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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.