Open Access Highly Accessed Research article

A genome-wide survey for SNPs altering microRNA seed sites identifies functional candidates in GWAS

Kris Richardson1*, Chao-Qiang Lai1, Laurence D Parnell1, Yu-Chi Lee1 and Jose M Ordovas123

Author Affiliations

1 Nutrition and Genomics Laboratory, Jean Mayer United States Department of Agriculture Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA

2 Department of Cardiovascular Epidemiology and Population Genetics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain

3 Instituto Madrileño de Estudios Avanzados (IMDEA) Alimentacion, Madrid, Spain

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BMC Genomics 2011, 12:504  doi:10.1186/1471-2164-12-504

Published: 13 October 2011

Additional files

Additional file 1:

SNPs identified to abrogate MRESSs in LD with GWAS SNPs. All MRESS SNP minor allele frequencies (MAF) reported are for the CEU pilot panel of the 1000 Genomes Project, except where indicted. *indicates MAF in low coverage 1000genomes CEU panel. Abbreviations: GWAS SNP = SNP reported in GWAS, Proxy = MRESS SNP in LD with GWAS SNP, SNP coord = genomic coordinate of MRESS SNP, PhastCon = conservation score, PID = PubMed accession, SVR = miRSVR score, S-T = seed type.

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Additional file 2:

CNM SNPs in LD with GWAS SNPs. CNM SNPs in LD with variants association with disease traits. All CNM SNP minor allele frequencies (MAF) reported are for the CEU pilot panel of the 1000 Genomes Project, except where indicted. * indicates MAF in low coverage 1000genomes CEU panel. Abbreviations: GWAS SNP = SNP reported in GWAS, Proxy = CNM SNP in LD with GWAS SNP, SNP coord = genomic coordinate of CNM SNP, PMID = PubMed accession, PS = miRanda Pairing Score, ES = miRanda energy score, S-T = seed type.

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Additional file 3:

CNM SNPs in LD with GWAS variants and showing co-expression of miR and mRNA. CNM SNPs in LD with variants association with disease traits. All minor allele frequencies (MAF) reported are for the CEU pilot panel of the 1000 Genomes Project, except where indicted. * indicates MAF in low coverage 1000genomes CEU panel. Abbreviations: PMID = PubMed accession, PS = miRanda Pairing Score, ES = miRanda energy score, S-T = seed type, miRlit = evidence of miR and mRNA expression collected from the literature, where numbers indicate pubmed ids, except those beginning with GDS, which indicate the Geoprofile dataset ID for which expression was demonstrated. Co = The number of cell and tissue samples in the mimiRNA database for which co-expression of miR and mRNA were found. eQTL = Reports available eQTL data in the mUTHER study, where F = -Fat cell biopsy (n = 160), L = LCL cells (n = 166), and S = skin cell biopsy (n = 160).

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