rs72928978

This variant is located in the TPCN2 gene.

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GWAS Catalog Trait Associations (5)

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

hair color

Morgan MD et al. “Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability.” Nature Communications 9(1):5271 (2018)
Allele A
OR 1.39
p 6.0e-48
N 283,920
Major Consortium StudyLarge GWAS
European

actinic keratosis

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 G
OR 0.07
p 6.0e-23
N 412,119
Major Consortium StudyLarge GWAS
European

skin cancer

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 G
OR 0.06
p 3.0e-14
N 431,198
Major Consortium StudyLarge GWAS
European

skin neoplasm

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 G
OR 0.07
p 3.0e-14
N 429,041
Major Consortium StudyLarge GWAS
European

type 2 diabetes mellitus

Mahajan A et al. “Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.” Nature Genetics 50(4):559-571 (2018)
Allele G
OR 1.05
p 2.0e-8
N 452,244
Large GWAS
multi-ancestry
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ClinVar annotation

Benign★★★☆
2 submitters1 publication
View on ClinVar →

About TPCN2

This gene encodes a putative cation-selective ion channel with two repeats of a six-transmembrane-domain. The protein localizes to lysosomal membranes and enables nicotinic acid adenine dinucleotide phosphate (NAADP) -induced calcium ion release from lysosome-related stores. This ubiquitously expressed gene has elevated expression in liver and kidney. Two common nonsynonymous SNPs in this gene strongly associate with blond versus brown hair pigmentation.[provided by RefSeq, Dec 2009]

View all TPCN2 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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