rs9895661

This is a regulatory region variant variant in the BCAS3 gene.

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GWAS Catalog Trait Associations (28)

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

glomerular filtration rate

Stanzick KJ et al. “Discovery and prioritization of variants and genes for kidney function in >1.2 million individuals.” Nature Communications 12(1):4350 (2021)
Allele C
OR 0.01
p 1.0e-169
N 1,201,930
Large GWAS
multi-ancestry
Wuttke M et al. “A catalog of genetic loci associated with kidney function from analyses of a million individuals.” Nature Genetics 51(6):957-972 (2019)
Allele C
OR 0.01
p 1.0e-106
N 765,348
Large GWAS
multi-ancestry
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 0.04
p 8.0e-55
N 571,227
Major Consortium StudyLarge GWAS
multi-ancestry
Sinnott-Armstrong N et al. “Genetics of 35 blood and urine biomarkers in the UK Biobank.” Nature Genetics 53(2):185-194 (2021)
Allele C
OR 0.07
p 4.0e-98
N 355,731
Major Consortium StudyLarge GWAS
multi-ancestry
Graham SE et al. “Sex-specific and pleiotropic effects underlying kidney function identified from GWAS meta-analysis.” Nature Communications 10(1):1847 (2019)
Allele C
OR 14.92
p 3.0e-50
N 350,514
Meta-analysisLarge GWAS
multi-ancestry
Hellwege JN et al. “Mapping eGFR loci to the renal transcriptome and phenome in the VA Million Veteran Program.” Nature Communications 10(1):3842 (2019)
Allele C
OR 0.01
p 2.0e-57
N 280,722
Major Consortium StudyLarge GWAS
multi-ancestry
Hughes O et al. “Genome-wide study investigating effector genes and polygenic prediction for kidney function in persons with ancestry from Africa and the Americas.” Cell Genomics 4(1):100468 (2024)
Allele C
OR 8.26
p 1.0e-16
N 145,732
Large GWAS
multi-ancestry
Mahajan A et al. “Trans-ethnic Fine Mapping Highlights Kidney-Function Genes Linked to Salt Sensitivity.” American Journal of Human Genetics 99(3):636-646 (2016)
Allele C
OR 1.00
p 8.0e-14
N 71,638
Large GWAS
multi-ancestry
Hishida A et al. “Genome-Wide Association Study of Renal Function Traits: Results from the Japan Multi-Institutional Collaborative Cohort Study.” American Journal of Nephrology 47(5):304-316 (2018)
Allele C
OR 0.01
p 1.0e-20
N 11,283
Large GWAS
East Asian

uric acid measurement

Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele C
OR 0.06
p 7.0e-78
N 153,950
Large GWAS
East Asian
Nakatochi M et al. “Genome-wide meta-analysis identifies multiple novel loci associated with serum uric acid levels in Japanese individuals.” Communications Biology 2:115 (2019)
Allele C
OR 0.03
p 2.0e-9
N 210,206
Meta-analysisLarge GWAS
multi-ancestry
Flanagan J et al. “Population-specific reference panel improves imputation quality for genome-wide association studies conducted on the Japanese population.” Communications Biology 7(1):1665 (2024)
Allele C
OR 0.04
p 1.0e-19
N 181,927
Large GWAS
East Asian
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 0.03
p 3.0e-22
N 129,405
Large GWAS
East Asian
Cho SK et al. “Polygenic analysis of the effect of common and low-frequency genetic variants on serum uric acid levels in Korean individuals.” Scientific Reports 10(1):9179 (2020)
Allele C
OR 0.10
p 2.0e-8
N 6,881
Large GWAS
East Asian

hemoglobin measurement

Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele T
OR 0.02
p 4.0e-65
N 928,679
Large GWAS
multi-ancestry
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 T
OR —
p 1.0e-50
N 746,431
Large 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 T
OR 0.02
p 3.0e-35
N 502,921
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 T
OR 0.04
p 1.0e-36
N 408,112
Large GWAS
European

urate measurement

Cho C et al. “Large-scale cross-ancestry genome-wide meta-analysis of serum urate.” Nature Communications 15(1):3441 (2024)
Allele T
OR 0.05
p 3.0e-63
N 1,029,323
Meta-analysisLarge GWAS
multi-ancestry
Major TJ et al. “A genome-wide association analysis reveals new pathogenic pathways in gout.” Nature Genetics 56(11):2392-2406 (2024)
Allele T
OR 0.04
p 2.0e-38
N 630,117
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 T
OR 0.02
p 2.0e-21
N 394,642
Large GWAS
European
Sinnott-Armstrong N et al. “Genetics of 35 blood and urine biomarkers in the UK Biobank.” Nature Genetics 53(2):185-194 (2021)
Allele T
OR 0.03
p 1.0e-18
N 355,426
Major Consortium StudyLarge GWAS
multi-ancestry
Tin A et al. “Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.” Nature Genetics 51(10):1459-1474 (2019)
Allele T
OR 0.04
p 1.0e-12
N 346,213
Large GWAS
European, South Asian, East Asian, African American or Afro-Caribbean, Hispanic or Latin American
Boocock J et al. “Genomic dissection of 43 serum urate-associated loci provides multiple insights into molecular mechanisms of urate control.” Human Molecular Genetics 29(6):923-943 (2020)
Allele T
OR 0.05
p 5.0e-12
N 131,709
Large GWAS
multi-ancestry

erythrocyte count

Vuckovic D et al. “The Polygenic and Monogenic Basis of Blood Traits and Diseases.” Cell 182(5):1214-1231.e11 (2020)
Allele T
OR 0.04
p 3.0e-35
N 408,112
Large GWAS
European
Jee YH et al. “Genome-wide association studies in a large Korean cohort identify quantitative trait loci for 36 traits and illuminate their genetic architectures.” Nature Communications 16(1):4935 (2025)
Allele T
OR 0.01
p 4.0e-35
N 928,679
Large GWAS
multi-ancestry
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 T
OR 0.03
p 1.0e-25
N 405,357
Major Consortium StudyLarge 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 T
OR 0.03
p 5.0e-12
N 172,952
Large GWAS
European

nephrolithiasis

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 3.0e-29
N 435,154
Major Consortium StudyLarge GWAS
European
Cao X et al. “Trans-ancestry GWAS identifies 59 loci and improves risk prediction and fine-mapping for kidney stone disease.” Nature Communications 16(1):3473 (2025)
Allele C
OR 1.11
p 2.0e-26
N 975,370
Large GWAS
multi-ancestry

bladder calculus

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 0.10
p 3.0e-27
N 433,456
Major Consortium StudyLarge GWAS
European

serum creatinine amount, glomerular filtration rate

Pattaro C et al. “Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.” Nature Communications 7:10023 (2016)
Allele T
OR 0.01
p 3.0e-22
N 118,448
Large GWAS
European
Gorski M et al. “1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function.” Scientific Reports 7:45040 (2017)
Allele T
OR 0.01
p 4.0e-21
N 110,517
Meta-analysisLarge GWAS
European

calcium measurement

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele T
OR 0.03
p 3.0e-21
N 399,133
Large GWAS
multi-ancestry
Sinnott-Armstrong N et al. “Genetics of 35 blood and urine biomarkers in the UK Biobank.” Nature Genetics 53(2):185-194 (2021)
Allele T
OR 0.03
p 3.0e-15
N 325,659
Major Consortium StudyLarge GWAS
multi-ancestry

urolithiasis

Sakaue S et al. “A cross-population atlas of genetic associations for 220 human phenotypes.” Nature Genetics 53(10):1415-1424 (2021)
Allele T
OR 0.12
p 5.0e-21
N 667,072
Large GWAS
multi-ancestry
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Research that mentions this SNP (2)

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NPT1/SLC17A1 Is a Renal Urate Exporter in Humans and Its Common Gain‐of‐Function Variant Decreases the Risk of Renal Underexcretion Gout
AssociationN=3,103Toshinori Chiba et al.(2015)· Arthritis &amp; Rheumatology

This replication study analyzed 2255 variants in LD with GWAS-identified gout/serum urate susceptibility loci in 1255 Han Chinese gout patients and 1848 controls. Twenty-three variants (41%) showed nominal association (p<0.05), with the strongest signal at ABCG2 rs1481012 (p=8.96×10⁻¹¹, OR=1.890). Previous gout-associated loci including ABCG2, SLC2A9, GCKR, ALDH2, and CNIH2 were replicated, while cumulative genetic risk scores showed that individuals with ≥8 risk alleles had significantly increased gout risk (OR=16.361 for ≥12 alleles).

Traits studied:GoutSerum urate concentrations
PubMedDOIMetascience Observatory
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Association between gout and polymorphisms in GCKR in male Han Chinese
AssociationN=3,103Jing Wang et al.(2012)· Human Genetics

This replication study examined 2,255 variants in linkage disequilibrium with GWAS-identified gout/urate susceptibility loci in 1,255 Han Chinese gout patients and 1,848 controls. Twenty-three variants (41% of 56 LD-pruned variants) showed nominal association with gout (p < 0.05), with the strongest signals at ABCG2 (rs1481012, OR=1.890, p=8.96×10⁻¹¹) and SLC2A9 (rs11722228, OR=1.619, p=2.40×10⁻⁶). Cumulative genetic risk score analysis demonstrated increasing gout risk with growing numbers of risk alleles (OR=16.361 for ≥12 alleles vs ≤5 reference).

Traits studied:GoutSerum urate levels
PubMedDOIMetascience Observatory

About BCAS3

Enables several functions, including acetyltransferase activator activity; beta-tubulin binding activity; and histone acetyltransferase binding activity. Involved in cellular response to estrogen stimulus; positive regulation of catalytic activity; and positive regulation of transcription by RNA polymerase II. Located in euchromatin; nucleus; and phagophore assembly site. Implicated in Hengel-Maroofian-Schols syndrome. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Jul 2025]

View all BCAS3 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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