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Table 1 GWAS loci and the associated pigmentary and cancer phenotypes

From: Moderate- to low-risk variant alleles of cutaneous malignancies and nevi: lessons from genome-wide association studies

Chromosomal region/locus (SNP region) [Reference] Pigmentation status Cancer phenotype
MC1R (RHC, NRHC) multiple SNPs [18, 19, 28] Blonde/red hair, freckling Skin sensitivity, CM, BCC
TYR (rs1126809, rs1042602, rs1393350) [24, 26, 28, 29] Blue versus green eyes, freckling Skin sensitivity, CM, BCC
TYRP1 (rs1408799) [25, 26] Blonde hair (weak), brown eyes, green eyes (weak) CM
ASIP haplotype (rs1015362 [G], rs4911414 [T]) [25, 26] Red and blonde hair, Freckling CM, BCC, skin sensitivity
TPCN2 (rs35264875 [T], rs3829241 [A]) [25] Blonde hair versus brown CM and BCC (weak)
SLC24A4 (rs12896399) [24] Blonde hair, green eyes brown eyes (weak) Skin sensitivity (weak)
KITLG (rs12821256) [24] Blonde hair Not known
6p25.3 (rs1540771) [24] Blonde hair, freckling Skin sensitivity (weak)
OCA2 (rs1667394, rs7495174) [24] Blonde hair, green and brown eyes Skin sensitivity (weak)
9p21 adjacent to MTAP (rs7023329) [28] Blonde hair, green and brown eyes, freckling Skin sensitivity, CM
9p21 adjacent to CDKN2A/B [12] No association BCC, no association to CM
KRT5, G138E substitution [12] No association BCC, no association to CM
7q32 adjacent to KLF14 [12] No association BCC, no association to CM
MTAP rs4636294 ref [37] Not known CM
PLA2G6 (rs2284063) [37] Not known CM
  1. BCC, basal cell carcinoma; CM, cutaneous melanoma; NRHC, non-red hair color variants; RHC, red hair color variants.