Table 3 Fine-mapping results

From: Genome-wide association analysis of plasma lipidome identifies 495 genetic associations

Locus

Variant

Function

Gene

CADD

Finnish enrichm.

MAF

Traits (P-value)

PCSK9

rs11591147-T

missense

PCSK9

10.4

3.10

0.033

CE 18:2;0 (2e-14),

3 SMs: SM 34:1;2 (2e-19), c3 (1e-14), c8 (2e-13)

GCKR

rs1260326-T

missense

GCKR

13.2

1.07

0.349

2 DAGs: DAG 18:1;0_18:2;0 (1e-12), 16 TAGs: TAG 50:4;0 (4e-22),

c2 (4e-13), c3 (1e-17)

SMIM13

rs1292311927-T*

splice_region

ELOVL2

22.9

FIN-specific

0.004

c6 (2e-7)

LPL

rs268-G

missense

LPL

21.3

1.01

0.023

3 TAGs: TAG 54:4;0 (1e-9)

LIPC

rs201563586-A*

missense

LIPC

24.9

FIN-specific

0.002

c2 (8e-8)

 

rs113298164-T

missense

LIPC

24.1

4.41

0.017

5 PCs: PC 18:0;0_18:2;0 (1e-12),

PC O-16:2;0/18:0;0 (3e-12),

5 PEs: PE 16:0;0_20:4;0 (4e-47),

c2 (3e-62), c3 (2e-7), c4 (2e-10),

c5 (4e-15), c7 (2e-7), c10 (1e-10)

LCAT

rs4986970-T

missense

LCAT

23.2

0.83

0.028

c7 (1e-16)

ABHD3

rs1253048206-G*

intergenic

 

11.8

 

0.017

c2 (3e-6)

 

rs186249276-T*

missense

ABHD3

23.7

29.64

0.004

c2 (4e-19), c3 (5e-12)

APOE

rs7412-T

missense

APOE

26.0

0.56

0.053

5 CEs: CE 18:2;0 (2e-14), c3 (3e-23), c6 (2e-18), c7 (2e-53), c8 (2e-65), c11 (4e-14)

 

rs429358-C

missense

APOE

16.7

1.29

0.189

2 CEs: CE 20:2;0 (9e-12), c7 (1e-29), c9 (8e-12)

SPHK2

rs61751862-C*

missense

SPHK2

22.1

2.45

0.031

c8 (6e-16)

LINC01722

rs61738161-A*

missense

SPTLC3

18.0

2.24

0.086

3 Cers: Cer 42:2;2 (3e-17), c8 (7e-19)

HNF4A

rs1800961-T

missense

HNF4A

21.4

1.41

0.052

2 CEs: CE 18:3;0 (1e-10), c2 (1e-10)

AGPAT3

rs62229686-T*

missense

AGPAT3

16.3

1.44

0.039

c3 (7e-17)

  1. Locus gene name in italic, variant rsid-minor allele, *variants reaching only low PIP (<0.1) in UKB, function variant function from VEP, gene gene name from VEP in italic, MAF minor-allele frequency, Finnish enrichm. Finnish enrichment calculated as ratio of MAF between our Finnish data and non-Finnish-non-Swedish-non-Estonian European samples in gnomAD v2.1. Bolded if >2. Variants not detected outside Finland in gnomAD are marked as FIN-specific.
  2. Variants with a CADD score >10 and a high PIP (>0.9) in GeneRISK are listed. Traits for which the variant reaches a high PIP are listed and, in the case of multiple species of a lipid class, the number of species and the species for which the variant reaches the lowest P-value are given. Two-sided P-values calculated using a linear-mixed-model (uv) and canonical correlation analysis (mv) are reported.
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