Table 1 List of high-confidence colocalizing expression and splicing QTLs with POAG and IOP GWAS loci

From: Integrating genetic regulation and single-cell expression with GWAS prioritizes causal genes and cell types for glaucoma

Lead GWAS varianta

RS ID

Nearest Gene/s

Total # colocalizing e/sGenesb

Colocalizing GTEx e/sQTLs based on eCAVIAR and enloc and significant MRc

Colocalizing retina eQTL (eCAVIAR)d

POAG GWAS ancestrye

Colocalizing with IOP GWASf

chr1:171636338:G:A

rs74315329

MYOC

1

PIGC (s)*

–

CA

No

chr1:165768467:G:C

rs2790053

TMCO1, TMCO1-AS1 (RP11-466F5.8)

2

TMCO1 (e,s), TMCO1-AS1 (e)*

TMCO1-AS1

CA,EU

Yes

chr9:22051671:G:C

rs944801

CDKN2B-AS1

3

CDKN2B-AS1 (s)

–

CA,EU

No

chr4:7902636:G:A

rs938604

AFAP1

2

AFAP1 (e)*

–

CA

Yes

chr17:10127866:G:A

rs9913911

GAS7

1

GAS7 (e)*

–

CA,EU

Yes

chr9:126628521:C:T

rs3829849

LMX1B

4

LMX1B (e)

–

CA,EU

Yes

chr7:116522252:T:A

rs10257125

CAV1

2

CAV2 (e,s)*

–

CA,EU

Yes

chr11:86657064:C:T

rs10792871

ME3

4

PRSS23 (e)*, ME3 (e)*

PRSS23

CA,EU

Yes

chr9:133255801:C:T

rs8176749

ABO

1

ABO (e)*

–

CA

Yes

chr15:73928957:C:T

rs1550437

LOXL1

2

LOXL1 (e,s)*

–

CA,EU

No

chr3:186411027:G:A

rs56233426

DGKG

2

DGKG (e)

DGKG

CA,EU

Yes

chr17:46010134:G:A

rs41543317

MAPT

9

–

KANSL1, LRRC37A2, LRRC37A

EU

No**

chr3:188349165:G:T

rs6787621

LPP

1

LPP (e,s)*

–

CA

Yes

chr1:36147354:C:A

rs4652902

TRAPPC3

1

–

COL8A2

CA

Yes

chr22:28712241:G:A

rs5752776

CHEK2

5

TTC28 (e)*

–

CA,EU

No**

chr1:37605594:C:T

rs6687545

GNL2, RSPO1

7

GNL2 (e,s)*, MEAF6 (e)*

MEAF6

EU

Yes

chr11:47447887:G:A

rs7111873

RAPSN

8

–

PSMC3

CA

No**

chr2:12811195:C:T

rs12623251

TRIB2

1

TRIB2 (e)

–

CA,EU

No

chr15:57261634:T:A

rs2431023

TCF12

2

ZNF280D (e), TCF12 (e)

–

CA,EU

No

chr11:130412183:C:T

rs2875238

ADAMTS8

2

RP11-121M22.1 (e,s)*, ADAMTS8 (e)

–

CA

No

chr14:74618126:G:A

rs754458

LTBP2, AREL1

4

NPC2 (e)*

NPC2

CA

Yes

chr7:134835770:C:A

rs10237321

CALD1

1

CALD1 (e)

–

CA

No

chr6:134051012:G:C

rs2811688

SLC2A12

3

SLC2A12 (e)*, TBPL1 (e)

SLC2A12

CA,EU

No

  1. aVariant chromosome positions are in genome build 38.
  2. bTotal number of target genes of expression and splicing QTLs (e/sGenes) in any of the 49 GTEx tissues or retina that colocalized with a given POAG cross-ancestry GWAS locus based on eCAVIAR (CLPP > 0.01) and/or enloc (RCP > 0.1).
  3. ce/sGenes from 49 GTEx tissues that significantly colocalized with a POAG cross-ancestry and/or European GWAS locus based on both eCAVIAR (CLPP > 0.01) and enloc (RCP > 0.1), and displayed significant Mendelian Randomization (MR) results (FDR < 0.05) using the European POAG GWAS meta-analysis. e, eQTL. s, sQTL.
  4. dTarget gene/s of retina eQTLs that significantly colocalized (CLPP > 0.01) with POAG cross-ancestry (CA) or European (EU) GWAS loci and displayed significant MR results (FDR < 0.05).
  5. eAncestry of POAG GWAS meta-analysis, cross-ancestry (CA) or European (EU), that colocalized with the e/sQTLs in the given locus. The GWAS variants are ordered based on their POAG effect size (odds ratio) in descending order.
  6. fThis column states whether the POAG colocalizing e/sQTLs significantly colocalized with the IOP GWAS and showed significant MR results (FDR < 0.05) with IOP. No colocalization with IOP GWAS suggests IOP-independent mechanisms. List of tissues in which the e/sQTLs colocalized with the POAG or IOP GWAS loci is given in Supplementary Data 7-12. *e/sQTLs where pleiotropy-robust sensitivity testing of significant MR results could be performed (≥3 LD-independent e/sVariants (instrumental variables)). All these genes were robust to horizontal pleiotropy (P > 0.05). **Loci associated with IOP, but for which colocalization was not found for the specific e/sGenes. A similar list of high-confidence colocalizing e/sQTLs with IOP is given in Supplementary Data 15.
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