rs6020611 — PTPN1

Intronic PTPN1 tag SNP in the PTP1B regulatory LD block; the minor A allele is associated with elevated total and LDL cholesterol in lean men

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PTP1B's Genetic Shadow — The Intronic PTPN1 Tag SNP rs6020611

Protein tyrosine phosphatase 1B (PTP1B), encoded by the PTPN1 gene on chromosome 20q13, is one of the most rigorously validated drug targets in metabolic medicine. Its job is to put the brakes on insulin signaling: once insulin binds its receptor and activates a phosphorylation cascade, PTP1B dephosphorylates the activated insulin receptor11 dephosphorylates the activated insulin receptor
removes phosphate groups from key tyrosine residues on the insulin receptor, switching off downstream glucose uptake signals and its substrates, terminating the signal. In lean tissues, this dampening is normal and necessary. In people with elevated PTP1B activity or expression, however, insulin signaling is chronically suppressed — a molecular origin of insulin resistance that precedes clinical type 2 diabetes by years or decades.

rs6020611 sits deep within intron 7 of PTPN1, at GRCh38 position chr20:50,578,070. It does not alter any amino acid.

The Evidence

The most direct evidence for rs6020611 comes from Bauer et al. 201022 Bauer et al. 2010
Bauer F et al. PTPN1 polymorphisms are associated with total and low-density lipoprotein cholesterol. Eur J Cardiovasc Prev Rehabil. 2010 Feb;17(1):28-34, who genotyped four PTPN1 tag SNPs in 382 Dutch Caucasian men aged 40–80. The minor (A) alleles of rs6020611, rs6067484, and rs1060402 were each associated with higher total plasma cholesterol and LDL (P<0.05), specifically in men with BMI below 26 kg/m². Haplotypes combining these minor alleles showed borderline significance for the same lipid phenotypes.

Evidence level is moderate: the cholesterol finding for rs6020611 specifically derives from a single modest-sized cohort (n=382) and is specific to lean men; it awaits replication at scale.

Practical Actions

Carrying the A allele — particularly in the AA genotype — does not guarantee elevated cholesterol. The most actionable implication is monitoring: lean individuals carrying A alleles should track fasting LDL periodically. Reducing saturated fat intake lowers the hepatic substrate for LDL production.

Nutrient Interactions

dietary carbohydrate altered_metabolism
dietary fat altered_metabolism

Genotype Interpretations

What each possible genotype means for this variant.

GG Common Form Normal

Common genotype — normal PTP1B haplotype, no elevated cholesterol risk

rs6020611 GG represents the population-major genotype at this intronic PTPN1 locus. No specific dietary or monitoring actions are indicated by this genotype for this variant.

AG Heterozygous Carrier Intermediate

One copy of the risk allele — mild haplotype tagging for PTPN1-associated metabolic risk

Bauer et al. (2010) found that minor allele carriers — including heterozygotes — showed elevated total cholesterol and LDL specifically in lean men (BMI <26 kg/m²). At a single copy, the effect size is modest.

AA Risk Homozygous High Risk

Two copies of the risk allele — stronger PTPN1 haplotype signal for elevated LDL and impaired insulin signaling

The Bauer 2010 study found the minor allele association with LDL was significant (p<0.05) in lean men, and haplotype combinations of the three minor-allele tag SNPs (including rs6020611) reached borderline significance for elevated LDL.