Table 1 The top loci associated with FA and the three most common types of FA in 2,197 discovery samples of European ancestry.

From: Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children

SNP

CHR

Position

Nearest gene

Allele*

MAF†

P for SNP–phenotype association‡

      

FA

PA

Egg allergy

Milk allergy

The five top loci for FA

 rs12121623

1

54931396

SSBP3|ACOT11

G/T

0.13

3.1 × 10−7

0.024

0.046

0.053

 rs1318710

4

101436201

EMCN

A/G

0.10

2.6 × 10−6

0.002

0.020

0.207

 rs777717

2

195954734

LOC645314|SLC39A10

C/T

0.08

4.7 × 10−6

0.008

0.057

0.214

 rs10994607

10

62760742

RHOBTB1

C/T

0.04

7.1 × 10−6

0.250

0.028

4.6 × 10−5

 rs6942407

7

86861313

LOC100289677|TP53TG1

G/A

0.21

8.2 × 10−6

7.6 × 10−4

0.016

0.003

The five top loci for PA

 rs9275596

6

32681631

HLA-DQB1|HLA-DQA2

T/C

0.35

0.006

6.8 × 10−10

0.509

0.247

 rs7192

6

32411646

HLA-DRA

G/T

0.39

0.175

5.5 × 10−8

0.293

0.468

 rs862942

14

26492233

STXBP6|NOVA1

T/C

0.07

2.7 × 10−4

3.0 × 10−6

0.169

0.026

 rs4584173

8

135336557

LOC100129104|ZFAT

T/C

0.40

0.031

3.6 × 10−6

0.168

0.386

 rs10878354

12

66384885

HMGA2|LLPH

G/A

0.23

0.031

5.1 × 10−6

0.603

0.451

The five top loci for egg allergy

 rs7717393

5

155753914

SGCD

C/G

0.07

0.067

0.627

1.4 × 10−6

2.7 × 10−4

 rs5961136

23

54802520

ITIH5L

T/G

0.39

0.251

0.067

2.4 × 10−6

0.900

 rs250585

16

23401076

COG7

G/A

0.17

0.003

0.101

3.8 × 10−6

0.021

 rs16823014

2

169817713

ABCB11

G/A

0.05

0.352

0.563

4.4 × 10−6

0.052

 rs6498482

16

13987719

LOC729993|ERCC4

T/C

0.39

0.022

0.158

4.8 × 10−6

0.006

The five top loci for milk allergy

 rs9898058

17

47818821

FAM117A

C/T

0.15

7.7 × 10−5

0.014

0.016

1.1 × 10−6

 rs17032597

2

67055115

LOC100289292|ETAA1

C/A

0.29

0.003

0.568

0.074

1.6 × 10−6

 rs78405116

11

1892562

LSP1

G/T

0.03

0.015

0.423

0.775

1.7 × 10−6

 rs10994613

10

62780127

RHOBTB1|TMEM26

G/A

0.03

1.6 × 10−5

0.997

0.036

4.8 × 10−6

 rs7833294

8

58008281

IMPAD1|LOC286177

C/T

0.02

0.281

0.504

0.066

7.3 × 10−6

  1. CHR, chromosome; FA, food allergy; MAF, minor allele frequency; MQLS, modified quasi-likelihood score; PA, peanut allergy; SNP, single-nucleotide polymorphism.
  2. Only the genotyped SNP with the minimum P-value based on the MQLS test is shown for each gene.
  3. *Major/minor allele.
  4. †The MAF was calculated using the genotyping data from parents of European ancestry.
  5. ‡P-value was generated using the MQLS test in the 2,197 discovery samples.
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