Manhattan Plot

Genome-wide association study (GWAS) visualization. Plot -log10(P) values across all chromosomes with genome-wide and suggestive significance threshold lines.

Visualization Parameters

Upload GWAS summary statistics and generate the Manhattan plot

Upload Data File

TSV/CSV with SNP, CHR, BP and P columns

Required Files

data.tsv — GWAS results: SNP ID, chromosome, position, P value

Format

Row = one SNP variant
SNP: variant identifier (e.g., rs12345)
CHR: chromosome number (numeric; "chr" prefix auto-removed)
BP: base-pair position on the chromosome
P: association P value (0 < P ≤ 1)
Column aliases auto-detected: chr/CHROM, pos/POS, pvalue/PValue

GWAS Data

SNP	CHR	BP	P
rs1000000	1	12458	3.2e-01
rs1000001	1	37892	1.5e-02
rs1000002	1	62104	7.8e-03
rs1400891	2	3751245	1.1e-09

Manhattan Plot

Upload data and click Generate, or run with example data

Documentation

Input format: a tab- or comma-separated table of GWAS summary statistics with columns SNP, CHR, BP, P. Common aliases (chr/CHROM, pos/POS, pvalue) are recognized automatically.

Threshold lines: red dashed line = genome-wide significance (P = 5×10^-8); blue dashed line = suggestive significance (P = 1×10^-5). SNPs above the suggestive line are highlighted in red.

Typical use: visualize the output of the GWAS Analysis module in the Genomics workflow, or any PLINK/GEMMA-style association result.