Table 1 Single variant association and functional prediction for variants contributing to the gene-level significance.

From: Impact of low-frequency coding variants on human facial shape

Chr

Gene

Gene info

Gene-level association

Variant-level association

Modulea

MultiSKAT P-valuea

SNP

Pos (hg19)

Ref/Altb

Functionc

CADD scored

MAF (%)

Modulee

MultiPhen P-valuee

6

HFE

Homeostatic iron regulator, binds to transferrin receptor (TFR) and reduces its affinity for iron-loaded transferrin

5, 22

1.51E-10

rs149342416

26,087,686

G/C

Arg6Ser

15.3

0.09

22

0.07

rs143662783

26,087,718

C/G

Thr17Ile

13.4

0.09

5

0.87

11

NECTIN1

Nectin 1, cell adhesion molecule

27

2.54E-07

rs142863092

119,548,369

G/A

Arg210His

25.2

0.09

27

1.08E−03

rs137991779

119,549,425

G/A

Gly44Ser

29.2

0.11

27

0.15

13

CARS2

Cysteinyl-tRNA synthetase 2, mitochondrial

10, 20

5.22E-10

rs151097801

111,296,817

C/T

Pro138Leu

22.4

0.09

20

0.12

rs117788141

111,357,899

G/A

Val69Ile

28

0.09

10

0.01

14

LTB4R

Leukotriene B4 receptor 1, receptor for extracellular ATP > UTP and ADP

20

6.88E-08

rs143666989

24,780,865

A/G

Gln332Arg

16.6

0.11

20

0.11

rs148153989

24,780,915

A/T

Met349Leu

12.5

0.09

20

0.59

16

TELO2

Telomere length regulation protein homolog, regulate DNA damage response

10

1.19E-09

rs140903666

1,544,313

G/A

Ala11Thr

6.3

0.22

10

8.21E−04

rs144863771

1,544,314

C/A

Ala11Asp

10.7

0.22

10

8.21E−04

rs147858841

1,555,541

C/T

Ala132Val

9.4

0.11

10

0.43

23

AR

Androgen receptor, steroid hormone receptors

18

1.77E-07

rs142280455

66,905,875

A/G

Ser598Gly

22.4

0.13

18

0.81

rs137852591

66,941,751

C/G

Gln267Glu

25

0.13

18

3.91E−03

23

FTSJ1

Putative tRNA (cytidine(32)/guanosine(34)-2′-O)-methyltransferase

1, 6, 12, 28

2.46E-10

rs142932029

48,341,118

G/A

Ser161Asn

7.4

0.08

28

1.59E−14

rs201095751

48,341,414

C/T

Splice site

0.1

0.11

12

0.1

  1. aFor genes associated with multiple facial modules, the most significant module is in bold and only its p-value is shown.
  2. bAlleles are listed as alternative/reference alleles on the forward strand of the reference genome.
  3. cFor missense variant, amino acid substitution is given.
  4. dBioinformatic prediction of variant effect, higher score indicates greater damaging effect.
  5. eVariants were tested against all module(s) with gene-level significance, and for genes associated with multiple modules, only the module yielding the smallest p-value in the variant-level test is shown.
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