Table 1 Lead variants associated with the skin color identified through meta-analysis of GWAS (P < 5 × 10−8)

From: Mapping and annotating genomic loci to prioritize genes and implicate distinct polygenic adaptations for skin color

rsID

GRCh37

Traits

Nearest or colocalized genes

Function

A1

A2

L*

a*

b*

EAF

β

s.e.

P

β

s.e.

P

β

s.e.

P

Previously unreported loci

 rs7520584

1:54000726

(L*),a*

GLIS1

intronic

G

A

−0.029

0.007

1.93 × 10−5

0.040

0.007

4.71 × 10−9

0.008

0.007

2.18 × 10−1

0.497

 rs702488

1:54204324

L*,a*

GLIS1

upstream

T

C

−0.045

0.008

3.36 × 10−8

0.048

0.008

2.71 × 10−9

0.015

0.008

6.01 × 10−2

0.231

 rs7529037

1:205637501

L*,(a*),(b*)

SLC45A3*, RAB29*, NUCKS1*, PM20D1*

intronic

G

C

0.046

0.007

1.89 × 10−11

−0.032

0.007

3.22 × 10−6

−0.031

0.007

5.34 × 10−6

0.457

 rs75998173

1:219110527

(L*),a*

MIR548F3

regulatory

G

A

0.077

0.020

1.45 × 10−4

−0.113

0.020

2.16 × 10−8

−0.057

0.020

5.23 × 10−3

0.029

 rs9853827

3:139002193

L*,a*

PISRT1, MRPS22

regulatory

T

A

0.039

0.007

1.57 × 10−8

−0.042

0.007

1.14 × 10−9

−0.010

0.007

1.69 × 10−1

0.409

 rs7667134

4:166643609

a*,b*

LINC01179, KLHL2*

intronic

T

A

−0.016

0.007

1.86 × 10−2

0.058

0.007

7.48 × 10−17

−0.041

0.007

3.02 × 10−9

0.401

 rs9361843

6:82287485

L*,a*,(b*)

BCKDHB, TENT5A*

intergenic

T

A

0.038

0.007

3.68 × 10−8

−0.038

0.007

2.42 × 10−8

−0.023

0.007

8.78 × 10−4

0.438

 rs6977057

7:96399494

(L*),a*

SEM1, LOC105375414, DLX6*

intergenic

C

T

−0.039

0.007

5.01 × 10−8

0.040

0.007

1.76 × 10−8

0.000

0.007

9.78 × 10−1

0.335

 rs3740342

10:88428718

(L*),a*,(b*)

LDB3*, OPN4*

intronic

T

C

−0.024

0.007

5.57 × 10−4

0.039

0.007

1.58 × 10−8

0.023

0.007

9.07 × 10−4

0.454

 rs2957668

11:10404382

L*,a*

CAND1.11, CTR9*

intronic

T

C

−0.040

0.007

5.21 × 10−9

0.052

0.007

4.66 × 10−14

−0.004

0.007

5.67 × 10−1

0.483

 rs10899491

11:78106305

L*

GAB2, USP35*

intronic

C

T

−0.039

0.007

2.73 × 10−8

0.016

0.007

2.29 × 10−2

0.006

0.007

3.62 × 10−1

0.380

 rs9924126

16:81283598

b*

BCO1

intronic

G

A

−0.007

0.007

3.36 × 10−1

0.011

0.007

1.38 × 10−1

0.041

0.007

2.49 × 10−8

0.321

Previously reported loci

 rs6689641

1:110720400

L*,(a*),b*

SLC6A17*

intronic

G

A

0.053

0.007

1.65 × 10−13

−0.036

0.007

3.90 × 10−7

−0.072

0.007

7.11 × 10−24

0.344

 rs10173066

2:33057305

(L*),b*

LINC00486, LTBP1*

intronic

C

G

0.029

0.007

2.56 × 10−5

−0.009

0.007

1.89 × 10−1

−0.057

0.007

2.10 × 10−16

0.417

 rs10929285

2:234613677

b*

UGT1A6, SNORC*

intronic

T

G

0.008

0.007

2.44 × 10−1

0.003

0.007

6.93 × 10−1

−0.054

0.007

6.35 × 10−15

0.427

 rs3773364

3:12189968

(L*),a*

SYN2

intronic

G

A

−0.035

0.007

5.04 × 10−7

0.052

0.007

3.32 × 10−14

0.019

0.007

5.53 × 10−3

0.455

 rs77310623

6:146871819

L*,(a*),b*

RAB32

intronic

A

G

0.097

0.013

9.64 × 10−14

−0.054

0.013

3.86 × 10−5

−0.088

0.013

1.29 × 10−11

0.074

 rs800884

8:116502628

L*,b*

TRPS1

intronic

C

A

0.059

0.009

1.08 × 10−11

−0.012

0.009

1.56 × 10−1

0.052

0.009

1.63 × 10−9

0.193

 rs16935073

9:16795790

L*,b*

BNC2

intronic

C

A

0.085

0.007

5.39 × 10−34

−0.019

0.007

7.29 × 10−3

−0.085

0.007

9.59 × 10−35

0.423

 rs72620727

12:89110410

L*,a*,b*

KITLG, LINC02458, TMTC3*

intergenic

C

A

0.101

0.007

1.22 × 10−46

−0.048

0.007

1.31 × 10−11

−0.108

0.007

3.37 × 10−53

0.375

 rs10846744

12:125312425

a*,b*

SCARB1

intronic

G

C

0.021

0.007

3.73 × 10−3

−0.058

0.007

3.77 × 10−15

−0.119

0.007

2.48 × 10−59

0.323

 rs728404

15:28200042

L*,a*,b*

OCA2

intronic

C

T

−0.178

0.011

1.08 × 10−62

0.061

0.007

7.78 × 10−9

0.157

0.011

5.32 × 10−50

0.117

 rs74653330

15:28228553

L*,a*,b*

OCA2

missense

T

C

0.345

0.014

2.37 × 10−137

−0.127

0.014

5.12 × 10−20

−0.375

0.014

3.64 × 10−162

0.065

 rs12598316

16:89916600

L*,(b*)

SPIRE2*, DEF8*, CPNE7*

intronic

A

C

0.059

0.010

5.06 × 10−9

−0.002

0.010

8.20 × 10−1

−0.052

0.010

2.95 × 10−7

0.132

 rs33932559

16:89986025

L*,b*

MC1R

missense

C

T

0.118

0.019

6.39 × 10−10

−0.024

0.019

2.12 × 10−1

−0.126

0.019

3.66 × 10−11

0.033

 rs2240751

19:3548231

a*,(b*)

MFSD12

missense

G

A

−0.017

0.007

1.95 × 10−2

0.040

0.007

2.57 × 10−8

0.030

0.007

4.12 × 10−5

0.332

  1. See Supplementary Data 1 for detailed information on previously reported variants. See Supplementary Data 4 for results in the replication GWAS and summary statistics of association between lead variants and raw phenotypes (without the inverse normal transformation). Colocalized genes in skin tissues are marked with asterisks. Abbreviations: GRCh37, chromosome number and base pair position (GRCh37/hg19); traits, genome-wide significant trait (nominally significant (P < 0.05/23) trait); A1, effective allele; A2, non-effective allele; β, coefficient of each SNP estimated by linear regression; s.e., standard error; EAF, effective allele frequency in the study sample; P, P-value of β.
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