Table 2 Information for the 19 example genetic clusters

From: Phenotypic and genetic associations of quantitative magnetic susceptibility in UK Biobank brain imaging

Related function

Brain regions

Cluster no.

Lead IDP

Npair

rsID

MAF

Gene

Genetic function (cluster)

eQTL

−log10 (Pdis)

Iron homeostasis

Pallidum, substantia nigra, putamen, caudate, hippocampus, thalamus, amygdala, accumbens

6

QSM pallidum (L)

15

rs11884632

0.256

SLC40A1

Downstream, intron

WDR75, SLC40A1, C2orf88, AC013439.4

71.271

10

T2* putamen (L)

18

rs4428180

0.151

TFP1:TF

Intron

TF

42.458

12

QSM SN (L)

7

rs9867473

0.571

TFRC

UTR3

MUC20, MIR570

14.562

27

QSM putamen (R)

21

rs1800562

0.077

HFE

Exon (missense)

RP1-221C16.8, U91328.19

48.973

66

QSM thalamus (L)

1

rs1131488

0.282

HMBS

Exon (synonymous)

VPS11, HMBS, RP11-110I1.14

7.8271

Metal ion transport

Caudate, putamen, pallidum, substantia nigra, accumbens, WMH

15

QSM pallidum (R)

18

rs13107325

0.070

SLC39A8

Exon (missense), intron

–

105.51

47

QSM caudate (L)

24

rs4348791

0.395

SLC39A12

Upstream, intron

SLC39A12

100.55

Calcium homeostasis

Caudate, pallidum, substantia nigra, putamen

49

QSM caudate (R)

10

rs11012783

0.386

CACNB2

Intergenic

CACNB2, SLC39A12-AS1

75.579

60

T2* caudate (R)

3

rs11013321

0.395

CACNB2

Intron

–

9.0318

68

T2* putamen (R)

3

rs73192811

0.074

TPCN1

Intron

RITA1

10.406

70

QSM putamen (R)

1

rs10842717

0.376

ITPR2

Intron

–

7.7763

16

QSM pallidum (L)

12

rs13105682

0.057

BANK1

Intron

–

46.911

18

QSM pallidum (L)

7

rs76062146

0.028

BANK1

Intron

–

14.353

20

QSM pallidum (L)

2

rs71614699

0.012

BANK1

Intron

–

10.914

Myelin and glia

Thalamus, hippocampus, pallidum, putamen

11

QSM pallidum (L)

3

rs34457487

0.554

MOBP

Intron

–

15.932

74

QSM putamen (L)

3

rs7203922

0.310

PLLP

Upstream, intron

–

10.575

80

QSM thalamus (L)

4

rs1126642

0.043

GFAP

Exon (missense)

–

11.181

Extracellular matrix

Pallidum, substantia nigra, WMH

9

QSM pallidum (L)

5

a

0.017

COL3A1

Intron

–

9.5122

25

QSM WMH

2

rs10052710

0.197

VCAN

Intron

–

18.745

  1. Lead IDP and rsID represent the top IDP/variant pair in each group. Npair indicates the number of IDP/variant pairs included in each genetic cluster. The –log10 (Pdis) values provided are two-sided, unadjusted values from the main discovery cohort. Genetic function refers to the position of the cluster’s variants with regards to the corresponding gene.
  2. SN, substantia nigra; R, right; L, left; UTR, untranslated region; MAF, minor allele frequency; eQTL, expression quantitative trait loci.
  3. a2:189666936_ATTTGACACTCCTGATTCATCAC_A
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