Table 2

Twenty-six genome-wide associated loci with GCAT traits and reported in the GWAS Catalog

GeneSNPChr:position*ImputedInfoGWAS Catalog traits†StudiesPublished yearGCAT traitβSEP values
CCDC141rs1510416852:179725237Yes0.998Resting heart rate12016heart_rate_c2.060.3611.2×10−8**
CCDC141, LOC105373766rs791466582:179786068Yes0.971Diastolic blood pressure12017heart_rate_c2.3590.37493.4×10−10
SLC45A2rs168919825:33951693Yes0.985Hair colour, eye colour, black versus non-black hair colour, skin sensitivity to sun, squamous cell carcinoma, melanoma, monobrow62010, 2015, 2016, 2017skin_color−0.5460.0212.2×10−130
DUSP22, IRF4rs77733246:382559Yes0.986Crohn’s disease, inflammatory bowel disease12015freckling_phototype_score0.2810.0456.5×10−10**
IRF4rs122035926:396321NoBlack versus blond hair colour, black versus red hair colour, hair colour, eye colour, freckling, progressive supranuclear palsy, non-melanoma skin cancer, tanning, sunburns, facial pigmentation, skin colour saturation, cutaneous squamous cell carcinoma, squamous cell carcinoma, basal cell carcinoma92008, 2010, 2011, 2013, 2015, 2016hair_color_phototype_score1.9150.1182.8×10−57
IRF4, LOC105374875rs623894246:422631Yes0.882Blond versus non-blond hair colour, brown versus non-brown hair colour, light versus dark hair colour, lung cancer in ever smokers22015, 2017freckling_phototype_score−0.9260.0731.6×10−35
LOC105374875rs122100506:475489NoTanning, basal cell carcinoma, schizophrenia42009, 2011, 2012, 2016hair_phototype_score1.0250.1231.7×10−16
RNU2-47P, TYRP1rs14087999:12672097NoBlue versus green eyes, eye colour22008, 2013eye_phototype_score0.4530.0712.2×10−10
BNC2- LOC1053759839:16884586Yes0.991Cutaneous squamous cell carcinoma, basal cell carcinoma22−0.0890.0163.4×10−8**
LOC107984363, TYRrs112680911:89017961Yes0.993Tanning, sunburns, cutaneous squamous cell carcinoma, squamous cell carcinoma, basal cell carcinoma42013, 2016skin_color−1.6720.2823.5×10−9**
LOC105370627rs1289639914:92773663NoBlond versus brown hair colour, blue versus green eyes, black versus blond hair colour, hair colour, eye colour42007, 2008, 2010, 2013phototype_score0.0930.0161.9×2.5−8**
OCA2rs1185501915:28335820NoBlack versus blond hair colour, black versus red hair colour12008hair_color−0.5480.0222.4×10−121
HERC2rs166739415:28530182NoBlond versus brown hair colour, blue versus green eyes, blue versus brown eyes, eye colour22007, 2012eye_color−0.6080.022.8×10−176
SPG7, RPL13rs6768985416:89625227Yes0.902Stromal cell-derived factor 1 alpha levels12016eye_color2.2840.2787.9×10−11
SPATA33rs3506302616:89736157Yes0.987Facial pigmentation, squamous cell carcinoma22015, 2016hair_color_red3.1120.3095.4×10−17
CDK10rs25832216:89755903NoBlack versus red hair colour, melanoma52008, 2009, 2011, 2014, 2017hair_color_red2.4310.2671.2×10−13
FANCArs1293126716:89818732Yes0.989Hair colour, freckling, skin sensitivity to sun22015, 2017hair_color_red3.2180.3113.9×10−18
MC1Rrs180500716:89986117NoFreckles, blond versus brown hair colour, red versus non-red hair colour, skin sensitivity to sun, basal cell carcinoma, tanning, hair colour, sunburns, non-melanoma skin cancer, perceived skin darkness, cutaneous squamous cell, melanoma72007, 2011, 2013, 2015, 2016, 2017hair_color_red3.6150.3267.7×10−22
DEF8rs14697236516:90022693Yes0.974Red versus non-red hair colour, light versus dark hair colour, brown versus non-brown hair colour12015hair_color0.4420.0523×10−17
AFG3L1Prs806316016:90054709Yes0.988Brown versus non-brown hair colour, light versus dark hair colour, red versus non-red hair colour12015hair_color_red2.5770.2778.9×10−15
TSPAN10rs974734717:79606820Yes0.982Myopia12016hair_color_phototype_score−0.5260.0871.8×10−9**
HMGN1P31- CDH2018:58840518Yes0.953Deep ovarian and/or rectovaginal disease with dense12017handedness0.0450.0083.9×10−8**
SMARCA4, LDLR19:11193949Yes0.999Cholesterol, total12017icd9_code3_272−0.5010.0793.2×10−10
LDLRrs651172019:11202306NoLDL cholesterol, carotid intima media thickness, cardiovascular disease risk factors, lipoprotein-associated phospholipase A2 activity and mass, cholesterol, total, metabolite levels, lipid metabolism phenotypes, Abdominal aortic aneurysm122008, 2009, 2010, 2011, 2012, 2013icd9_code3_272−0.4930.0819.4×10−10**
RPL41P1- LINC0143220:22000281NoMale-pattern baldness12016hair_loss_400.190.0326.2×10−9**
LINC01432rs116031220:22050503NoMale-pattern baldness12008hair_loss_400.1930.0321.9×10−9**
  • *Chr:position based on hg19.

  • †GWAS Catalog traits based on GWAS Catalog database (release V.1.0, e90, 27 September 2017).

  • 5×10−8 threshold for univariate GWAS and 5×10−10 threshold accounting for multiple phenotypes.

  • GWAS, genome-wide association studies; LDL, low-density lipoprotein.

  • _c for heart-rate_c, means calculated-imputed variable.