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Table 2 The top hit probes identified in SMR analyses

From: Exploring genes for immunoglobulin A nephropathy: a summary data-based mendelian randomization and FUMA analysis

eQTL data

Probe

Gene

CHR

Top SNP

OR (95% CI)

PeQTL

PGWAS

Beta

SE

PSMR

PHEIDI

Q value

CAGE

ILMN_2150787

HLA-C

6

rs2523578

1.14 (1.11–1.17)

1.55 × 10− 65

2.62 × 10− 24

− 0.2378

0.0272

2.10 × 10− 18

9.48 × 10− 12

5.73 × 10− 13

ILMN_1682717

IER3

6

rs2233980

0.85 (0.83–0.88)

2.05 × 10− 60

5.47 × 10− 22

− 0.2065

0.0249

1.07 × 10− 16

1.89 × 10− 03

7.30 × 10− 12

ILMN_1661439

FLOT1

6

rs3130985

0.85 (0.83–0.88)

6.93 × 10− 37

2.55 × 10− 22

− 0.2666

0.0345

1.16 × 10− 14

2.68 × 10− 02

3.53 × 10− 10

ILMN_1700067

BTN3A2

6

rs9393710

0.89 (0.86–0.92)

9.06 × 10− 237

3.86 × 10− 12

0.0832

0.0123

1.24 × 10− 11

9.13 × 10− 08

2.11 × 10− 07

ILMN_1820787

BTN2A1

6

rs3734544

0.91 (0.88–0.94)

3.34 × 10− 189

1.40 × 10− 10

− 0.0877

0.0140

3.60 × 10− 10

1.40 × 10− 08

3.93 × 10− 06

ILMN_1721113

HLA-C

6

rs9266075

1.08 (1.05–1.1)

2.99 × 10− 183

5.90 × 10− 10

− 0.0867

0.0143

1.35 × 10− 09

1.12 × 10− 03

1.02 × 10− 05

ILMN_1803945

HCP5

6

rs2596495

0.85 (0.83–0.88)

5.73 × 10− 14

1.58 × 10− 21

0.4716

0.0798

3.48 × 10− 09

3.20 × 10− 02

1.94 × 10− 05

ILMN_2044927

RNF5

6

rs192471087

0.91 (0.89–0.94)

2.49 × 10− 37

1.28 × 10− 10

− 0.1974

0.0343

8.59 × 10− 09

1.29 × 10− 04

3.00 × 10− 05

ILMN_1804571

ZKSCAN4

6

rs13200462

0.89 (0.86–0.92)

2.61 × 10− 19

1.37 × 10− 13

− 0.3193

0.0558

1.08 × 10− 08

1.88 × 10− 02

3.00 × 10− 05

ILMN_1660436

HSPA1A

6

rs494620

1.07 (1.05–1.1)

1.40 × 10− 74

1.81 × 10− 09

0.1417

0.0248

1.10 × 10− 08

2.16 × 10− 09

3.00 × 10− 05

GTEx

ENSG00000271581.1

XXbac-BPG248L24.12

6

rs9266244

1.14 (1.11–1.17)

1.52 × 10− 16

2.96 × 10− 24

0.2043

0.0319

1.44 × 10− 10

4.34 × 10− 07

6.22 × 10− 06

ENSG00000186470.9

BTN3A2

6

rs68112369

0.89 (0.86–0.92)

9.15 × 10− 70

1.14 × 10− 11

0.1088

0.0172

2.28 × 10− 10

1.07 × 10− 03

6.22 × 10− 06

ENSG00000224389.4

C4B

6

rs1270942

0.87 (0.84–0.9)

3.63 × 10− 19

1.44 × 10− 16

− 0.1233

0.0203

1.23 × 10− 09

5.84 × 10− 02

1.48 × 10− 05

ENSG00000244731.3

C4A

6

rs116667074

0.87 (0.84–0.9)

5.15 × 10− 19

1.67 × 10− 15

0.1382

0.0233

2.88 × 10− 09

1.08 × 10− 01

1.96 × 10− 05

ENSG00000214894.2

LINC00243

6

rs3094222

0.85 (0.83–0.88)

8.03 × 10− 12

3.93 × 10− 22

− 0.3086

0.0553

2.38 × 10− 08

5.63 × 10− 03

1.04 × 10− 04

ENSG00000204644.5

ZFP57

6

rs2747431

0.93 (0.91–0.96)

2.03 × 10− 85

5.51 × 10− 08

− 0.0566

0.0108

1.62 × 10− 07

7.31 × 10− 05

4.88 × 10− 04

ENSG00000204536.9

CCHCR1

6

rs1265087

0.93 (0.91–0.95)

4.64 × 10− 22

1.01 × 10− 08

− 0.2081

0.0423

8.60 × 10− 07

7.49 × 10− 04

1.91 × 10− 03

ENSG00000137312.10

FLOT1

6

rs3094222

0.85 (0.83–0.88)

3.74 × 10− 08

3.93 × 10− 22

− 1.3396

0.2802

1.74 × 10− 06

1.11 × 10− 02

2.49 × 10− 03

ENSG00000231852.2

CYP21A2

6

rs7763805

0.89 (0.86–0.92)

2.24 × 10− 10

5.15 × 10− 13

− 0.1665

0.0349

1.85 × 10− 06

3.40 × 10− 01

2.49 × 10− 03

ENSG00000204622.6

HLA-J

6

rs1611336

1.07 (1.04–1.09)

6.54 × 10− 20

8.13 × 10− 08

0.1162

0.0251

3.78 × 10− 06

4.10 × 10− 04

4.10 × 10− 03

  1. For a full list of the significant probes identified in the SMR analyses, please see Additional file 1: Table S4. The GWAS summarized data were provided by the study of Sakaue et al. and can be downloaded at http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90018001-GCST90019000/GCST90018866/harmonised/. The CAGE and GTEx eQTL data can be downloaded at https://cnsgenomics.com/data/SMR/#eQTLsummarydata.
  2. OR (95% CI) is the odds ratio and the corresponding 95% confidence interval for the top SNPs. PeQTL is the P value of the top associated cis-eQTL in the eQTL analysis, and PGWAS is the P value for the top associated cis-eQTL in the GWAS analysis. Beta is the estimated effect size in SMR analysis, SE is the corresponding standard error, PSMR is the P value for SMR analysis and PHEIDI is the P value for the HEIDI test
  3. CAGE Consortium for the Architecture of Gene Expression, CHR chromosome, CI confidence interval, eQTL expression quantitative trait loci, GTEx Genotype-Tissue Expression, HEIDI heterogeneity in dependent instruments, OR odds ratio, SNP single-nucleotide polymorphism, SMR summary data-based Mendelian randomization, FDR false discovery rate, GWAS genome-wide association studies, IgAN immunoglobulin A nephropathy
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BMC Medical Genomics

ISSN: 1755-8794

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