These files contain the cis-eQTL results from the MuTHER study. Please see the following publication for information on data generation and analysis parameters:

Mapping cis and trans regulatory effects across multiple tissues in twins
Grundberg, E, Small KS, Hedman ÅK, Nica AC, Buil, A, Keildson S, Bell JT, Yang TP, Meduri E, Barrett A, Nisbett, J, Sekowska M, Wilk, A, Shin SY, Glass D, Travers M, Min JL, Ring S, Ho K, Thorleifsson G, Kong A, Thorsteindottir U, Ainali C, Dimas AS, Hassanali N, Ingle C, Knowles D, Krestyaninova M,  Lowe CE, Di Meglio P, Montgomery SB, Parts L, Potter S, Surdulescu G, Tsaprouni, L, Tsoka S, Bataille V, Durbin R, Nestle FO, O’Rahilly S, Soranzo N, Lindgren CM, Zondervan KT, Ahmadi KA, Schadt EE, Stefansson K, Davey Smith G,  McCarthy MI, Deloukas P, Dermitzakis EM, Spector TD, for the MuTHER consortium

Nature Genetics, 2012 Sep 2;44(10):1084-1089. doi: 10.1038/ng.2394. Epub 2012 Sep 2.


The cis results are presented in two sets of files "Top" results per tissue and all tested associations per chromosome.  
-All coordinates are in Build 36.  
-The "A1" column lists the reference/effect allele.  
-Autosomal genotypes were generated with IMPUTE 2 with a HapMap2 reference panel. Only directly genotyped SNPs were analyzed for chromosome 23.   



TOP RESULTS FILES:
MuTHER_top_cis_eQTL_per_probe_Fat.txt
MuTHER_top_cis_eQTL_per_probe_LCL.txt
MuTHER_top_cis_eQTL_per_probe_SKINtxt

For each tissue, this file lists the most significant cis SNP association for each probe in the tissue specified in the file name.  The association at the same SNP-probe pair in the other two tissues are included for comparison.    


FULL RESULTS FILES:
MuTHER_cis_results_chr[1-23].txt
These files list the association results for all tested cis SNP-probe pairs in all three tissues. Files are divided by chromosome.