rs7679673

This is a intron variant variant in the LOC124900868 gene.

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GWAS Catalog Trait Associations (10)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

prostate carcinoma

Verma A et al. “Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.” Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele C
OR 0.11
p 6.0e-54
N 573,692
Major Consortium StudyLarge GWAS
multi-ancestry
Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele C
OR 0.10
p 2.0e-15
N 301,559
Large GWAS
multi-ancestry
Conti DV et al. “Trans-ancestry genome-wide association meta-analysis of prostate cancer identifies new susceptibility loci and informs genetic risk prediction.” Nature Genetics 53(1):65-75 (2021)
Allele C
OR 1.10
p 3.0e-35
N 234,253
Meta-analysisLarge GWAS
multi-ancestry
Emami NC et al. “A Large-Scale Association Study Detects Novel Rare Variants, Risk Genes, Functional Elements, and Polygenic Architecture of Prostate Cancer Susceptibility.” Cancer Research 81(7):1695-1703 (2021)
Allele C
OR 1.14
p 4.0e-18
N 208,253
Large GWAS
European
Schumacher FR et al. “Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci.” Nature Genetics 50(7):928-936 (2018)
Allele C
OR 1.13
p 1.0e-49
N 140,254
Large GWAS
European
Hoffmann TJ et al. “A large multiethnic genome-wide association study of prostate cancer identifies novel risk variants and substantial ethnic differences.” Cancer Discovery 5(8):878-91 (2015)
Allele C
OR 1.12
p 5.0e-8
N 46,378
Large GWAS
multi-ancestry
Berndt SI et al. “Two susceptibility loci identified for prostate cancer aggressiveness.” Nature Communications 6:6889 (2015)
Allele C
OR 1.12
p 4.0e-9
N 7,541
Large GWAS
European

smoking status measurement, chronic obstructive pulmonary disease

Kim W et al. “Genome-Wide Gene-by-Smoking Interaction Study of Chronic Obstructive Pulmonary Disease.” American Journal of Epidemiology 190(5):875-885 (2021)
Allele A
OR —
p 2.0e-13
N 200,766
Large GWAS
European

platelet volume

Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele A
OR 0.01
p 2.0e-12
N 394,642
Large GWAS
European

granulocyte count

Astle WJ et al. “The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.” Cell 167(5):1415-1429.e19 (2016)
Allele A
OR 0.02
p 1.0e-10
N 169,822
Large GWAS
European

neutrophil count, basophil count

Astle WJ et al. “The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.” Cell 167(5):1415-1429.e19 (2016)
Allele A
OR 0.02
p 2.0e-10
N 170,143
Large GWAS
European

neutrophil count, eosinophil count

Astle WJ et al. “The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.” Cell 167(5):1415-1429.e19 (2016)
Allele A
OR 0.02
p 2.0e-10
N 170,384
Large GWAS
European

myeloid leukocyte count

Astle WJ et al. “The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.” Cell 167(5):1415-1429.e19 (2016)
Allele A
OR 0.02
p 3.0e-10
N 169,219
Large GWAS
European

chronic obstructive pulmonary disease

Kim W et al. “Genome-Wide Gene-by-Smoking Interaction Study of Chronic Obstructive Pulmonary Disease.” American Journal of Epidemiology 190(5):875-885 (2021)
Allele A
OR 0.91
p 8.0e-9
N 200,766
Large GWAS
European

neutrophil count

Chen MH et al. “Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations.” Cell 182(5):1198-1213.e14 (2020)
Allele A
OR —
p 1.0e-32
N 627,215
Large GWAS
multi-ancestry
Vuckovic D et al. “The Polygenic and Monogenic Basis of Blood Traits and Diseases.” Cell 182(5):1214-1231.e11 (2020)
Allele A
OR 0.02
p 9.0e-21
N 408,112
Large GWAS
European
Loya H et al. “A scalable variational inference approach for increased mixed-model association power.” Nature Genetics 57(2):461-468 (2025)
Allele A
OR 0.02
p 2.0e-26
N 394,642
Large GWAS
European
Astle WJ et al. “The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.” Cell 167(5):1415-1429.e19 (2016)
Allele A
OR 0.02
p 2.0e-10
N 170,702
Large GWAS
European
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Research that mentions this SNP (5)

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Associations of prostate cancer risk variants with disease aggressiveness: results of the NCI-SPORE Genetics Working Group analysis of 18,343 cases
AssociationN=18,343Brian T. Helfand et al.(2015)· Human Genetics

A case-case association study of 18,343 prostate cancer patients (16,515 European, 1,828 African-American) evaluating 36 validated PC-risk SNPs found that rs2735839 (G allele) on chromosome 19q13 in the KLK3 gene was significantly and inversely associated with aggressive disease and high Gleason scores in both populations (p = 9.343 × 10⁻⁸ overall, p = 1.042 × 10⁻⁵ European, p = 2.0 × 10⁻⁴ African-American).

Traits studied:Gleason scoreProstate cancer aggressivenessProstate cancer high-grade disease
PubMedDOIMetascience Observatory
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A genome-wide association study of prostate cancer in West African men
AssociationN=932Michael Blaise Cook et al.(2014)· Human Genetics

Genome-wide association study of 474 prostate cancer cases and 458 controls from West African men identified a novel prostate cancer susceptibility locus at 10p14 marked by rs7918885 (p=1.29×10⁻⁷), localized to an intron of the lncRNA gene RP11-543F8.2. A stratified analysis by Gleason score revealed additional associations including rs34575154 in PCDHA1 at 5q31.3 (p=3.66×10⁻⁸) for high-grade disease and rs985081 at Xq28 (p=8.66×10⁻⁹) for low-grade disease. Validation in the African Ancestry Prostate Cancer GWAS Consortium showed limited replication, with only rs2993385 at 10p14 reaching nominal significance (p<0.05), highlighting population-specific genetic architecture.

Traits studied:Prostate cancerProstate cancer (high-grade/Gleason score ≥7)Prostate cancer (low-grade/Gleason score <7)
PubMedDOIMetascience Observatory
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Common variants at 8q24 are associated with prostate cancer risk in Taiwanese men
ReviewMarcelo Chen et al.(2010)· The Prostate

Systematic literature review of 22 GWAS studies identifying 53 SNPs in 29 genomic loci associated with aggressive and progressive prostate cancer, particularly in low-grade disease. Functional analysis of 21 SNPs revealed involvement in the MYC/POU5F1B pathway (rs1447295, rs6983267, rs4242382), androgen receptor pathway (rs17021918, rs10486567, rs7679673, rs2939244), and PSA/KLK3 biomarkers (rs2735839, rs10993994). SNPs were integrated with somatic copy number aberration data, with 17 SNPs found in regions of recurrent CNAs predictive of progression; notably, rs1447295 and 7 other SNPs cluster in 8q24 gain regions harboring MYC.

Traits studied:Aggressive prostate cancerBiochemical recurrenceGleason score upgradeLow-grade prostate cancerMetastatic prostate cancerProstate cancerProstate cancer progression
PubMedDOIMetascience Observatory
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Prostate cancer risk‐associated variants reported from genome‐wide association studies: Meta‐analysis and their contribution to genetic Variation
Meta-analysisN=600,000Kim ST et al.(2010)· The Prostate

This meta-analysis of genome-wide association studies identified 30 prostate cancer risk-associated SNPs in Caucasian populations. The SNPs had odds ratios ranging from 1.12-1.47, except rs16901979 (OR=1.80). These 30 SNPs collectively explained approximately 13.5% of the total genetic variance in prostate cancer risk, with individual SNPs explaining 0.2-0.9% of variance.

Traits studied:Prostate cancer risk
PubMedDOIMetascience Observatory
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Association of genetic polymorphisms at 8q24 with the risk of prostate cancer in a Japanese population
ReviewNaoki Terada et al.(2008)· The Prostate

This systematic review identified 53 unique SNPs in 29 genomic loci associated with aggressive prostate cancer progression and poor outcomes from GWAS studies. Functional studies implicated 21 SNPs as modulating the androgen receptor pathway, MYC oncogene, and PSA-related genes, with rs1447295 and rs10993994 being replicated across multiple populations and associated with unfavorable pathological features in low-grade prostate cancer.

Traits studied:Biochemical recurrenceGleason score upgradeMetastasisPSA recurrenceProstate cancer aggressivenessProstate cancer progression
PubMedDOIMetascience Observatory

This variant is in our database but has no known associations or PRS memberships yet.

Gene information from NCBI Gene. Variant classifications from ClinVar.

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