Additional file 1: of MARV: a tool for genome-wide multi-phenotype analysis of rare variants

marv_chr1-5.result. Original results files outputted from MARV from the case study using NFBC1966 data. (RESULT 17825 kb

SNPs associated with circulating chemerin levels at genome-wide significant levels.

<p>Inflation factor of all single studies were negligible (maximum λ = 1.014 in the Sorbs cohort). No inflation of meta-analysis results was observed (λ = 0.99). Positions of SNPs are given according to HapMap2 CEU, Release 24, dbSNP-build 126, NCBI 36 as the reference panel. Effect directions are given for the coding allele. <i>ß</i> Beta coefficient of regression model.</p><p>Chr: chromosome; <i>β</i>: beta; SE: standard error; <i>LRRC61</i>: leucine rich repeat containing 61; <i>ACTR3C</i>: ARP3 actin-related protein 3 homolog C; <i>RARRES2</i>: retionic acid receptor responder 2; <i>REPIN1</i>: replication initiator 1; <i>ZBED6CL</i>: ZBED6 C-terminal like.</p><p>SNPs associated with circulating chemerin levels at genome-wide significant levels.</p

eQTL analysis for rs7806429 in PBMCs of the Sorbs cohort.

<p>eQTL analysis for rs7806429 in PBMCs of the Sorbs cohort.</p

Association of rs7806429 with <i>RARRES2</i> expression in subcutaneous and visceral adipose tissue.

<p>Linear regression analyses adjusted for age and BMI (and sex for the total cohort). Subjects with T2D were not included in the analyses.</p><p>SC: subcutaneous; VIS: visceral; β: beta.</p><p>Association of rs7806429 with <i>RARRES2</i> expression in subcutaneous and visceral adipose tissue.</p

Regional association plot for the top-hit of association with chemerin levels on chromosome 7.

<p>Regional association plot for the top-hit of association with chemerin levels on chromosome 7.</p

Correlation of serum chemerin concentrations with anthropometric parameters and markers of glucose metabolism, serum lipids and renal function in the Sorbs cohort.

<p>Associations were assessed in a linear regression model adjusting for age, sex and BMI (except for analysis of BMI itself). HOMA-IR was calculated as published by Matthews et al. <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004854#pgen.1004854-Matthews1" target="_blank">[35]</a>. The Stumvoll Index refers to Stumvoll ISI_{(0 and 120 min) and} Stumvoll ISI_{(0 and 30 min)}<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004854#pgen.1004854-Stumvoll1" target="_blank">[36]</a>. Glomerular filtration rate (GFR) was calculated using the MDRD formula. <i>ß</i> Beta coefficient of linear regression model.</p><p>Correlation of serum chemerin concentrations with anthropometric parameters and markers of glucose metabolism, serum lipids and renal function in the Sorbs cohort.</p

Regional association plots for LDL cholesterol association in the SardiNIA study.

<p>Association plots for a study of 2,432 Sardinian individuals for five Metabochip fine-mapping regions using 1000 Genomes data as reference set and Affymetrix genotypes (left panels : A,C,E,G,H) or Metabochip genotypes (right panels : B,D,F,H,J) as target sets. The figures plot −log₁₀ of the association p-value within the region and recombination rate (blue lines) as a function of position on the chromosome. Blue, green, and red dots and triangles indicate genotyped and imputed SNPs with minor allele frequencies less than 0.02, greater than or equal 0.02 and less than 0.05, and greater than or equal 0.05, respectively. Gene positions and structures are displayed in the lower panel.</p

Summary of Metabochip SNPs by SNP category.

<p> <i>Numbers in parenthesis represents the proportion of the SNPs in the previous column. A SNP may fall into multiple categories.</i></p

Coverage of 257 Metabochip fine-mapping regions.

<p>Fraction of 1000 Genomes Project SNPs in strong linkage disequilibrium (r²≥.8) with HapMap 3 (green squares) or Metabochip (blue dots) SNPs as a function of minor allele frequencies: (A) 1000 Genomes Pilot 1 SNPs, (B) 1000 Genomes Phase 1 SNPs (May 2011 release).</p

Summary of Metabochip SNPs by trait: Fine-mapping and replication.

<p> <i>SNP counts are numbers of SNPs successfully manufactured on the Metabochip array.</i></p>*<p> <i>Waist-to-hip ratio and waist circumference were adjusted for body mass index.</i></p