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From SNPedia

obesity risk
Geno Mag Summary
(C;C) 3.1 ~1.7x increased obesity risk
(C;T) 2.5 ~1.3x increased obesity risk
(T;T) 0.1 normal obesity risk
ReferenceGRCh38 38.1/141
is asnp
is mentioned by
1000 genomesrs1421085
23andMe allrs1421085
SNP Nexus

GWAS Ctlgrs1421085
Max Magnitude3.1
? (C;C) (C;T) (T;T) 28
rs1421085 is a SNP located in the first intron of the FTO (fat mass and obesity associated) gene on chromosome 16. This SNP showed the most association with obesity in the original work by Dina et al [PMID 17496892].

[PMID 26287746] The rs1421085 T-to- C single-nucleotide alteration underlies the association between FTO and obesity by disrupting ARID5B-mediated repression of IRX3 and IRX5. This disruption leads to a developmental shift from browning to whitening programs and loss of mitochondrial thermogenesis

Within the FTO gene, many SNPs appear to be co-inherited. The SNP showing the strongest association with body weight (i.e. body mass index, BMI) is not rs1421085, although this SNP is one of co-inherited SNPs in the FTO gene region. For more information, refer to the FTO gene or the most studied of FTO SNPs, rs9930506. [PMID 17658951OA-icon.png]

However, in one study of 583 extremely obese women with several FTO SNPs, the strongest association was indeed with rs1421085 (p=3.04x10-10, OR = 1.75, CI: 1.47-2.08).[PMID 18218107OA-icon.png]

  • Note: The three FTO SNPs, rs1421085, rs17817449, and rs9939609, are in strong linkage disequilibrium (pairwise r2>0.97), and there are two primary haplotypes, C-G-A (42.0 %) and T-T-T (55.5 %).

[PMID 18719664] This SNP is also associated with adult obesity in Mexicans.

[PMID 19153581] rs17782313(C) more snacking, however rs1421085(C) did not influence eating behavior

[PMID 18551112] rs1421085(C) and rs17817449(G) significantly associated with increased BMI. Our results suggest that FTO may be one of the worldwide obesity-risk genes.

GWAS snp
PMID [PMID 19151714]
Trait Obesity
Title Genome-wide association study for early-onset and morbid adult obesity identifies three new risk loci in European populations
Risk Allele C
P-val 1E-28
Odds Ratio 1.39 [1.27-1.51]

[PMID 19322589OA-icon.png] Analysis of FTO gene variants with measures of obesity and glucose homeostasis in the IRAS Family Study


[PMID 19818665] Apolipoprotein E genotype is associated with serum C-reactive protein but not abdominal aortic aneurysm

[PMID 20373279] FTO Genotype and Weight Gain in Obese and Normal Weight Adults From a Norwegian Population Based Cohort (the HUNT Study)

[PMID 20502638OA-icon.png] Risk of Type 2 Diabetes and Obesity Is Differentially Associated with Variation in FTO in Whites and African-Americans in the ARIC Study

[PMID 21248310OA-icon.png] Examining Overweight and Obesity as Risk Factors for Common Mental Disorders Using Fat Mass and Obesity-Associated (FTO) Genotype-Instrumented Analysis: The Whitehall II Study, 1985-2004

[PMID 21796137] Association of variations in the FTO, SCG3 and MTMR9 genes with metabolic syndrome in a Japanese population

[PMID 22590636OA-icon.png] Prevalence and Determinants of Metabolic Syndrome among Women in Chinese Rural Areas

[PMID 17928949] FTO polymorphisms in oceanic populations.

[PMID 18159244OA-icon.png] Genome wide association (GWA) study for early onset extreme obesity supports the role of fat mass and obesity associated gene (FTO) variants.

[PMID 18379722OA-icon.png] Variations in the FTO gene are associated with severe obesity in the Japanese.

[PMID 18487448OA-icon.png] Common variation in the fat mass and obesity-associated (FTO) gene confers risk of obesity and modulates BMI in the Chinese population.

[PMID 18572014] FTO gene associates to metabolic syndrome in women with polycystic ovary syndrome.

[PMID 18599522OA-icon.png] FTO variants are associated with obesity in the Chinese and Malay populations in Singapore.

[PMID 18647953OA-icon.png] Fat mass-and obesity-associated (FTO) gene variant is associated with obesity: longitudinal analyses in two cohort studies and functional test.

[PMID 19079261OA-icon.png] Six new loci associated with body mass index highlight a neuronal influence on body weight regulation.

[PMID 19255736] Combined effects of MC4R and FTO common genetic variants on obesity in European general populations.

[PMID 19557161OA-icon.png] Genome-wide association scan meta-analysis identifies three Loci influencing adiposity and fat distribution.

[PMID 20075150OA-icon.png] Utility of genetic and non-genetic risk factors in prediction of type 2 diabetes: Whitehall II prospective cohort study.

[PMID 20080751OA-icon.png] Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3.

[PMID 20127379OA-icon.png] From monogenic to polygenic obesity: recent advances.

[PMID 20381893OA-icon.png] The genetics of obesity: FTO leads the way.

[PMID 20404173OA-icon.png] A commonly carried allele of the obesity-related FTO gene is associated with reduced brain volume in the healthy elderly.

[PMID 20421936OA-icon.png] Two new Loci for body-weight regulation identified in a joint analysis of genome-wide association studies for early-onset extreme obesity in French and german study groups.

[PMID 20442772OA-icon.png] Common SNPs in FTO gene are associated with obesity related anthropometric traits in an island population from the eastern Adriatic coast of Croatia.

[PMID 20703240] Polymorphisms in NRXN3, TFAP2B, MSRA, LYPLAL1, FTO and MC4R and their effect on visceral fat area in the Japanese population.

[PMID 21102551OA-icon.png] Analysis of FTO gene variants with obesity and glucose homeostasis measures in the multiethnic Insulin Resistance Atherosclerosis Study cohort.

[PMID 21283731OA-icon.png] FTO and MC4R gene variants are associated with obesity in polycystic ovary syndrome.

[PMID 21317302OA-icon.png] FTO polymorphisms are associated with adult body mass index (BMI) and colorectal adenomas in African-Americans.

[PMID 21318054OA-icon.png] Rs9939609 variant of the fat mass and obesity-associated gene and trunk obesity in adolescents.

[PMID 22187296] Variants of the FTO gene in obese children and their impact on body composition and metabolism before and after lifestyle intervention.

[PMID 22189543OA-icon.png] Genetic variants in FTO associated with metabolic syndrome: a meta- and gene-based analysis.

[PMID 22513296OA-icon.png] Obesity susceptibility loci and dietary intake in the Look AHEAD Trial.

GET Evidence
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.289062

[PMID 23136261OA-icon.png] Fat mass and obesity gene and cognitive decline: The Atherosclerosis Risk in Communities Study

[PMID 23342142OA-icon.png] Association of FTO Polymorphisms with Obesity and Obesity-Related Outcomes in Portuguese Children.

[PMID 23341774OA-icon.png] A Systematic Mapping Approach of 16q12.2/FTO and BMI in More Than 20,000 African Americans Narrows in on the Underlying Functional Variation: Results from the Population Architecture using Genomics and Epidemiology (PAGE) Study

GWAS snp
PMID [PMID 23636237OA-icon.png]
Trait Dietary macronutrient intake
Title Genome-wide meta-analysis of observational studies shows common genetic variants associated with macronutrient intake.
Risk Allele C
P-val 1E-9
Odds Ratio .10 [0.061-0.139] % increase

[PMID 24106974] Association between fat mass and obesity-associated (FTO) gene and hip fracture susceptibility

GWAS snp
PMID [PMID 23563607OA-icon.png]
Trait Obesity
Title Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
Risk Allele C
P-val 6E-39
Odds Ratio 1.45 [NR]
GWAS snp
PMID [PMID 23563609OA-icon.png]
Trait Obesity (early onset extreme)
Title Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity.
Risk Allele C
P-val 3E-28
Odds Ratio 1.44 [1.35-1.54]

[PMID 24348519OA-icon.png] EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children

[PMID 22761283OA-icon.png] Multigene interactions and the prediction of depression in the Wisconsin Longitudinal Study.

[PMID 22801903OA-icon.png] Impact of FTO genotypes on BMI and weight in polycystic ovary syndrome: a systematic review and meta-analysis.

[PMID 23849767OA-icon.png] Effects of FTO RS9939906 and MC4R RS17782313 on obesity, type 2 diabetes mellitus and blood pressure in patients with hypertension.

[PMID 24863145OA-icon.png] FTO genotype and aging: pleiotropic longitudinal effects on adiposity, brain function, impulsivity and diet

“Genetic associations with traits in 23andMe customers.” 23andMe White Paper.

[PMID 25074273] Association of obesity with rs1421085 and rs9939609 polymorphisms of FTO gene

[PMID 26935496] The Frequencies of Haplotypes of FTO Gene Variants and Their Association with the Distribution of Body Fat in Non-Obese Poles.

Risk rs1421085(C;C)
Alt rs1421085(C;C)
Reference rs1421085(T;T)
Significance Other
Disease OBESITY (BMIQ14)
Variation info
Gene FTO
Reversed 0
HGVS NC_000016.9:g.53800954T>C
CLNSRC OMIM Allelic Variant
CLNACC RCV000201907.1,