Table 2 Peaks detected with conditional analysis of the EYS locus and associated non-synonymous variants.

From: A hypomorphic variant in EYS detected by genome-wide association study contributes toward retinitis pigmentosa

 

Peak 1

Peak 2

Peak 3

dbSNP rsID

rs76960013

rs59178556

rs79476654

Gene info

EYS:intron

EYS:intron

EYS:intron

Ref/Alt

A/G

C/A

T/C

ToMMo AF

0.0414

0.2161

0.0005

Odds ratio

3.95

1.83

16.46

P-value

1.18E−13

3.79E−10

2.45E−08

Linked variant

G843E

S2556C

S1653Kfs

dbSNP rsID

rs74419361

rs66462731

rs527236065

ToMMo AF

0.0171

0.214

0.0044

Odds ratio

3.75

1.79

NA†

P-value

1.06E−09

1.56E−09*

NA†

Corrleation (r2)

0.68

0.97

0.78

PolyPhen-2

Damaging

Possibly damaging

No data

SIFT

Damaging

Damaging/tolerated

Damaging

MutationTaster

Disease causing

Polymorphism

Disease causing

CADD score

23.8

22.9

No data

  1. Information on the three independent peaks detected in this study and exonic variants in linkage disequilibrium are presented.
  2. *P-value for S2556C was calculated after conditional analysis.
  3. †The odds ratio and P-value for S1653Kfs was not available (NA), because the variant was not included in the imputed genotypes of the GWAS analysis.
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