We report that the chromosome 1q41 locus (most significant SNP rs4373767) is associated with AL in a meta-analysis of three GWAS performed in the study cohorts consisting of Chinese adults, Chinese children, and Malay adults. The discovery of chromosome 1q41 as a locus for high myopia in our data is further supported by validation in two independent Japanese cohorts, and the observed genetic effects are highly consistent across all five studies. The pseudogene ZC3H11B and two nearby genes SLC30A10 and LYPLAL1 were found to be expressed in the human retina and sclera. The potential roles in regulating myopia at three candidate genes were further implicated by the concordant changes in the pattern of transcription and protein expression in the mouse model.
pseudogene belongs to the CCCH-type zinc finger family, whereas such type of zinc finger protein has been shown as a RNA-binding motif to facilitate the mRNA processing at transcription 
. Emerging evidence suggests that pseudogenes, resembling known genes but not producing proteins, play a significant role in pathological conditions by competing for binding sites to regulate the transcription of its protein-coding counterpart 
. Although the function of the ZC3H11B
in humans is presently unknown, the implicated role of the murine gene ZC3H11A
(conserved gene of ZC3H11B
in mouse) in myopia development is in keeping with previous findings that several zinc finger proteins are involved in myopia 
. Given their role as transcription factors 
, zinc finger protein ZENK
has been proposed to function as a messenger in modulating the visual signaling cascade in the chicken retina, where the expression of the ZENK
was suppressed by the condition of minus defocus (induced myopic eye growth) and enhanced by positive defocus (induced hyperopic eye growth) 
. Similarly, it has been reported that ZENK
knockout mice had elongated AL and a myopic shift in refraction 
. Moreover, early growth response gene type1 EGR-1
(the human homologue of ZENK
) has been shown to activate transforming growth factor beta 1 gene TGFB1
by binding its promoter 
, a gene that is implicated to be associated with myopia 
. Another zinc protein finger protein 644 isoform ZNF644
has recently been identified to be responsible for high myopia using whole genome exome sequencing in a Han Chinese family 
, whereas its influence on “myopia genes” remains to be elucidated. In light of this, the observation that ZC3H11B is abundantly expressed in retina and sclera, together with the significant down-regulation of the coding counterpart ZC3H11A
in myopic mice eyes, suggests it may promote or inhibit the transcription of ocular growth genes vital in myopia development.
One of the two neighboring genes SLC30A10
is an efflux transporter that reduces cytoplasmic zinc concentrations 
. The SLC30
zinc transporters are expressed abundantly in human RPE cells, and the retina has been observed to possess the highest concentration of zinc in the human body 
. Zinc deficiency in the intracellular retina has thus been implicated in the pathogenesis of age-related macular degeneration (AMD) 
, and in RPE-photoreceptor complex deficits, which can affect visual signal transduction from retina to sclera and lead to visual impairment 
functions as a triglyceride lipase and this gene has been shown to be up-regulated in subcutaneous adipose tissue in obese individuals 
. While the relationship between LYPLAL1
and myopia is unknown, elevated saturated-fat intake has been proposed to influence myopia development through the retinoid receptor pathway 
. Interestingly, the SNPs pinpointing chromosome 1q41 in our study are 1 Mb away from the transforming growth factor beta 2 gene (TGFβ2
) which has been implicated in the down-regulation of mRNA levels in myopia progression of an induced tree shrew myopia model 
. None of these nearby genes, however, are within the LD block containing our identified SNPs.
Chromosome 1q41 is a previously reported locus for refraction from a linkage analysis of 486 pedigrees in the Beaver Dam Eye Study, US 
. Using microsatellite markers, Klein et al
identified novel regions of linkage to SE on chromosome 1q41, whereas the peak spanned a broad region near Marker D1S2141 (multipoint P
). This result however was not replicated in a subsequent genome-wide linkage scan for SE with denser SNP markers, partially due to varying information of linkage conveyed by SNPs versus microsatellites 
. The identified variants at chromosome 1q41 in our study were noted to exhibit weaker, albeit still significant, association with SE in SCES and SCORM (rs4373767, SCES/SCORM: P
, respectively; Table S3
), but not in SiMES (3.51×10−1
), which is consistent with the lower correlation of AL and SE seen in the SiMES data, partially from increasing lens opalescence in the Malay population 
Our data have shown that genetic variants on chromosome 1q41 influence the physiological attribute of AL and are also associated with high myopia. Elongation of AL is the major underlying structural determinant of high myopia, mostly accompanied with prolate eyeballs and thinning of the sclera, macula and retina 
. Thus, high myopia is also defined as AL of >26 mm in some studies 
. It is possible that genes involved in a quantitative trait (refraction or underlying AL) also play a role in the extreme forms of the trait (high myopia) 
. Two recent GWAS performed in general Caucasians population have identified genetic variants for quantitative refraction at chromosome 15q14 
and 15q25 
, of which the locus on 15q14 was subsequently confirmed to be associated with high myopia in the Japanese 
. Our GWAS results herein highlight AL QTLs relevant for high myopia predisposition, which advances our understanding of the genetic etiology of myopia at different levels of severity.
The meta-analysis of three GWAS in our discovery suggests that the quantitative trait locus at chromosome 1q41 accounts for variation in AL in both school children and adults, regardless of age differences. Notably, the early-onset of myopia in childhood may continuously progress toward high myopia in later life, while adult-onset of myopia is usually in the low or moderate form 
. The significant association on chromosome 1q41 for high myopia in adults and children thus also implicates this locus identified for AL is likely to be associated with early-onset myopia.
The prevalence of myopia among Asian population is considerably higher than in Caucasians 
. Although distinct genetic mechanisms governing myopia may exist for populations with different genetic backgrounds, we believe there are polymorphisms involved in refractive variation that are shared across populations. However, the allele frequencies of these identified SNPs vary across populations. For instance, the minor C allele of rs4373767 was a major allele in the HapMap Africans and Europeans with frequency of 0.92 and 0.62 respectively. Four distinct linkage disequilibrium (LD) blocks existed in 50 kb region encapsulating our top SNPs in the HapMap Africans, whereas high LD was observed for the Chinese, Malays and Japanese populations. Such heterogeneity may confer different statistical power and confound the transferability of the same variants across populations 
. In addition, we note that the variability in refraction attributed to AL may vary in different ethnic groups. For example, AL has been reported to account for a larger proportion of the variation in refraction in East-Asian children compared to their Caucasian counterparts 
, therefore the increased power of refraction may reflect more variation in factors other than pure elongation of AL in certain ethnic groups.
In conclusion, our findings suggest that common variants at chromosome 1q41 are associated with AL and high myopia in a pediatric and an adult cohort, the latter incorporating Chinese, Malay and Japanese populations. Further evaluation of causal variants and underlying pathway mechanisms may contribute to early identification of children at highest risk of developing myopia, and eventually lead to appropriate interventions to retard the progression of myopia.