2.3x10-67 European
(IGAP 2013: Stage 1)
Lambert et al., 2013b
GWAS G 0.686 14,895 (total) OR = 1.64
European Lo et al., 2019c
GWAS C   12,738 | 13,850 p=5.08x10-7 Mixed 
(ADGC Transethnic LOAD: APOE4 carriers)
Jun et al., 2017b
C   10,352 | 9,207


(APOE-Stratified Analysis)

(IGAP - APOE4 carriers) Jun et al., 2016b
Whole Exome Meta-analysis     5,740 | 5,096 p=5.0 x10-11 Mostly European
Bis et al., 2018b
GWAS C 0.321 4,010 | 4,672 OR = 0.65
[CI = 0.60-0.71]
European, U.S. Wang et al., 2021c
Targeted G 0.663 2,302 | 17,096 p=1.08x10-18 East Asian Choi et al., 2019
Targeted C 0.35 1,873 | 1,443d HetLODe=7.96  (PDT)=98.39 p<0.001
χ2 (Pearson) = 171.62
Caucasian Thornton-Wells et al., 2008
Meta-analysis C vs G   1,113 | 978 OR = 0.58
(Alzgene Dec 1, 2005 data)
Bertram et al., 2007

a24,087 LOAD cases; 47,793 offspring of parents with AD
bData from the National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (NIAGADS), rs440446, Aug 2022
cData from GWAS Catalog rs440446, August 2022
dFamily-based: 1,422 cases, 744 controls; and case-control: 451 cases, 699 controls
eHetLOD = herogeneity LOD score; PDT= pedigree disequilibrium test

OR=odds ratio, GWAS=genome-wide association study. Statistically significant associations (as assessed by the authors) are in bold. For data retrieved from NIAGADS, GWAS p-values <5x10-8 and whole-exome association p-values <1x10-3 are in bold. All data retrieved from the GWAS catalog (p-values <1x10-5) are in bold.
All genome-wide association studies in this table included >2,000 cases, and all targeted association studies included >500 cases (subgroups within a study may be smaller).

This table is meant to convey the range of results reported in the literature. As specific analyses, including co-variates, differ among studies, this information is not intended to be used for quantitative comparisons, and readers are encouraged to refer to the original papers. Thresholds for statistical significance were defined by the authors of each study. (Significant results are in bold.) Note that data from some cohorts may have contributed to multiple studies, so each row does not necessarily represent an independent dataset. While every effort was made to be accurate, readers should confirm any values that are critical for their applications.

Last Updated: 05 Dec 2022


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Mutations Citations

  1. APOE C130R (ApoE4)
  2. APOE c.-286T>G (rs405509)
  3. APOE R176C (ApoE2)

Paper Citations

  1. . A newly identified polymorphism in the apolipoprotein E enhancer gene region is associated with Alzheimer's disease and strongly with the epsilon 4 allele. Neurology. 1996 Jul;47(1):196-201. PubMed.
  2. . Sequence diversity and large-scale typing of SNPs in the human apolipoprotein E gene. Genome Res. 2000 Oct;10(10):1532-45. PubMed.
  3. . Gene polymorphism in apolipoprotein E and presenilin-1 in patients with late-onset Alzheimer's disease. Chin Med J (Engl). 2000 Apr;113(4):340-4. PubMed.
  4. . Apolipoprotein E -491 promoter polymorphism is an independent risk factor for Alzheimer's disease in the Chinese population. Neurosci Lett. 2003 Oct 16;350(1):25-8. PubMed.
  5. . Comprehensive association analysis of APOE regulatory region polymorphisms in Alzheimer disease. Neurogenetics. 2004 Dec;5(4):201-8. Epub 2004 Sep 29 PubMed.
  6. . Regulatory region single nucleotide polymorphisms of the apolipoprotein E gene and the rate of cognitive decline in Alzheimer's disease. Hum Mol Genet. 2007 Sep 15;16(18):2199-208. Epub 2007 Jul 5 PubMed.
  7. . Comprehensive analysis of APOE and selected proximate markers for late-onset Alzheimer's disease: patterns of linkage disequilibrium and disease/marker association. Genomics. 2007 Jun;89(6):655-65. Epub 2007 Apr 16 PubMed.
  8. . Genetic association study on in and around the APOE in late-onset Alzheimer disease in Japanese. Genomics. 2009 May;93(5):441-8. Epub 2009 Feb 3 PubMed.
  9. . The algorithm for Alzheimer risk assessment based on APOE promoter polymorphisms. Alzheimers Res Ther. 2016 May 19;8(1):19. PubMed.
  10. . APOE ɛ4, rs405509, and rs440446 promoter and intron-1 polymorphisms and dementia risk in a cohort of elderly Finns-Helsinki Birth Cohort Study. Neurobiol Aging. 2019 Jan;73:230.e5-230.e8. Epub 2018 Sep 12 PubMed.
  11. . A new polymorphism in the APOE promoter associated with risk of developing Alzheimer's disease. Hum Mol Genet. 1998 Mar;7(3):533-40. PubMed.
  12. . APOE and aging-related cognitive change in a longitudinal cohort of men. Neurobiol Aging. 2016 Aug;44:151-158. Epub 2016 May 10 PubMed.
  13. . Associations of apolipoprotein E gene with ischemic stroke and intracranial atherosclerosis. Eur J Hum Genet. 2008 Aug;16(8):955-60. Epub 2008 Feb 27 PubMed.
  14. . ApoE epsilon3-haplotype modulates Alzheimer beta-amyloid deposition in the brain. Am J Med Genet. 2002 Apr 8;114(3):288-91. PubMed.
  15. . Haplotype architecture of the Alzheimer's risk in the APOE region via co-skewness. Alzheimers Dement (Amst). 2020;12(1):e12129. Epub 2020 Nov 11 PubMed.
  16. . APOE Promoter Polymorphism-219T/G is an Effect Modifier of the Influence of APOE ε4 on Alzheimer's Disease Risk in a Multiracial Sample. J Clin Med. 2019 Aug 16;8(8) PubMed.
  17. . Apolipoprotein E gene polymorphisms and thrombosis and restenosis after coronary artery stenting. J Lipid Res. 2004 Dec;45(12):2221-6. Epub 2004 Oct 1 PubMed.
  18. . Relations of APOE promoter polymorphisms to LDL cholesterol and markers of subclinical atherosclerosis in young adults. J Lipid Res. 2006 Jun;47(6):1298-306. Epub 2006 Mar 9 PubMed.
  19. . Polymorphisms of +2836 G>A in the apoE gene are strongly associated with the susceptibility to essential hypertension in the Chinese Hui population. Genet Mol Res. 2014 Feb 27;13(1):1212-9. PubMed.
  20. . Gender differences in genetic risk profiles for cardiovascular disease. PLoS One. 2008;3(10):e3615. Epub 2008 Oct 31 PubMed.
  21. . Interactions of functional apolipoprotein E gene promoter polymorphisms with smoking on aortic atherosclerosis. Circ Cardiovasc Genet. 2008 Dec;1(2):107-16. Epub 2008 Oct 15 PubMed.
  22. . Genetic determinants of serum lipid levels in Chinese subjects: a population-based study in Shanghai, China. Eur J Epidemiol. 2009;24(12):763-74. Epub 2009 Nov 4 PubMed.
  23. . Comprehensive evaluation of the association of APOE genetic variation with plasma lipoprotein traits in U.S. whites and African blacks. PLoS One. 2014;9(12):e114618. Epub 2014 Dec 12 PubMed.
  24. . Apolipoprotein E-C1-C4-C2 gene cluster region and inter-individual variation in plasma lipoprotein levels: a comprehensive genetic association study in two ethnic groups. PLoS One. 2019;14(3):e0214060. Epub 2019 Mar 26 PubMed.
  25. . The association of the apolipoprotein E gene promoter polymorphisms and haplotypes with serum lipid and lipoprotein concentrations. Atherosclerosis. 2005 Mar;179(1):161-7. Epub 2004 Dec 10 PubMed.
  26. . Apolipoprotein E genetic variants interact with Mediterranean diet to modulate postprandial hypertriglyceridemia in coronary heart disease patients: CORDIOPREV study. Eur J Clin Invest. 2019 Aug;49(8):e13146. Epub 2019 Jun 23 PubMed.
  27. . Leveraging Polygenic Functional Enrichment to Improve GWAS Power. Am J Hum Genet. 2019 Jan 3;104(1):65-75. Epub 2018 Dec 27 PubMed.
  28. . APOE genotype-function relationship: evidence of -491 A/T promoter polymorphism modifying transcription control but not type 2 diabetes risk. PLoS One. 2011;6(10):e24669. Epub 2011 Oct 18 PubMed.
  29. . The APOE -219G/T and +113G/C polymorphisms affect insulin resistance among Turks. Metabolism. 2011 May;60(5):655-63. Epub 2010 Aug 17 PubMed.
  30. . APOE polymorphisms and the development of diabetic nephropathy in type 1 diabetes: results of case-control and family-based studies. Diabetes. 2000 Dec;49(12):2190-5. PubMed.
  31. . Association of apolipoprotein E promoter polymorphisms with bone structural traits is modified by dietary saturated fat intake - the Cardiovascular Risk in Young Finns study. Bone. 2011 May 1;48(5):1058-65. Epub 2011 Jan 23 PubMed.
  32. . A susceptible haplotype within APOE gene influences BMD and intensifies the osteoporosis risk in postmenopausal women of Northwest India. Maturitas. 2010 Nov;67(3):239-44. PubMed.
  33. . Association between an intronic apolipoprotein E polymorphism and bone mineral density in Singaporean Chinese females. Bone. 2010 Sep;47(3):503-10. Epub 2010 May 28 PubMed.
  34. . Polymorphisms of genes in the lipid metabolism pathway and risk of biliary tract cancers and stones: a population-based case-control study in Shanghai, China. Cancer Epidemiol Biomarkers Prev. 2008 Mar;17(3):525-34. Epub 2008 Feb 22 PubMed.
  35. . Identification and characterization of transcriptional regulatory regions associated with expression of the human apolipoprotein E gene. J Biol Chem. 1988 Sep 15;263(26):13340-9. PubMed.
  36. . Haplotype analysis of APOE intragenic SNPs. BMC Neurosci. 2018 Apr 19;19(Suppl 1):16. PubMed.
  37. . Redefining transcriptional regulation of the APOE gene and its association with Alzheimer's disease. PLoS One. 2020;15(1):e0227667. Epub 2020 Jan 24 PubMed.
  38. . Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk. Nat Genet. 2019 Mar;51(3):404-413. Epub 2019 Jan 7 PubMed.
  39. . Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. Nat Genet. 2019 Mar;51(3):414-430. Epub 2019 Feb 28 PubMed.
  40. . Transethnic genome-wide scan identifies novel Alzheimer's disease loci. Alzheimers Dement. 2017 Jul;13(7):727-738. Epub 2017 Feb 7 PubMed.
  41. . Meta-analysis of 74,046 individuals identifies 11 new susceptibility loci for Alzheimer's disease. Nat Genet. 2013 Dec;45(12):1452-8. Epub 2013 Oct 27 PubMed.
  42. . Identification of genetic heterogeneity of Alzheimer's disease across age. Neurobiol Aging. 2019 Dec;84:243.e1-243.e9. Epub 2019 Mar 12 PubMed.
  43. . A novel Alzheimer disease locus located near the gene encoding tau protein. Mol Psychiatry. 2015 Mar 17; PubMed.
  44. . Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation. Mol Psychiatry. 2018 Aug 14; PubMed.
  45. . Similar Genetic Architecture of Alzheimer's Disease and Differential APOE Effect Between Sexes. Front Aging Neurosci. 2021;13:674318. Epub 2021 May 28 PubMed.
  46. . Confronting complexity in late-onset Alzheimer disease: application of two-stage analysis approach addressing heterogeneity and epistasis. Genet Epidemiol. 2008 Apr;32(3):187-203. PubMed.
  47. . Systematic meta-analyses of Alzheimer disease genetic association studies: the AlzGene database. Nat Genet. 2007 Jan;39(1):17-23. PubMed.

External Citations

  1. GWAS catalog
  2. dbSNP

Further Reading

No Available Further Reading

Protein Diagram

Primary Papers

  1. . A newly identified polymorphism in the apolipoprotein E enhancer gene region is associated with Alzheimer's disease and strongly with the epsilon 4 allele. Neurology. 1996 Jul;47(1):196-201. PubMed.

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