rs9939609 — FTO Intron 1 T>A

The First and Strongest Genetic Link to Common Obesity

In 2007, two genome-wide association studies¹¹ genome-wide association studies
Large-scale scans comparing genetic variants across thousands of individuals to identify disease-linked DNA changes simultaneously discovered that common variants in the first intron of the FTO (fat mass and obesity-associated) gene were powerfully associated with body mass index and obesity risk. Among the dozens of obesity-associated loci identified since, FTO remains the variant with the strongest and most consistent effect²² strongest and most consistent effect
Replicated across 200+ studies in diverse populations worldwide. Each copy of the A allele increases BMI by approximately 0.3-0.4 kg/m² and raises obesity risk by 20-30% — seemingly modest numbers that translate to 3-4 kg of additional body weight for AA homozygotes compared to TT individuals.

rs9939609 sits in a cluster of tightly linked SNPs (rs1421085³³ rs1421085
The functional variant that actually drives the effect, rs8050136, rs17817449) within intron 1 of FTO. For years after discovery, the mechanism remained opaque. FTO encodes an N6-methyladenosine (m6A) RNA demethylase, but direct FTO function didn't explain the obesity association — FTO-deficient mice are lean, not obese. The breakthrough came in 2015 when researchers discovered that the obesity-associated variants don't primarily affect FTO at all. Instead, they function as long-range enhancers⁴⁴ long-range enhancers
Regulatory DNA elements that control gene expression from distances up to millions of base pairs away that regulate IRX3 and IRX5 expression in preadipocytes during a critical developmental window.

The Mechanism: A Thermostat for Fat Burning

The risk variant disrupts a binding site for the ARID5B transcriptional repressor, leading to doubled expression of IRX3 and IRX5⁵⁵ doubled expression of IRX3 and IRX5
Measured in human preadipocytes from individuals with AA vs TT genotypes during early adipocyte differentiation. This developmental shift is decisive: preadipocytes normally differentiate into a mixture of white adipocytes⁶⁶ white adipocytes
Energy-storing cells with large lipid droplets and minimal mitochondria and beige adipocytes⁷⁷ beige adipocytes
Thermogenic cells that burn calories to produce heat, similar to brown fat. Elevated IRX3/IRX5 shifts the balance decisively toward white adipocytes, reducing mitochondrial thermogenesis by 5-fold and doubling lipid storage capacity. CRISPR editing experiments confirmed causality — repairing the rs1421085 risk allele in patient-derived cells restored normal IRX3/IRX5 levels and increased thermogenesis 7-fold.

The Evidence: Replicated Across Populations and Ages

The original 2007 discovery analyzed 38,759 participants⁸⁸ 38,759 participants
Combined from 13 European cohorts and found that 16% of adults homozygous for the risk allele (AA) weighed ~3 kg more and had 1.67-fold increased obesity odds compared to TT individuals. This association appeared from age 7 onward and reflected a specific increase in fat mass, not lean tissue. Subsequent replication extended to East and South Asians⁹⁹ East and South Asians
Meta-analysis of 96,551 individuals: BMI +0.26 kg/m² per allele, OR 1.25 for obesity, African populations, and Latino cohorts, though effect sizes vary — the A allele is far rarer in East Asian populations (12% frequency vs 42% in Europeans) but confers similar per-allele effects.

FTO also increases type 2 diabetes risk OR 1.13¹⁰¹⁰ OR 1.13
Meta-analysis of 41,504 Scandinavian subjects, p = 4.5×10⁻⁸, an effect that persists after adjusting for BMI (OR 1.11), suggesting FTO influences metabolic health partly independent of body weight. The variant also associates with dyslipidemia¹¹¹¹ dyslipidemia
Particularly elevated LDL-C in metabolically healthy individuals with excess weight, cardiovascular disease¹²¹² cardiovascular disease
In men with abnormal glucose metabolism, and metabolic syndrome¹³¹³ metabolic syndrome
OR 1.42 in a Korean study.

Practical Implications: Exercise as a Genetic Override

The most clinically actionable FTO finding emerged from a landmark 2011 meta-analysis¹⁴¹⁴ 2011 meta-analysis
Combining 45 studies of adults (218,166 participants) and 9 studies of children (19,268) examining whether physical activity modifies genetic obesity risk. The results were striking: the FTO risk allele increased obesity odds by 1.30-fold per allele in inactive individuals but only 1.22-fold in physically active individuals — a 27% attenuation¹⁵¹⁵ 27% attenuation
The association was 27% weaker in active vs inactive groups of genetic risk. This represents one of the most robust gene-environment interactions in human genetics. Physical activity doesn't eliminate FTO's effect, but it substantially blunts it — AA individuals who exercise regularly have obesity risk comparable to inactive AT heterozygotes.

The mechanism likely involves compensatory increases in energy expenditure. Exercise interventions in FTO risk allele carriers demonstrate efficacy for weight loss, with some studies showing A carriers lose more weight¹⁶¹⁶ A carriers lose more weight
On high-protein hypocaloric diets compared to TT individuals, possibly because the thermogenic deficit is more responsive to intervention.

Behavioral Pathways: Appetite and Eating Control

Beyond thermogenesis, FTO influences eating behavior¹⁷¹⁷ eating behavior
Studies in children and adults show consistent associations with appetite regulation. Risk allele carriers report reduced satiety responsiveness¹⁸¹⁸ satiety responsiveness
The ability to stop eating when full, measured by validated questionnaires and increased food responsiveness¹⁹¹⁹ food responsiveness
External cue-driven eating and responsiveness to food availability. Children and adolescents with one or two A alleles exhibit more frequent loss-of-control eating episodes²⁰²⁰ loss-of-control eating episodes
Feeling unable to stop eating even when uncomfortably full and preferentially select higher-fat foods at buffet meals. Studies measuring postprandial hormone responses found that A allele carriers have blunted satiety signals²¹²¹ A allele carriers have blunted satiety signals
Reduced peptide YY and GLP-1 responses after meals, providing a biological substrate for reduced fullness perception.

Interactions: Macronutrient Composition and Meal Timing

FTO genotype may interact with diet composition, though findings are mixed. Some evidence suggests A carriers respond better to higher-protein diets²²²² A carriers respond better to higher-protein diets
Reduced food cravings and greater satiety with 25% vs 15% protein intake during weight loss, possibly compensating for impaired satiety signaling. Other studies report differential responses to dietary fat²³²³ dietary fat
Risk allele carriers may have slower weight loss on high-fat vs high-carbohydrate diets, though the evidence remains inconsistent. Recent work suggests interactions with meal timing²⁴²⁴ meal timing
The common FTO polymorphism interacts with sleeping and eating windows to affect T2D predisposition, with risk allele carriers potentially benefiting from earlier eating windows and alignment with circadian rhythms.

Related Variants and Broader Context

rs9939609 is in near-perfect linkage disequilibrium with rs1421085²⁵²⁵ rs1421085
r² > 0.97, this variant disrupts the ARID5B binding motif and is likely the functional driver, rs8050136, and rs17817449 — most FTO studies examine one or more of these tightly linked variants interchangeably. Beyond the common variants, rare loss-of-function mutations in FTO cause a Mendelian syndrome of severe growth retardation and developmental delay²⁶²⁶ severe growth retardation and developmental delay
OMIM #612938, distinct from common variant effects on adiposity, highlighting that FTO's normal function is essential for development while common variants subtly tune thermogenic capacity.

FTO remains a powerful demonstration that genetic predisposition to obesity is neither deterministic nor immutable — the same variant that increases risk 1.67-fold in sedentary individuals has attenuated effects in those who remain physically active. For AA carriers, this knowledge transforms genetic risk from an abstract statistic into a concrete call to action.