Additional file 1 of A genome-wide association study of mammographic texture variation

Additional file 1: Fig. S1. Correlations between the four V assessments. Fig. S2. Quantile-quantile plots of the GWAS meta-analysis results. Fig. S3. Manhattan plots of the GWAS meta-analysis results. Fig. S4. Quantile-quantile plots of the P value of heterogeneity. Table S2. Sources of summary statistics of breast cancer risk and breast cancer risk factors for calculating genetic correlation. Table S3. Sources of summary statistics of breast cancer risk and breast cancer risk factors for the SNP-set test

Additional file 9: Figure S5. of Deep targeted sequencing of 12 breast cancer susceptibility regions in 4611 women across four different ethnicities

MAF distribution for SNVs in the 1000 Genomes Project but not in this study. (DOCX 49 kb

Association analysis of BCC-loci and mKC susceptibility from the combined analyses (Harvard cohorts, FHS and RS).

<p>Association analysis of BCC-loci and mKC susceptibility from the combined analyses (Harvard cohorts, FHS and RS).</p

Manhattan plot of the GWAS associations for mKCs in the discovery sample (FHS and Harvard cohorts).

<p>The observed -log10 p-values (Y-axis) of the association between the SNPs and susceptibility for mKC are shown. All SNP are represented by dots and displayed per chromosome (X-axis).</p

Imputation quality score by minor allele frequency for the three platform families.

<p>Imputation quality score by minor allele frequency for the three platform families.</p

GWAS datasets in HPFS, NHS, NHSII and PHS.

<p>GWAS datasets in HPFS, NHS, NHSII and PHS.</p

QQ-plot for GWAS analysis of body mass index based on 20,283 individuals.

<p>QQ-plot for GWAS analysis of body mass index based on 20,283 individuals.</p

Manhattan plot for GWAS analysis of venous thromboembolism based on 1,364 cases and 17,628 controls.

<p>Manhattan plot for GWAS analysis of venous thromboembolism based on 1,364 cases and 17,628 controls.</p

Associations for known body mass index SNPs based on 20,283 individuals.

<p>Associations for known body mass index SNPs based on 20,283 individuals.</p

Overlap in SNPs across genotype platforms.

<p>Overlap in SNPs across genotype platforms.</p