Table 2 Genetic loci associated with the ALPS-indexes

From: Genome-wide association study unravels mechanisms of brain glymphatic activity

Region

Lead variant

Annotation

GWAS in UKB discovery cohort

 

SNP

chr:position

EA/NEA

MAF

Function

Closest gene(s)

Phenotype

Effect (β)a

SEa

p-valuea

2p23.3

rs3769136

2:27168743

C/T

0.3668

intronic

DPYSL5

Mean/Left/Right

0.064

0.008

8.18 × 10−16

7p22.3

rs2533872b

7:2883004

C/G

0.2962

intronic

GNA12

Mean/Left/Right

−0.062

0.009

2.40 × 10−13

12q23.3

rs12146713

12:106476805

C/T

0.0915

intronic

NUAK1

Mean/Left/Right

−0.091

0.013

2.48 × 10−12

11p15.1

rs2702723c

11:19498582

T/A

0.4573

intronic

NAV2

Mean/Left/Right

−0.051

0.008

2.60 × 10−11

16q24.2

rs4843555b

16:87231160

T/C

0.4433

intergenic

C16orf95

Mean/Left/Right

0.05

0.008

1.53 × 10−10

17q21.31

17:44289832_A_G

17:44289832

G/A

0.4404

intronic

KANSL1

Mean/Right

−0.046

0.008

3.64 × 10−09

3q28

rs61067594

3:190650833

A/G

0.4046

intergenic

GMNC

Right

0.047

0.008

4.65 × 10−09

22q13.1

rs4239889b, c

22:38140352

G/T

0.332

intronic

NOL12:TRIOBP

Mean/Left/Right

−0.049

0.008

6.76 × 10−09

2p22.2

rs2717493

2:37122552

A/G

0.4751

intronic

STRN

Mean/Left

0.043

0.008

1.89 × 10−08

3q26.2

3:170972928_AAT_A

3:170972928

A/AAT

0.2773

intronic

TNIK

Mean/Left

0.048

0.009

2.21 × 10−08

2q23.3

rs776546277

2:151966287

TCTGA/T

0.4672

intergenic

AC018731.3

Mean

0.043

0.008

2.31 × 10−08

20q13.12

rs6012259

20:46374885

G/C

0.2147

intronic

SULF2

Mean/Right

−0.053

0.01

2.66 × 10−08

14q23.2

rs3783324

14:100350017

C/T

0.1551

intronic

EML1

Mean/Right

−0.055

0.01

2.95 × 10−08

12q23.1

rs10778024

12:100196655

C/A

0.4215

intronic

ANKS1B

Right

0.044

0.008

3.96 × 10−08

9q31.3

rs10817103

9:113649502

T/C

0.1272

intronic

LPAR1

Mean

0.067

0.012

4.01 × 10−08

11q12.2

rs174538

11:61560081

A/G

0.3131

UTR5

TMEM258

Mean

−0.045

0.008

4.72 × 10−08

5q15

5:92872910_GA_G

5:92872910

G/GA

0.0308

ncRNA_intronic

NR2F1-AS1

Mean/Right

−0.097

0.018

4.95 × 10−08

  1. P values and β effects were computed by GWAS via PLINK in a linear additive regression model (two-sided test), adjusting for age, age2, sex, imaging center, and the first ten genetic principal components (PCs). P values shown are original values. GWAS analyses were adjusted for age, age2, sex, imaging site, and the first ten genetic principal components.
  2. Chr chromosome, EA effect allele, GWAS genome-wide association study, NEA non-effect allele, MAF minor allele frequency, SE standard error, SNP single nucleotide polymorphism.
  3. aFrom the GWAS results for the first phenotype reported in the “Phenotype” column.
  4. bFor these loci, the lead SNP was different in analyses of the right ALPS-index (lead SNP in the GWAS of mean ALPS-index → right ALPS-index: rs2533872 → rs2644291; rs4843555 → rs4843550; rs4239889 → rs1894526).
  5. cFor these loci, the lead SNP was different in analyses of the left ALPS-index (lead SNP in the GWAS of mean ALPS-index → left ALPS-index: rs2702723 → rs2702721; rs4239889 → rs4820303).
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