Web-based Myopia Genetics Hub

Welcome

The Web-based Myopia Genetics Hub (WMGH) platform incorporates three specialized genetic databases focused on myopia: the Simple Myopia-Associated Pathogenic Variants Dataset, the Syndromic Myopia-Associated Pathogenic Variants Dataset, and the Myopia-Associated Risk Variants Dataset. Researchers can upload their existing genotype data to generate personalized assessments of myopia risk. Two formats of test-ready data templates are offered to streamline validation experiments.

How to Use

Navigate between sections with just a few clicks:

Simple Myopia-Associated Pathogenic Variants Dataset: Pathogenic variants linked to simple myopia ( 308 records ).
Syndromic Myopia-Associated Pathogenic Variants Dataset: Pathogenic variants linked to 23 myopia-related disorders ( 45,422 records ).
Myopia-Associated Risk Variants Dataset: Genetic risk variants associated with myopia ( 785 records ).
Myopia Risk Prediction: PRS-based myopia risk prediction ( processes 1,000 samples in seconds ).

Data Sources and Model Construction

Figure 1. Construction of the WMGH Platform for Myopia Genetic Analysis

This platform was constructed as a modular, reproducible resource for the collection, annotation, integration, and visualization of genetic variants associated with myopia. Figure 1 describes the detailed collection and processing workflow of the database. The platform comprises three primary variant datasets as described above, alongside a polygenic risk score (PRS) model optimized for the Han Chinese population. Each dataset is stored as a tab-delimited plain-text file (.txt) and aligned to the hg38 human reference genome assembly via liftOver. All variant identifiers (RSIDs) were cross-checked between the original sources (GWAS Catalog, ClinVar, and OMIM) and dbSNP to confirm consistency in genomic coordinates (hg38) and allele designation. All identifiers follow dbSNP conventions. Gene names are standardized to HGNC symbols. Each dataset is accompanied by machine-readable metadata including date of last update, source database version (GWAS Catalog, ClinVar, and OMIM), genome build version (GRCh38/hg38), reference URLs to original publications and database entries.

Figure 2. Construction and Application of Myopia PRS Prediction Models

The PRS model was trained on genotype data from 2,900 unrelated Han Chinese individuals provided by WeGene, including 2,308 samples in the training set and 592 samples in the independent test set. Figure 2 shows how the model is built in detail. We extracted 416 myopia-associated SNPs from GWAS summary statistics as candidate predictors. Genotypes were imputed to the hg38 build and subjected to quality control (call rate ≥ 98%, MAF ≥ 1%). The output of the myopia risk prediction model is stored in sum_final.txt, which serves as the parameter file for model inference. This file contains crucial information for each variant, including variant identifier (RSID), chromosome number (CHR), genomic position (POS), reference allele (a0), effect allele (a1), effect size/SNP weight (beta), and genotype coding (geno). When predicting personal myopia risk, the platform matches uploaded genotype data against the RSIDs in sum_final.txt. It calculates weighted PRS scores using the beta values and turns them into personal myopia risk probabilities, as illustrated in Figure 2. A probability ≥ 0.5 indicates predicted myopia, while a probability < 0.5 indicates predicted non-myopia. AUC consistency between the training and test sets demonstrates the model's generalizability and its ability to maintain predictive performance on new data.

Paper describing this work has been received in Frontiers of Computer Science （FCS） special column “ Code & Data ”.

Cited as: Yan WANG, Haoyi WENG, Minxi BI, Gang CHEN, Xinghu QIN, Likun WANG. WMGH: a comprehensive genetic platform to facilitate myopia research and risk prediction in Han Chinese individuals. Front. Comput. Sci. , 2026, DOI: 10.1007/s11704-026-60291-9

Citations

Li Z, Qu J, Xu X, et al. A genome-wide association study reveals association between common variants in an intergenic region of 4q25 and high-grade myopia in the Chinese Han population[J]. Human molecular genetics, 2011, 20(14): 2861-2868.
Guggenheim J A, Clark R, Cui J, et al. Whole exome sequence analysis in 51,624 participants identifies novel genes and variants associated with refractive error and myopia[J]. Human molecular genetics, 2022, 31(11): 1909-1919.
Meguro A, Yamane T, Takeuchi M, et al. Genome-wide association study in Asians identifies novel loci for high myopia and highlights a nervous system role in its pathogenesis[J]. Ophthalmology, 2020, 127(12): 1612-1624.
Tang S M, Li F F, Lu S Y, et al. Association of the ZC3H11B, ZFHX1B and SNTB1 genes with myopia of different severities[J]. British Journal of Ophthalmology, 2020, 104(10): 1472-1476.
Lanca C, Kassam I, Patasova K, et al. New polygenic risk score to predict high myopia in Singapore Chinese children[J]. Translational vision science & technology, 2021, 10(8): 26-26.
Jiang C, Melles R B, Yin J, et al. A multiethnic genome-wide analysis of 19,420 individuals identifies novel loci associated with axial length and shared genetic influences with refractive error and myopia[J]. Frontiers in Genetics, 2023, 14: 1113058.

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Email: qinxh@bjfu.edu.cn, wanglk@pku.edu.cn

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Simple Myopia-Associated Pathogenic Variants Dataset

This table contains pathogenic/likely pathogenic variants linked to simple myopia. The current criteria for determining whether a variant is pathogenic are relatively strict. This may lead to the omission of some potentially pathogenic variants. Based on the above considerations, we have also retained some variants of uncertain pathogenicity for user reference. Users can filter and select them as needed. Descriptions of each variable are provided below.

CHR: Chromosome number.
POSITION: Genomic position of the variant.
RSID: SNP ID from dbSNP.
SYMBOL: Gene symbol associated with the variant.
VARIANT_TYPE:
- Single Nucleotide Variant (SNV): A change of a single nucleotide in the genome.
- Multiple Nucleotide Variant (MNV): A variation involving changes in multiple adjacent nucleotides.
- Deletion: A deletion of one or more nucleotides from the genome.
- Duplication: A duplication of a segment of the genome.
- Insertion: An addition of one or more nucleotides into the genome.
- Indel: A variation where both insertion and deletion occur.
- Microsatellite: A short, repetitive sequence of DNA.
- Inversion: A segment of the genome is reversed end to end.
GENOMIC_CONTEXT: The location and functional impact of a genetic variant.
- Intron Variant: A variant located within a non-coding intron; usually neutral.
- Frameshift Variant: Alters the reading frame, typically causing significant protein changes.
- Missense Variant: Changes a single amino acid in the protein sequence; may impact function.
- Splice Polypyrimidine Tract Variant: Affects the splicing polypyrimidine tract; impacts RNA splicing.
- Stop Gained: Introduces a premature stop codon, truncating the protein.
- Stop Lost: Removes a stop codon, potentially extending the protein.
- Synonymous Variant: Does not change the amino acid sequence; typically neutral.
- Upstream Gene Variant: A variant before a gene; may affect gene regulation.
- Splice Donor Variant: Alters the splice donor site; disrupts RNA splicing.
- Inframe Deletion: Deletes amino acids without shifting the reading frame.
- Non Coding Transcript Exon Variant: Located in a non-coding RNA exon; may alter RNA function.
- Non Coding Transcript Variant: Found in non-coding RNA; could alter function.
- Splice Region Variant: Near the splice site; may disrupt RNA splicing.
- Downstream Gene Variant: A variant after a gene; may affect regulation.
- Splice Donor 5th Base Variant: Affects the 5th base of the splice donor site; impacts splicing.
- 3 Prime UTR Variant: In the 3' untranslated region; affects RNA stability.
- Splice Donor Region Variant: Located in the splice donor region; may disrupt splicing.
- Splice Acceptor Variant: Alters the splice acceptor site; disrupts RNA splicing.
- Start Lost: Removes the start codon; may prevent protein translation.
- 5 Prime UTR Variant: In the 5' untranslated region; may affect translation efficiency.
- Coding Sequence Variant: Alters the protein-coding sequence; may impact function.
- NMD Transcript Variant: Targets transcripts for nonsense-mediated decay.
- Inframe Insertion: Inserts amino acids without shifting the reading frame.
- Protein Altering Variant: Changes the structure or function of the protein.
- Intergenic Variant: Located between genes; usually neutral.
- Stop Retained Variant: Retains a stop codon; typically neutral.
- Start Retained Variant: Retains a start codon; typically neutral.
- Incomplete Terminal Codon Variant: Affects the terminal codon; may impact translation termination.
REF: Reference allele.
ALT: Alternate allele.
gnomAD_AF: Alternate allele frequency in the general population from gnomAD.
gnomAD_EAS_AF: Alternate allele frequency in East Asian population from gnomAD.
gnomAD_EUR_AF: Alternate allele frequency in European population from gnomAD.
gnomAD_AMR_AF: Alternate allele frequency in American population from gnomAD.
gnomAD_AFR_AF: Alternate allele frequency in African population from gnomAD.
gnomAD_SAS_AF: Alternate allele frequency in South Asian population from gnomAD.
PUBMED: Related research articles (PubMed IDs).
DATABASE: The source database for the genetic variant (e.g., ClinVar or OMIM).

Select a Chromosome:

Select a Variant Type:

Select a Genomic Context:

Select a Database:

Select an Inheritance:

Select Pathogenicity:

Syndromic Myopia-Associated Pathogenic Variants Dataset

This table contains pathogenic/likely pathogenic variants linked to 23 myopia-related disorders. Descriptions of each variable are provided below.

CHR: Chromosome number.
POSITION: Genomic position of the variant.
RSID: SNP ID from dbSNP.
SYMBOL: Gene symbol associated with the variant.
VARIANT_TYPE:
- Single Nucleotide Variant (SNV): A change of a single nucleotide in the genome.
- Multiple Nucleotide Variant (MNV): A variation involving changes in multiple adjacent nucleotides.
- Deletion: A deletion of one or more nucleotides from the genome.
- Duplication: A duplication of a segment of the genome.
- Insertion: An addition of one or more nucleotides into the genome.
- Indel: A variation where both insertion and deletion occur.
- Microsatellite: A short, repetitive sequence of DNA.
- Inversion: A segment of the genome is reversed end to end.
REF: Reference allele.
ALT: Alternate allele.
gnomAD_AF: Alternate allele frequency in the general population from gnomAD.
gnomAD_EAS_AF: Alternate allele frequency in East Asian population from gnomAD.
gnomAD_EUR_AF: Alternate allele frequency in European population from gnomAD.
gnomAD_AMR_AF: Alternate allele frequency in American population from gnomAD.
gnomAD_AFR_AF: Alternate allele frequency in African population from gnomAD.
gnomAD_SAS_AF: Alternate allele frequency in South Asian population from gnomAD.
PUBMED: Related research articles (PubMed IDs).
DISORDER: The name of the disorder(s) associated with the variant. Multiple disorders are separated by semicolons.
DATABASE: The source database for the genetic variant (ClinVar or OMIM).
INHERITANCE: Mode of inheritance: AD (Autosomal Dominant), AR (Autosomal Recessive), XL (X-linked).
PATHOGENIC: Pathogenicity classification (Pathogenic/Likely-Pathogenic).

Select a Disorder:

Select a Chromosome:

Select a Variant Type:

Select a Database:

Select an Inheritance:

Select Pathogenicity:

Myopia-Associated Risk Variants Dataset

This table contains genetic variants that may increase or decrease the risk of developing myopia. Descriptions of each variable are provided below.

CHR: Chromosome number.
POSITION: Genomic position of the variant.
RSID: SNP ID from dbSNP.
SYMBOL: Gene symbol associated with the variant.
VARIANT_TYPE:
- Single Nucleotide Variant (SNV): A change of a single nucleotide in the genome.
- Multiple Nucleotide Variant (MNV): A variation involving changes in multiple adjacent nucleotides.
- Deletion: A deletion of one or more nucleotides from the genome.
- Duplication: A duplication of a segment of the genome.
- Insertion: An addition of one or more nucleotides into the genome.
- Indel: A variation where both insertion and deletion occur.
- Microsatellite: A short, repetitive sequence of DNA.
- Inversion: A segment of the genome is reversed end to end.
GENOMIC_CONTEXT: The location and functional impact of a genetic variant.
- Intron Variant: A variant located within a non-coding intron; usually neutral.
- Frameshift Variant: Alters the reading frame, typically causing significant protein changes.
- Missense Variant: Changes a single amino acid in the protein sequence; may impact function.
- Splice Polypyrimidine Tract Variant: Affects the splicing polypyrimidine tract; impacts RNA splicing.
- Stop Gained: Introduces a premature stop codon, truncating the protein.
- Stop Lost: Removes a stop codon, potentially extending the protein.
- Synonymous Variant: Does not change the amino acid sequence; typically neutral.
- Upstream Gene Variant: A variant before a gene; may affect gene regulation.
- Splice Donor Variant: Alters the splice donor site; disrupts RNA splicing.
- Inframe Deletion: Deletes amino acids without shifting the reading frame.
- Non Coding Transcript Exon Variant: Located in a non-coding RNA exon; may alter RNA function.
- Non Coding Transcript Variant: Found in non-coding RNA; could alter function.
- Splice Region Variant: Near the splice site; may disrupt RNA splicing.
- Downstream Gene Variant: A variant after a gene; may affect regulation.
- Splice Donor 5th Base Variant: Affects the 5th base of the splice donor site; impacts splicing.
- 3 Prime UTR Variant: In the 3' untranslated region; affects RNA stability.
- Splice Donor Region Variant: Located in the splice donor region; may disrupt splicing.
- Splice Acceptor Variant: Alters the splice acceptor site; disrupts RNA splicing.
- Start Lost: Removes the start codon; may prevent protein translation.
- 5 Prime UTR Variant: In the 5' untranslated region; may affect translation efficiency.
- Coding Sequence Variant: Alters the protein-coding sequence; may impact function.
- NMD Transcript Variant: Targets transcripts for nonsense-mediated decay.
- Inframe Insertion: Inserts amino acids without shifting the reading frame.
- Protein Altering Variant: Changes the structure or function of the protein.
- Intergenic Variant: Located between genes; usually neutral.
- Stop Retained Variant: Retains a stop codon; typically neutral.
- Start Retained Variant: Retains a start codon; typically neutral.
- Incomplete Terminal Codon Variant: Affects the terminal codon; may impact translation termination.
REF: Reference allele.
ALT: Alternate allele.
OR: Odds ratio associated with the risk allele, indicating the relative risk.
BETA: Effect size or direction of the association for the variant.
P_VALUE: Statistical significance of the association for the variant.
gnomAD_AF: Alternate allele frequency in the general population from gnomAD.
gnomAD_EAS_AF: Alternate allele frequency in East Asian population from gnomAD.
gnomAD_EUR_AF: Alternate allele frequency in European population from gnomAD.
gnomAD_AMR_AF: Alternate allele frequency in American population from gnomAD.
gnomAD_AFR_AF: Alternate allele frequency in African population from gnomAD.
gnomAD_SAS_AF: Alternate allele frequency in South Asian population from gnomAD.
PUBMED: Related research articles (PubMed IDs).
DATABASE: The source database for the genetic variant (GWAS Catalog).

Select a Chromosome:

Select a Variant Type:

Select a Genomic Context:

Upload your data in either of the two formats below:

PLINK files: .bim, .bed, .fam. Need an example template? Download a sample PLINK file set.
When uploading PLINK format files, please select and upload all three files (.bim, .bed, and .fam) at the same time.
TXT file: Column headers should be RSID (SNP IDs from dbSNP), and row names should be sample IDs. A sample TXT file is provided to help you get started.
SNP List: SNPs used in our myopia prediction model: SNP_list.txt.

Upload Your Genetic Data:

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