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Table 2 Functional candidate genes that are missed depending on the gene definition

From: Genetic distance as an alternative to physical distance for definition of gene units in association studies

Chromosomea

Phenotypeb

van der Harst et al.

SRR ≥ 2c

± 50 Kbc

nsSNP

    

1q23

MCHC

OR6Y1, OR10Z1, SPTA1

-

OR6Y1

1q44

RBC

TRIM58

-

-

6p21

MCH

HFE

HFE

HFE

6p21

RBC

HLA-DQA1

-

-

10q11

MCV

MARCH8

-

-

11q13

MCV

RPS6KB2

-

-

11q13

HB

ARHGEF17

-

-

12q24

HB

SH2B3

-

-

12q24

MCV

ACADS

-

-

16q22

RBC

CTRL, PSMB10

-

CTRL, PSMB10

19p13

MCV

UBXD1, NUDT19

UBXD1

UBXD1

22q11

MCV

YDJC

YDJC

-

22q12

MCH

FBXO7, TMPRSS6

-

-

 

∑ nsSNP

18

-3

-5

eQTL

    

4q27

MCV

CCNA2

-

-

6p23

MCH

GMPR

-

-

6p21

RBC

HLA-DQA1/HLA-DQA2

HLA-DQA2

HLA-DQA2

8p11

MCHC

C8orf40

-

-

10q11

MCV

MARCH8

-

-

11p15

HB

AKIP1/C11orf16, NRIP3

-

NRIP3

11q13

MCV

RPS6KB2, PTPRCAP/COROB1

-

-

11q13

HB

ARHGEF17

-

-

15q22

MCV

PTPLAD1

-

PTPLAD1

15q25

MCHC

DNAJA4

-

-

16q22

RBC

DUS2L

-

DUS2L

17q11

MCH

ERAL1, TRAF4

-

ERAL1

17q12

RBC

CDK12

-

-

17q25

HB

PGS1

-

-

18q21

MCH

C18orf25

-

-

19p13

MCH

CALR, FARSA

-

-

22q11

MCV

UBE2L3

-

-

22q13

MCV

ECGF1

-

-

 

∑ eQTL

25

-1

-5

 

Total

43

-4

-10

  1. aLoci in chromosome 17q21 were excluded from analysis because it contains a common inversion polymorphism of approximately 900 kb in populations with European ancestry that shows exceptional LD and inheritance [26].
  2. bPhenotypes were: MHCH = Mean cell haemoglobin concentration, RBC = Red blood cell count, MCH = Mean cell haemoglobin, MCV = Mean cell volume and HB = Haemoglobin.
  3. cGenes that did not overlap with the SRR ≥ 2 or the ± 50 Kb definition are indicated: - no differences with the functional candidate genes highlighted by van der Harst et al. [20]; genes that were highlighted by van der Harst et al. [20] but whose definition did not overlap with the top associated SNP.
  4. Functional candidates were selected in van der Harst et al. [20] because they contained nsSNP (upper rows) or were regulated by eQTL (lower rows) in LD with the top associated SNP.