rs6834314 — HSD17B13

Intergenic tag SNP in near-perfect linkage disequilibrium with the HSD17B13 splice variant (rs72613567); the G allele tags HSD17B13 loss-of-function and is associated with reduced risk of NAFLD, NASH, cirrhosis, and lower liver enzymes — effects entirely attributable to LD rather than independent function

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HSD17B13 rs6834314 — A Tag SNP Telling the Same Story as rs72613567

In 2011, a landmark genome-wide association study scanning 61,089 individuals of Caucasian and Asian Indian descent identified an intergenic variant near the HSD17B13 gene on chromosome 4 as one of the strongest signals for plasma ALT concentrations — a key marker of liver injury: Chambers JC et al. Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nature Genetics, 201111 Chambers JC et al. Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nature Genetics, 2011. That variant was rs6834314, and its protective G allele was associated with lower liver enzyme levels in the general population. However, subsequent functional work established that rs6834314 itself has no direct effect on HSD17B13 gene expression or enzyme activity. Its associations are entirely a consequence of linkage disequilibrium22 linkage disequilibrium
Two variants are in LD when they co-occur on the same chromosome more often than expected by chance; r² measures how predictively one tags the other with the causal splice variant rs72613567 (D'=0.995, r²=0.93). Knowing your rs6834314 genotype tells you almost exactly what your rs72613567 genotype is — these two variants are nearly perfect proxies for each other.

The Mechanism

rs6834314 is located approximately 11 kb downstream of the HSD17B13 gene in an intergenic region and has no predicted regulatory or coding consequence. The variant's associations with liver disease risk, liver inflammation, and liver enzyme levels are entirely attributable to its co-inheritance with rs72613567, the adenine insertion adjacent to the splice donor site of intron 633 adenine insertion adjacent to the splice donor site of intron 6
rs72613567 disrupts the splice donor site, generating an aberrant truncated transcript (isoform D) that encodes a non-functional HSD17B13 protein with reduced enzymatic activity in HSD17B13. This was confirmed by Ma et al. (2019), who showed that rs6834314 genotype was not associated with hepatic HSD17B13 expression levels after accounting for the rs72613567 splice variant.

The Evidence

The clinical signal captured by rs6834314 mirrors the rs72613567 findings precisely, because the two variants tag the same underlying haplotype. In 768 Caucasian patients with biopsy-proven NAFLD, Ma et al. found the rs6834314 G allele (tagging the HSD17B13 loss-of-function haplotype) was associated with lower risk of liver inflammation (OR 0.77), reduced hepatocyte ballooning (OR 0.67), fewer Mallory-Denk bodies (OR 0.68), and lower serum transaminases and GGT. In the general population cohort (Michigan Genomics Initiative), the G allele was associated with a 21% reduction in cirrhosis risk (OR 0.79, p=7.5×10⁻⁴): Ma Y et al. 17-Beta Hydroxysteroid Dehydrogenase 13 Is a Hepatic Retinol Dehydrogenase Associated With Histological Features of Nonalcoholic Fatty Liver Disease. Hepatology, 201944 Ma Y et al. 17-Beta Hydroxysteroid Dehydrogenase 13 Is a Hepatic Retinol Dehydrogenase Associated With Histological Features of Nonalcoholic Fatty Liver Disease. Hepatology, 2019.

In a multi-ethnic Asian cohort, Seto et al. followed 165 biopsy-proven NAFLD patients for a mean of 89 months and found that each rs6834314 G allele was associated with lower odds of NAFLD (adjusted OR 0.59, 95% CI 0.40–0.87) and NASH (adjusted OR 0.48, 95% CI 0.31–0.75). Homozygous GG individuals showed markedly lower liver-related complication rates during follow-up. However, the protective effect was observed only in ethnic Chinese, not in Malays or Indians within the same cohort — likely reflecting population-specific LD patterns between rs6834314 and the causal rs72613567 insertion: Seto WK et al. Loss-of-function HSD17B13 variants, non-alcoholic steatohepatitis and adverse liver outcomes: results from a multi-ethnic Asian cohort. Clinical and Molecular Hepatology, 202155 Seto WK et al. Loss-of-function HSD17B13 variants, non-alcoholic steatohepatitis and adverse liver outcomes: results from a multi-ethnic Asian cohort. Clinical and Molecular Hepatology, 2021.

In Japanese patients with biopsy-proven NAFLD (n=290), rs6834314 G allele carriage abolished the fibrosis-promoting effect of PNPLA3 I148M: among HSD17B13 AA carriers, PNPLA3 GG conferred significantly higher advanced fibrosis risk (OR 2.4, p=0.041); among HSD17B13 AG/GG carriers, no such PNPLA3 effect was detected. The G allele was also associated with lower inflammation and ballooning prevalence: Seko Y et al. Attenuated effect of PNPLA3 on hepatic fibrosis by HSD17B13 in Japanese patients with non-alcoholic fatty liver disease. Liver International, 202066 Seko Y et al. Attenuated effect of PNPLA3 on hepatic fibrosis by HSD17B13 in Japanese patients with non-alcoholic fatty liver disease. Liver International, 2020.

Practical Implications

The clinical interpretation of rs6834314 is structurally identical to that of rs72613567, because they tag the same biological state. If your genome file includes rs6834314 but not rs72613567 (a scenario most likely on older Illumina arrays that predated specific addition of the HSD17B13 locus), your rs6834314 genotype tells you the same information: whether you carry the HSD17B13 loss-of-function haplotype. The G allele protective association with liver inflammation and fibrosis is real — it just originates from a functionally upstream cause.

One important caveat specific to rs6834314: because protection depends on LD, and LD patterns can differ between ancestral populations, the G allele is a reliable proxy for rs72613567 in European and East Asian populations (r²=0.93) but may be a less accurate proxy in other ancestries, particularly in populations not well-represented in the original LD reference panels.

Interactions

The most clinically important interaction is between the HSD17B13 loss-of-function haplotype (tagged by rs6834314 G) and PNPLA3 rs738409 (I148M). The high-risk PNPLA3 GG genotype strongly predicts advanced fibrosis in HSD17B13 AA carriers but not in G allele carriers — meaning the HSD17B13 protective haplotype functionally overrides much of the PNPLA3 fibrosis risk. This same interaction was originally described for rs72613567 in the Abul-Husn NEJM 2018 cohort and replicated here using rs6834314 as the proxy.

See also rs58542926 (TM6SF2 E167K), which operates in the same hepatic lipid droplet biology axis and further stratifies liver disease risk when combined with PNPLA3 and HSD17B13 genotypes.

Genotype Interpretations

What each possible genotype means for this variant.

AA No HSD17B13 Protection Normal

No protective HSD17B13 haplotype — standard liver disease risk baseline

You carry the common A/A genotype at rs6834314, which means you do not carry the HSD17B13 loss-of-function haplotype tagged by the G allele. About 59% of people of European descent share this genotype. Your HSD17B13 enzyme is expected to be fully active — and since HSD17B13 loss-of-function is protective against liver disease progression, the absence of the protective haplotype means your liver inflammation risk is at the population baseline, not reduced by this variant. Liver disease risk remains primarily determined by environmental factors (alcohol intake, metabolic health) and other genetic variants such as PNPLA3 and TM6SF2.

AG Partial HSD17B13 Protection (Likely Heterozygous) Beneficial

One copy of the protective HSD17B13 haplotype — meaningfully reduced liver disease risk

The rs6834314 G allele was associated with lower liver inflammation scores (OR 0.77), reduced hepatocyte ballooning (OR 0.67), and fewer Mallory-Denk bodies (OR 0.68) in biopsy-proven NAFLD patients. Lower serum transaminases (ALT, AST, GGT) are also associated with the G allele in population cohorts. The protection operates through reduced HSD17B13 enzymatic activity in the liver, decreasing the inflammatory cascade that drives progression from simple steatosis to NASH and fibrosis.

Note: rs6834314 serves as a proxy for rs72613567. If your genome file directly genotypes rs72613567, that result is more reliable. When only rs6834314 is available, it provides a high-fidelity inference, but interpret with slightly more uncertainty in non-European, non-East-Asian ancestries.

GG Full HSD17B13 Protection (Likely Homozygous) Beneficial

Two copies of the protective HSD17B13 haplotype — strongest genetic protection against liver disease progression

In the multi-ethnic Asian cohort (Seto et al.), homozygous GG individuals showed dramatically lower liver-related complication rates over 89 months of follow-up (HR 0.01, 95% CI 0.00–0.97 in one analysis). In Japanese NAFLD patients, GG homozygotes showed the lowest prevalence of advanced fibrosis, and the HSD17B13 protective haplotype completely abolished the elevated fibrosis risk from PNPLA3 I148M (GG genotype).

As with the AG genotype, interpret this result as a high-fidelity proxy for the causal rs72613567 II genotype, with slightly greater uncertainty in non-European, non-East-Asian ancestries where the LD relationship may differ. If your genome data directly genotypes rs72613567, prefer that result.