Table 1 Identified SNPs for GERD (Chromosomes 1–6)

From: Gastroesophageal reflux GWAS identifies risk loci that also associate with subsequent severe esophageal diseases

Chr

SNP

BP

A1/A2

OR [95% CI]

GERD adj. P

Meta

BE/EA P

Gene context

eQTL gene

PheWAS

1

rs1937450

66M

T/G

0.97 [0.96–0.98]

1.63 × 10−8

---

0.73

[PDE4B]; U4, −81303

 

Obesity (3.0 × 10−9)

1

rs7552188

98M

T/C

1.04 [1.03–1.06]

3.76 × 10−10

++?

0.54

[DPYD]

DPYD (1.9 × 10−7)

Obesity (2.1 × 10−10)

2

rs11901649

21M

G/A

1.03 [1.02–1.04]

2.14 × 10−8

++?

1.03 × 10−7

[APOB]

APOB (2.9 × 10−6)

 

2

rs4362541

68M

A/T

1.05 [1.03–1.06]

3.38 × 10−10

+++

0.0033

   

2

rs7609078

100M

G/A

1.04 [1.02–1.05]

2.54 × 10−9

+++

0.22

[AFF3]

 

Height (1.9 × 10−5)

3

rs74652506

43M

C/T

0.96 [0.94–0.97]

4.16 × 10−8

---

0.95

[ANO10]; SNRK, 51244

SNRK (3.2 × 10−8)

Obesity (2.0 × 10−7), Height (5.3 × 10−5)

3

rs7613875

50M

C/A

0.97 [0.96–0.98]

3.67 × 10−8

---

0.068

RBM6, −5962; MON1A, 4069

RBM6 (9.2 × 10−69);

BMI (6.9 × 10−33), EDU (3.6 × 10−28)

3

rs4676893

71M

A/T

1.04 [1.03–1.05]

5.24 × 10−10

+++

8.4 × 10−12

FOXP1,−86225

 

Obesity (5.4 × 10−9)

4

rs809955

141M

G/A

1.04 [1.03–1.05]

4.69 × 10−10

+++

0.014

[MAML3]; BC040304, −174408

 

Obesity (7.7 × 10−12), smoking (9.7 × 10−7)

5

rs10940767

29M

T/A

0.96 [0.95–0.98]

3.45 × 10−10

---

1.56 × 10−6

AK098570, −142143; LSP1P3, 74104

SPIP3 (2.0 × 10−21)

 

5

rs72771256

83M

G/A

1.04 [1.03–1.06]

2.96 × 10−8

+?+

0.046

HAPLN1, −49454; VCAN, 75804

 

Obesity (5.3 × 10−8)

6

rs7763910

26M

A/G

0.96 [0.95–0.98]

2.41 × 10−8

--+

0.040

[LOC285819]; BTN1A1, −28802; BTN2A1, 2789

BTN1A1 (5.3 × 10−5)

EDU (4.6 × 10−7), Height (2.8 × 10−6)

6

rs9266237

31M

G/C

0.96 [0.95–0.97]

1.46 × 10−9

--?

0.19

MICA, −42039; HLA-B, 532

HLA-B (1.9 × 10−22)

 
  1. Chr: (chromosome) and bp: base-pair position of SNP in hg19; A1/A2 refers to the effect allele and noneffect allele for the SNP; OR: GERD meta-analysis odds ratio and 95% confidence interval (confidence intervals were inflated by the square root of the LD-score regression intercept to account for potential residual stratification); GERD adj. P: adjusted P-value of SNP association in meta-analysis of UKBB, i.e., each SNP’s chi-squared value was divided by the intercept (1.04) from LD-score regression. 23andMe and QSkin for GERD; The column “Meta” shows the direction of risk association for the effect allele in order of the UKBB, 23andMe and QSkin GERD GWASs where “+” denotes increased risk, and “-” denotes decreased risk and “?” denotes that the result is missing for that study. P-value BE/EA shows P-value of SNP association for analysis of BE/EA samples. The “Gene context” column refers to the genes nearby (<200 kb) the most associated GERD SNP; brackets indicate that the peak SNP or those in LD (r2 > 0.8) are within the specified genes. The “-” sign after the genes indicates that the genes are located upstream of the top SNP, while the “+” after genes shows that the genes are located downstream of the top SNP. If any gene in the column has significant eQTL-association with the SNP from any of the 44 GTEx Tissues (https://gtexportal.org/), the gene is shown in eQTL column and the P-value quoted describes the strength of the relationship to the corresponding SNP. GWAS results for BMI, obesity, education, major depression, height and smoking were retrieved from https://genetics.opentargets.org, and are listed in the PheWAS column. More detailed eQTL and phewas results are in Supplementary Table 1. For each significant independent association a locuszoom plot is given in Supplementary Fig. 3.
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