Table 2.

Commonly used terms in systems genetics and their definitions

Term	Definition
Complex Disease	A disease caused by the interaction of multiple genetic and environmental factors
GWAS	Genome-Wide Association Study: A technique where changes in a phenotype are associated with changes in the genome. Other forms, such as EWAS (epigenome-wide association study) apply the same concept to other biological layers
QTL	Quantitative Trait Locus: A region (locus) of the genome which is significantly associated with a phenotype. QTLs are broken down into types that represent the biological layer to which they are referring. (eg eQTL for expression, pQTL for protein abundance, miRQTL for microRNAs, etc.)
SNP	Single Nucleotide Polymorphism
Cis/Trans	Sometimes called ‘local’ and ‘distant’, these terms refer to the mechanism of action between a SNP and its target in a QTL. When a SNP is affecting a gene on the same chromosome and within the same LD block, it is said to be acting in cis, while a SNP affecting the expression of a gene elsewhere on the genome (eg on another chromosome) is said to be acting in trans
Bisulfite Sequencing	A common means to query the methylome. Unmethylated cytosines are converted to Uracil by bisulfite treatment, resulting in a clear signature which can be detected during DNA sequencing.
ChIP	Chromatin Immunoprecipitation: The name for a class of approaches which determine if a given protein binds to a given region of DNA
3C	Chromosome Conformation Capture: A way to examine whether two locations on the genome interact with one another in 3-d space.
4C	Chromosome Conformation Capture-on-Chip: Captures interactions between one locus and the rest of the genome
Hi-C	Identifies all interactions between DNA in 3-d space in the genome
RIPseq	RNA Immunoprecipitation Sequencing: Maps which RNA sequences are bound by a given protein
ATACseq	Assay for Transposase-Accessible Chromatin using sequencing: An approach which identifies genome-wide chromatin accessibility
Polygenic Risk Score	A way to integrate the results of many QTLs together to calculate a single score which predicts the susceptibility of an individual to a disease based on their DNA.