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aFC specifications


Unique identifier OMICS_23423
Name aFC
Alternative name allelic Fold Change
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data A list of QTL.
Input format FASTQTL
Operating system Unix/Linux
Programming languages Python
Computer skills Advanced
Version 0.2
Stability Stable
vcf, pheno, qtl, geno, chr, log_xform
Maintained Yes



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  • person_outline Pejman Mohammadi <>
  • person_outline Tuuli Lappalainen <>

Publication for allelic Fold Change

aFC in publications

PMCID: 5776756
PMID: 29022597
DOI: 10.1038/nature24277

[…] 1) lay in open chromatin regions, while only 6.56% of evariants in the lowest tenth percentile (0.0266 <p < 0.189) lay in such regions ()., to determine the effect sizes of cis-eqtls, we used allelic fold change, a method that assumes an additive model of eqtl alleles on total gene expression, allowing for interpretation of effect sizes as a fold change between alleles (). 17.4% of egenes […]

PMCID: 5389726
PMID: 28334807
DOI: 10.1093/nar/gkx105

[…] the novel cis-regulatory variant rs7647481, label-free proteomics found the nonrisk allele binding transcription factors yy1 with a 6.6-fold (p = 2.94 × 10−3) and nfatc4 with a 2.6-fold (p = 0.01) allelic fold-change (table , figure ). for rs4684847, previously shown to abrogate a type 2 diabetes-specific homeobox tfbs and to infer with prrx1 homeobox protein binding (), proteomics found […]

PMCID: 3129675
PMID: 21418647
DOI: 10.1186/gb-2011-12-3-r25

[…] days, we observed a significant decrease in ae in 20% of loci that showed at least a two-fold difference in ae at baseline (defined as an allelic change of at least 1.25-fold, the 95th percentile of allelic fold change among untreated biological controls). only one of the imprinted loci showed a change in ae upon treatment (gnas). similarly, loci where the ae could be mapped to common snps [] […]

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aFC institution(s)
New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Institute for Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland; Swiss Institute of Bioinformatics, Geneva, Switzerland
aFC funding source(s)
Supported by the Common Fund of the Office of the Director of the National Institutes of Health (NIH); by the NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS; by a contract (HHSN268201000 029C); by an SAIC-F subcontract (10ST1035); by SAIC-F (HHSN261200800001E); by University of Miami grants DA006227 and DA033684 and to contract N01MH000028; by the University of Geneva (MH090941 and MH101814), the University of Chicago (MH090951, MH090937, MH101820, MH101825), the University of North Carolina–Chapel Hill (MH090936 and MH101819), Harvard University (MH090948), Stanford University (MH101782), Washington University St Louis (MH101810), and the University of Pennsylvania (MH101822).

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