Trait: skin pigmentation

Experimental Factor Ontology (EFO) Information
Identifier EFO_0003784
Description Coloration of the skin.
Trait category
Other trait
Synonyms 3 synonyms
  • Pigmentation, Skin
  • Pigmentations, Skin
  • Skin Pigmentations
Mapped terms 5 mapped terms
  • MeSH:D012880
  • MedDRA:10040910
  • NCIt:C35026
  • SNOMEDCT:370172004
  • SNOMEDCT:38962007
Child trait(s) suntan

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported
Note: This table shows all PGS for "skin pigmentation" and any child terms of this trait in the EFO hierarchy by default.
Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS001244
(GBE_BIN_FC30001727)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Ease of skin tanning (get mildly or occasionally tanned) suntan 958
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001244/ScoringFiles/PGS001244.txt.gz
PGS001245
(GBE_BIN_FC20001727)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Ease of skin tanning (get moderately tanned) suntan 2,693
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001245/ScoringFiles/PGS001245.txt.gz
PGS001246
(GBE_BIN_FC10001727)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Ease of skin tanning (get very tanned) suntan 4,130
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001246/ScoringFiles/PGS001246.txt.gz
PGS001247
(GBE_BIN_FC40001727)
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Ease of skin tanning (never tan, only burn) suntan 3,159
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001247/ScoringFiles/PGS001247.txt.gz
PGS001897
(portability-PLR_darker_skin0)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Skin color skin pigmentation 15,817
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001897/ScoringFiles/PGS001897.txt.gz
PGS001937
(portability-PLR_less_tanned)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Ease of skin tanning suntan 16,197
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS001937/ScoringFiles/PGS001937.txt.gz
PGS002110
(portability-ldpred2_darker_skin0)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Skin color skin pigmentation 275,831
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002110/ScoringFiles/PGS002110.txt.gz
PGS002155
(portability-ldpred2_less_tanned)
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Ease of skin tanning suntan 240,701
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002155/ScoringFiles/PGS002155.txt.gz
PGS002350
(pigment_TANNING.BOLT-LMM)
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Tanning suntan 1,109,311
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002350/ScoringFiles/PGS002350.txt.gz
PGS002422
(pigment_TANNING.P+T.0.0001)
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Tanning suntan 8,273
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002422/ScoringFiles/PGS002422.txt.gz
PGS002471
(pigment_TANNING.P+T.0.001)
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Tanning suntan 20,040
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002471/ScoringFiles/PGS002471.txt.gz
PGS002520
(pigment_TANNING.P+T.0.01)
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Tanning suntan 100,837
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002520/ScoringFiles/PGS002520.txt.gz
PGS002569
(pigment_TANNING.P+T.1e-06)
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Tanning suntan 4,792
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002569/ScoringFiles/PGS002569.txt.gz
PGS002618
(pigment_TANNING.P+T.5e-08)
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Tanning suntan 4,026
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002618/ScoringFiles/PGS002618.txt.gz
PGS002667
(pigment_TANNING.PolyFun-pred)
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Tanning suntan 123,613
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002667/ScoringFiles/PGS002667.txt.gz
PGS002716
(pigment_TANNING.SBayesR)
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Tanning suntan 947,237
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS002716/ScoringFiles/PGS002716.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM008729 PGS001244
(GBE_BIN_FC30001727)
 PSS003879|
African Ancestry|
4,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.52345 [0.50398, 0.54292] R²: 0.00289
Incremental AUROC (full-covars): -0.04291
PGS R2 (no covariates): 0.00485
PGS AUROC (no covariates): 0.46513 [0.44563, 0.48463]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008730 PGS001244
(GBE_BIN_FC30001727)
 PSS003880|
East Asian Ancestry|
1,541 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.54571 [0.50672, 0.5847] PGS R2 (no covariates): 0.00029
R²: 0.01015
Incremental AUROC (full-covars): -0.01074
PGS AUROC (no covariates): 0.50235 [0.46279, 0.54191]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008731 PGS001244
(GBE_BIN_FC30001727)
 PSS003881|
European Ancestry|
24,421 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.64487 [0.63683, 0.65291] R²: 0.06277
Incremental AUROC (full-covars): 0.03781
PGS R2 (no covariates): 0.05363
PGS AUROC (no covariates): 0.63901 [0.631, 0.64703]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008732 PGS001244
(GBE_BIN_FC30001727)
 PSS003882|
South Asian Ancestry|
6,616 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.5248 [0.50879, 0.54081] R²: 0.00212
Incremental AUROC (full-covars): -0.01511
PGS R2 (no covariates): 0.00013
PGS AUROC (no covariates): 0.50088 [0.48459, 0.51717]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008733 PGS001244
(GBE_BIN_FC30001727)
 PSS003883|
European Ancestry|
66,187 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get mildly or occasionally tanned) — AUROC: 0.63688 [0.63202, 0.64174] R²: 0.05636
Incremental AUROC (full-covars): 0.0631
PGS R2 (no covariates): 0.04114
PGS AUROC (no covariates): 0.61836 [0.61342, 0.62331]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008734 PGS001245
(GBE_BIN_FC20001727)
 PSS003820|
African Ancestry|
4,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get moderately tanned) — AUROC: 0.56845 [0.54941, 0.58748] R²: 0.0181
Incremental AUROC (full-covars): -0.00634
PGS R2 (no covariates): 0.00058
PGS AUROC (no covariates): 0.4935 [0.47406, 0.51294]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008735 PGS001245
(GBE_BIN_FC20001727)
 PSS003821|
East Asian Ancestry|
1,541 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get moderately tanned) — AUROC: 0.56854 [0.53942, 0.59766] R²: 0.0235
Incremental AUROC (full-covars): -0.00697
PGS R2 (no covariates): 3e-05
PGS AUROC (no covariates): 0.50505 [0.47505, 0.53504]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008736 PGS001245
(GBE_BIN_FC20001727)
 PSS003822|
European Ancestry|
24,421 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get moderately tanned) — AUROC: 0.60803 [0.60093, 0.61513] R²: 0.0505
Incremental AUROC (full-covars): 0.02684
PGS R2 (no covariates): 0.04554
PGS AUROC (no covariates): 0.59926 [0.59214, 0.60639]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008737 PGS001245
(GBE_BIN_FC20001727)
 PSS003823|
South Asian Ancestry|
6,616 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get moderately tanned) — AUROC: 0.53215 [0.51774, 0.54657] R²: 0.00473
Incremental AUROC (full-covars): -0.01571
PGS R2 (no covariates): 0.00011
PGS AUROC (no covariates): 0.4952 [0.4807, 0.5097]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008738 PGS001245
(GBE_BIN_FC20001727)
 PSS003824|
European Ancestry|
66,187 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get moderately tanned) — AUROC: 0.59038 [0.58606, 0.5947] R²: 0.03719
Incremental AUROC (full-covars): 0.0541
PGS R2 (no covariates): 0.03521
PGS AUROC (no covariates): 0.58661 [0.58228, 0.59094]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008739 PGS001246
(GBE_BIN_FC10001727)
 PSS003706|
African Ancestry|
4,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get very tanned) — AUROC: 0.55472 [0.5369, 0.57253] R²: 0.00767
Incremental AUROC (full-covars): -0.09744
PGS R2 (no covariates): 0.02303
PGS AUROC (no covariates): 0.42303 [0.40544, 0.44063]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008740 PGS001246
(GBE_BIN_FC10001727)
 PSS003707|
East Asian Ancestry|
1,541 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get very tanned) — AUROC: 0.57445 [0.54548, 0.60341] R²: 0.0252
Incremental AUROC (full-covars): 0.0116
PGS R2 (no covariates): 0.00504
PGS AUROC (no covariates): 0.53511 [0.50559, 0.56464]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008741 PGS001246
(GBE_BIN_FC10001727)
 PSS003708|
European Ancestry|
24,421 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get very tanned) — AUROC: 0.74853 [0.74163, 0.75543] R²: 0.19694
Incremental AUROC (full-covars): 0.07826
PGS R2 (no covariates): 0.20123
PGS AUROC (no covariates): 0.75019 [0.74322, 0.75717]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008742 PGS001246
(GBE_BIN_FC10001727)
 PSS003709|
South Asian Ancestry|
6,616 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get very tanned) — AUROC: 0.53071 [0.51584, 0.54558] R²: 0.00488
Incremental AUROC (full-covars): -0.02206
PGS R2 (no covariates): 0.00175
PGS AUROC (no covariates): 0.51457 [0.4998, 0.52934]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008743 PGS001246
(GBE_BIN_FC10001727)
 PSS003710|
European Ancestry|
66,187 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Get very tanned) — AUROC: 0.73548 [0.73096, 0.74] R²: 0.17513
Incremental AUROC (full-covars): 0.13981
PGS R2 (no covariates): 0.14977
PGS AUROC (no covariates): 0.71732 [0.71263, 0.72202]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008744 PGS001247
(GBE_BIN_FC40001727)
 PSS003924|
African Ancestry|
4,524 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Never tan, only burn) — AUROC: 0.72336 [0.70495, 0.74178] R²: 0.1468
Incremental AUROC (full-covars): -0.02841
PGS R2 (no covariates): 0.03694
PGS AUROC (no covariates): 0.40146 [0.38146, 0.42147]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008745 PGS001247
(GBE_BIN_FC40001727)
 PSS003925|
East Asian Ancestry|
1,541 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Never tan, only burn) — AUROC: 0.60911 [0.55312, 0.6651] R²: 0.06219
Incremental AUROC (full-covars): -0.04068
PGS R2 (no covariates): 0.00142
PGS AUROC (no covariates): 0.46835 [0.41763, 0.51907]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008746 PGS001247
(GBE_BIN_FC40001727)
 PSS003926|
European Ancestry|
24,421 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Never tan, only burn) — AUROC: 0.7732 [0.76576, 0.78064] R²: 0.23458
Incremental AUROC (full-covars): 0.08314
PGS R2 (no covariates): 0.24179
PGS AUROC (no covariates): 0.77686 [0.76951, 0.78422]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008747 PGS001247
(GBE_BIN_FC40001727)
 PSS003927|
South Asian Ancestry|
6,616 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Never tan, only burn) — AUROC: 0.54182 [0.51791, 0.56574] R²: 0.00258
Incremental AUROC (full-covars): -0.04265
PGS R2 (no covariates): 0.00055
PGS AUROC (no covariates): 0.48795 [0.46261, 0.51329]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM008748 PGS001247
(GBE_BIN_FC40001727)
 PSS003928|
European Ancestry|
66,187 individuals
 PGP000244 |
Tanigawa Y et al. PLoS Genet (2022)
 Reported Trait: Ease of skin tanning (Never tan, only burn) — AUROC: 0.74303 [0.7382, 0.74787] R²: 0.18357
Incremental AUROC (full-covars): 0.17233
PGS R2 (no covariates): 0.18165
PGS AUROC (no covariates): 0.74085 [0.73597, 0.74572]		 age, sex, UKB array type, Genotype PCs Full Model & PGS R2 is estimated using Nagelkerke's method
PPM010059 PGS001897
(portability-PLR_darker_skin0)
 PSS009393|
European Ancestry|
19,738 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.387 [0.375, 0.3988] sex, age, birth date, deprivation index, 16 PCs —
PPM010060 PGS001897
(portability-PLR_darker_skin0)
 PSS009167|
European Ancestry|
4,029 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.3235 [0.2955, 0.3509] sex, age, birth date, deprivation index, 16 PCs —
PPM010061 PGS001897
(portability-PLR_darker_skin0)
 PSS008721|
European Ancestry|
6,521 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.326 [0.3041, 0.3476] sex, age, birth date, deprivation index, 16 PCs —
PPM010063 PGS001897
(portability-PLR_darker_skin0)
 PSS008273|
South Asian Ancestry|
6,068 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.1171 [0.0921, 0.1418] sex, age, birth date, deprivation index, 16 PCs —
PPM010064 PGS001897
(portability-PLR_darker_skin0)
 PSS008050|
East Asian Ancestry|
1,506 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.0091 [-0.0418, 0.0599] sex, age, birth date, deprivation index, 16 PCs —
PPM010065 PGS001897
(portability-PLR_darker_skin0)
 PSS007837|
African Ancestry|
2,401 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.0775 [0.0374, 0.1173] sex, age, birth date, deprivation index, 16 PCs —
PPM010066 PGS001897
(portability-PLR_darker_skin0)
 PSS008941|
African Ancestry|
3,778 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.0247 [-0.0073, 0.0567] sex, age, birth date, deprivation index, 16 PCs —
PPM010062 PGS001897
(portability-PLR_darker_skin0)
 PSS008495|
Greater Middle Eastern Ancestry|
1,058 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.2918 [0.2352, 0.3465] sex, age, birth date, deprivation index, 16 PCs —
PPM010371 PGS001937
(portability-PLR_less_tanned)
 PSS009424|
European Ancestry|
19,578 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.4089 [0.3972, 0.4205] sex, age, birth date, deprivation index, 16 PCs —
PPM010372 PGS001937
(portability-PLR_less_tanned)
 PSS009198|
European Ancestry|
3,995 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.3298 [0.3018, 0.3572] sex, age, birth date, deprivation index, 16 PCs —
PPM010373 PGS001937
(portability-PLR_less_tanned)
 PSS008752|
European Ancestry|
6,490 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.3092 [0.287, 0.3311] sex, age, birth date, deprivation index, 16 PCs —
PPM010374 PGS001937
(portability-PLR_less_tanned)
 PSS008526|
Greater Middle Eastern Ancestry|
996 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.0834 [0.0207, 0.1454] sex, age, birth date, deprivation index, 16 PCs —
PPM010375 PGS001937
(portability-PLR_less_tanned)
 PSS008304|
South Asian Ancestry|
5,414 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.0218 [-0.0049, 0.0484] sex, age, birth date, deprivation index, 16 PCs —
PPM010376 PGS001937
(portability-PLR_less_tanned)
 PSS008081|
East Asian Ancestry|
1,651 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): -0.0042 [-0.0527, 0.0443] sex, age, birth date, deprivation index, 16 PCs —
PPM010377 PGS001937
(portability-PLR_less_tanned)
 PSS007868|
African Ancestry|
2,004 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): -0.0432 sex, age, birth date, deprivation index, 16 PCs —
PPM010378 PGS001937
(portability-PLR_less_tanned)
 PSS008972|
African Ancestry|
2,347 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): -0.0234 [-0.064, 0.0172] sex, age, birth date, deprivation index, 16 PCs —
PPM011735 PGS002110
(portability-ldpred2_darker_skin0)
 PSS009393|
European Ancestry|
19,738 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.3849 [0.3729, 0.3967] sex, age, birth date, deprivation index, 16 PCs —
PPM011736 PGS002110
(portability-ldpred2_darker_skin0)
 PSS009167|
European Ancestry|
4,029 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.3197 [0.2916, 0.3472] sex, age, birth date, deprivation index, 16 PCs —
PPM011737 PGS002110
(portability-ldpred2_darker_skin0)
 PSS008721|
European Ancestry|
6,521 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.3242 [0.3023, 0.3458] sex, age, birth date, deprivation index, 16 PCs —
PPM011738 PGS002110
(portability-ldpred2_darker_skin0)
 PSS008495|
Greater Middle Eastern Ancestry|
1,058 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.2964 [0.2399, 0.351] sex, age, birth date, deprivation index, 16 PCs —
PPM011739 PGS002110
(portability-ldpred2_darker_skin0)
 PSS008273|
South Asian Ancestry|
6,068 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.1163 [0.0914, 0.1411] sex, age, birth date, deprivation index, 16 PCs —
PPM011740 PGS002110
(portability-ldpred2_darker_skin0)
 PSS008050|
East Asian Ancestry|
1,506 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.0115 [-0.0394, 0.0623] sex, age, birth date, deprivation index, 16 PCs —
PPM011741 PGS002110
(portability-ldpred2_darker_skin0)
 PSS007837|
African Ancestry|
2,401 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.0842 [0.0442, 0.1239] sex, age, birth date, deprivation index, 16 PCs —
PPM011742 PGS002110
(portability-ldpred2_darker_skin0)
 PSS008941|
African Ancestry|
3,778 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Skin colour — — Partial Correlation (partial-r): 0.0232 [-0.0088, 0.0551] sex, age, birth date, deprivation index, 16 PCs —
PPM012090 PGS002155
(portability-ldpred2_less_tanned)
 PSS008526|
Greater Middle Eastern Ancestry|
996 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.0806 [0.0179, 0.1426] sex, age, birth date, deprivation index, 16 PCs —
PPM012087 PGS002155
(portability-ldpred2_less_tanned)
 PSS009424|
European Ancestry|
19,578 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.4051 [0.3933, 0.4168] sex, age, birth date, deprivation index, 16 PCs —
PPM012088 PGS002155
(portability-ldpred2_less_tanned)
 PSS009198|
European Ancestry|
3,995 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.3281 [0.3, 0.3555] sex, age, birth date, deprivation index, 16 PCs —
PPM012089 PGS002155
(portability-ldpred2_less_tanned)
 PSS008752|
European Ancestry|
6,490 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.3057 [0.2834, 0.3276] sex, age, birth date, deprivation index, 16 PCs —
PPM012091 PGS002155
(portability-ldpred2_less_tanned)
 PSS008304|
South Asian Ancestry|
5,414 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): 0.0246 [-0.0021, 0.0512] sex, age, birth date, deprivation index, 16 PCs —
PPM012092 PGS002155
(portability-ldpred2_less_tanned)
 PSS008081|
East Asian Ancestry|
1,651 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): -0.0075 [-0.056, 0.041] sex, age, birth date, deprivation index, 16 PCs —
PPM012093 PGS002155
(portability-ldpred2_less_tanned)
 PSS007868|
African Ancestry|
2,004 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): -0.0465 [-0.0903, -0.0025] sex, age, birth date, deprivation index, 16 PCs —
PPM012094 PGS002155
(portability-ldpred2_less_tanned)
 PSS008972|
African Ancestry|
2,347 individuals
 PGP000263 |
Privé F et al. Am J Hum Genet (2022)
 Reported Trait: Ease of skin tanning — — Partial Correlation (partial-r): -0.0194 [-0.06, 0.0212] sex, age, birth date, deprivation index, 16 PCs —
PPM013115 PGS002350
(pigment_TANNING.BOLT-LMM)
 PSS009843|
African Ancestry|
4,649 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013164 PGS002350
(pigment_TANNING.BOLT-LMM)
 PSS009844|
East Asian Ancestry|
864 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0014 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013213 PGS002350
(pigment_TANNING.BOLT-LMM)
 PSS009845|
European Ancestry|
42,556 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.1206 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013262 PGS002350
(pigment_TANNING.BOLT-LMM)
 PSS009846|
South Asian Ancestry|
6,976 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0003 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013452 PGS002422
(pigment_TANNING.P+T.0.0001)
 PSS009844|
East Asian Ancestry|
864 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013501 PGS002422
(pigment_TANNING.P+T.0.0001)
 PSS009845|
European Ancestry|
42,556 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0722 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013550 PGS002422
(pigment_TANNING.P+T.0.0001)
 PSS009846|
South Asian Ancestry|
6,976 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0001 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013403 PGS002422
(pigment_TANNING.P+T.0.0001)
 PSS009843|
African Ancestry|
4,649 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0008 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013599 PGS002471
(pigment_TANNING.P+T.0.001)
 PSS009843|
African Ancestry|
4,649 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013648 PGS002471
(pigment_TANNING.P+T.0.001)
 PSS009844|
East Asian Ancestry|
864 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0011 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013697 PGS002471
(pigment_TANNING.P+T.0.001)
 PSS009845|
European Ancestry|
42,556 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0729 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013746 PGS002471
(pigment_TANNING.P+T.0.001)
 PSS009846|
South Asian Ancestry|
6,976 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0001 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013795 PGS002520
(pigment_TANNING.P+T.0.01)
 PSS009843|
African Ancestry|
4,649 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0003 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013844 PGS002520
(pigment_TANNING.P+T.0.01)
 PSS009844|
East Asian Ancestry|
864 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0015 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013893 PGS002520
(pigment_TANNING.P+T.0.01)
 PSS009845|
European Ancestry|
42,556 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0582 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013942 PGS002520
(pigment_TANNING.P+T.0.01)
 PSS009846|
South Asian Ancestry|
6,976 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0003 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014040 PGS002569
(pigment_TANNING.P+T.1e-06)
 PSS009844|
East Asian Ancestry|
864 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM013991 PGS002569
(pigment_TANNING.P+T.1e-06)
 PSS009843|
African Ancestry|
4,649 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0001 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014089 PGS002569
(pigment_TANNING.P+T.1e-06)
 PSS009845|
European Ancestry|
42,556 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0703 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014138 PGS002569
(pigment_TANNING.P+T.1e-06)
 PSS009846|
South Asian Ancestry|
6,976 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0001 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014187 PGS002618
(pigment_TANNING.P+T.5e-08)
 PSS009843|
African Ancestry|
4,649 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014236 PGS002618
(pigment_TANNING.P+T.5e-08)
 PSS009844|
East Asian Ancestry|
864 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014285 PGS002618
(pigment_TANNING.P+T.5e-08)
 PSS009845|
European Ancestry|
42,556 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0696 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014334 PGS002618
(pigment_TANNING.P+T.5e-08)
 PSS009846|
South Asian Ancestry|
6,976 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0001 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014530 PGS002667
(pigment_TANNING.PolyFun-pred)
 PSS009846|
South Asian Ancestry|
6,976 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0001 age, sex, age*sex, assessment center, genotyping array, 10 PCs See pigment_TANNING.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014383 PGS002667
(pigment_TANNING.PolyFun-pred)
 PSS009843|
African Ancestry|
4,649 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0 age, sex, age*sex, assessment center, genotyping array, 10 PCs See pigment_TANNING.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014432 PGS002667
(pigment_TANNING.PolyFun-pred)
 PSS009844|
East Asian Ancestry|
864 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.0015 age, sex, age*sex, assessment center, genotyping array, 10 PCs See pigment_TANNING.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014481 PGS002667
(pigment_TANNING.PolyFun-pred)
 PSS009845|
European Ancestry|
42,556 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model when combined with BOLT-LMM vs. covariates alone): 0.1326 age, sex, age*sex, assessment center, genotyping array, 10 PCs See pigment_TANNING.mixweights file at http://data.broadinstitute.org/alkesgroup/polypred_results for combination weights
PPM014579 PGS002716
(pigment_TANNING.SBayesR)
 PSS009843|
African Ancestry|
4,649 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014628 PGS002716
(pigment_TANNING.SBayesR)
 PSS009844|
East Asian Ancestry|
864 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0019 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014677 PGS002716
(pigment_TANNING.SBayesR)
 PSS009845|
European Ancestry|
42,556 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0972 age, sex, age*sex, assessment center, genotyping array, 10 PCs —
PPM014726 PGS002716
(pigment_TANNING.SBayesR)
 PSS009846|
South Asian Ancestry|
6,976 individuals
 PGP000332 |
Weissbrod O et al. Nat Genet (2022)
 Reported Trait: Tanning — — Incremental R2 (full model vs. covariates alone): 0.0003 age, sex, age*sex, assessment center, genotyping array, 10 PCs —

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS008526 — — 996 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS009167 — — 4,029 individuals — European Poland (NE Europe) UKB —
PSS009424 — — 19,578 individuals — European UK (+ Ireland) UKB —
PSS008273 — — 6,068 individuals — South Asian India (South Asia) UKB —
PSS003924 — —
[
  • 798 cases
  • , 3,726 controls
]
 — African unspecified — UKB —
PSS003925 — —
[
  • 128 cases
  • , 1,413 controls
]
 — East Asian — UKB —
PSS003926 — —
[
  • 4,667 cases
  • , 19,754 controls
]
 — European non-white British ancestry UKB —
PSS003927 — —
[
  • 552 cases
  • , 6,064 controls
]
 — South Asian — UKB —
PSS003928 — —
[
  • 11,988 cases
  • , 54,199 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS008941 — — 3,778 individuals — African unspecified Nigeria (West Africa) UKB —
PSS009198 — — 3,995 individuals — European Poland (NE Europe) UKB —
PSS008304 — — 5,414 individuals — South Asian India (South Asia) UKB —
PSS008050 — — 1,506 individuals — East Asian China (East Asia) UKB —
PSS003820 — —
[
  • 1,138 cases
  • , 3,386 controls
]
 — African unspecified — UKB —
PSS003821 — —
[
  • 580 cases
  • , 961 controls
]
 — East Asian — UKB —
PSS003822 — —
[
  • 9,176 cases
  • , 15,245 controls
]
 — European non-white British ancestry UKB —
PSS003823 — —
[
  • 2,395 cases
  • , 4,221 controls
]
 — South Asian — UKB —
PSS003824 — —
[
  • 27,274 cases
  • , 38,913 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS003706 — —
[
  • 1,589 cases
  • , 2,935 controls
]
 — African unspecified — UKB —
PSS003707 — —
[
  • 605 cases
  • , 936 controls
]
 — East Asian — UKB —
PSS003708 — —
[
  • 5,648 cases
  • , 18,773 controls
]
 — European non-white British ancestry UKB —
PSS003709 — —
[
  • 2,117 cases
  • , 4,499 controls
]
 — South Asian — UKB —
PSS003710 — —
[
  • 13,602 cases
  • , 52,585 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS008972 — — 2,347 individuals — African unspecified Nigeria (West Africa) UKB —
PSS008721 — — 6,521 individuals — European Italy (South Europe) UKB —
PSS008081 — — 1,651 individuals — East Asian China (East Asia) UKB —
PSS007837 — — 2,401 individuals — African American or Afro-Caribbean Carribean UKB —
PSS009843 — — 4,649 individuals — African unspecified — UKB —
PSS009844 — — 864 individuals — East Asian — UKB —
PSS009845 — — 42,556 individuals — European Non-British European UKB —
PSS009846 — — 6,976 individuals — South Asian — UKB —
PSS003879 — —
[
  • 1,037 cases
  • , 3,487 controls
]
 — African unspecified — UKB —
PSS003880 — —
[
  • 251 cases
  • , 1,290 controls
]
 — East Asian — UKB —
PSS003881 — —
[
  • 5,255 cases
  • , 19,166 controls
]
 — European non-white British ancestry UKB —
PSS003882 — —
[
  • 1,622 cases
  • , 4,994 controls
]
 — South Asian — UKB —
PSS003883 — —
[
  • 14,769 cases
  • , 51,418 controls
]
 — European white British ancestry UKB Testing cohort (heldout set)
PSS009393 — — 19,738 individuals — European UK (+ Ireland) UKB —
PSS008495 — — 1,058 individuals — Greater Middle Eastern (Middle Eastern, North African or Persian) Iran (Middle East) UKB —
PSS008752 — — 6,490 individuals — European Italy (South Europe) UKB —
PSS007868 — — 2,004 individuals — African American or Afro-Caribbean Carribean UKB —