Chunk #13 — Online Methods — Functional Annotation of SNPs

Source

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence.

Embedded

yes

Text

categorical score based on information from expression quantitative trait loci (eQTLs) and chromatin marks, ranging from 1a to 7 with lower scores indicating an increased likelihood of having a regulatory function. Scores are as follows: 1a=eQTL + Transcription Factor (TF) binding + matched TF motif + matched DNase Footprint + DNase peak; 1b=eQTL + TF binding + any motif + DNase Footprint + DNase peak; 1c=eQTL + TF binding + matched TF motif + DNase peak; 1d=eQTL + TF binding + any motif + DNase peak; 1e=eQTL + TF binding + matched TF motif; 1f=eQTL + TF binding / DNase peak; 2a=TF binding + matched TF motif + matched DNase Footprint + DNase peak; 2b=TF binding + any motif + DNase Footprint + DNase peak; 2c=TF binding + matched TF motif + DNase peak; 3a=TF binding + any motif + DNase peak; 3b=TF binding + matched TF motif; 4=TF binding + DNase peak; 5=TF binding or DNase peak; 6=other; 7=Not available. The chromatin state represents the accessibility of genomic regions (every 200bp) with 15 categorical states predicted by a hidden Markov model based on 5 chromatin marks for 127 epigenomes in the Roadmap Epigenomics Project46. A lower state indicates higher