Table 1 Association results of the lead SNPs of novel genome-wide significant loci with haematological traits.

From: Insights into the genetic architecture of haematological traits from deep phenotyping and whole-genome sequencing for two Mediterranean isolated populations

Trait

Chr

Gene

Rs-id

Position

Type

A1*

A0*

AF*

AF Topmed

Beta

SE

P value

Pomak

White blood cell count

2

LOC105374834

rs551751343

81,484,692

Intron

T

C

0.004

0.0001

1.72

0.29

4.1 × 10–9

2

 

–

81,745,516

–

A

G

0.004

–

1.72

0.29

4.1 × 10–9

2

LOC102724542

rs1041582657

81,759,339

Intron

A

G

0.004

0.00001

1.72

0.29

4.1 × 10–9

2

 

rs556280089

81,954,850

Intergenic

T

C

0.004

0.00001

1.72

0.29

4.1 × 10–9

2

rs989421555

82,175,919

Intergenic

G

C

0.004

0.00009

1.72

0.29

4.1 × 10–9

2

–

82,474,946

–

G

A

0.004

–

1.72

0.29

4.1 × 10–9

2

rs576414992

82,654,697

Intergenic

G

C

0.004

0.00006

1.72

0.29

4.1 × 10–9

2

LOC105374831

rs73941786

82,835,859

Intron

C

A

0.004

0.00833

1.72

0.29

4.1 × 10–9

2

LOC105374834

rs190806297

83,537,814

Intron

A

G

0.004

0.00004

1.72

0.29

4.1 × 10–9

2

 

rs140340075

83,662,388

Intergenic

C

A

0.004

–

1.72

0.29

4.1 × 10–9

2

rs188113595

83,930,989

Intergenic

T

C

0.004

0.00144

1.72

0.29

4.1 × 10–9

2

rs573444805

84,150,305

Intergenic

G

C

0.004

0.00004

1.72

0.29

4.1 × 10–9

2

rs548781149

84,159,599

Intergenic

T

C

0.004

0.00004

1.72

0.29

4.1 × 10–9

2

–

84,341,726

–

C

C

0.004

–

1.72

0.29

4.1 × 10–9

2

–

84,464,745

–

T

G

0.004

–

1.72

0.29

4.1 × 10–9

2

–

84,535,416

–

C

C

0.004

–

1.72

0.29

4.1 × 10–9

Red cell distribution width

9

SVEP1

rs189173017

110,549,951

110,453,573

Intron

G

A

0.004

0.00294

− 1.90

0.30

8.4 × 10–10

Red cell distribution width

9

LPAR1

rs145221983

110,885,694

Intron

G

C

0.002

0.00178

− 2.64

0.39

3.9 × 10–11

platelet distribution width

20

APCDD1L

rs73183273

58,478,356

Intron

A

C

0.007

0.00483

1.44

0.23

4.1 × 10–9

MANOLIS

Red blood cell count

15

 

rs1320751535

101,913,651

Intergenic

G

A

0.009

0.00002

1.52

0.23

6.2 × 10–10

  1. Betas are reported in units of standard deviation of the traits. The lead SNP for the locus on chromosome 2 is represented by 16 variants in perfect linkage disequilibrium covering an area of 3 Mb.*A0 is the reference allele and A1 is the effect allele for which the allele frequency (AF) is reported in the current sample and in TopMed.
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