Infinium MethylationEPIC v2.0 Manifest Column Headings
This article provides detailed descriptions of the column headings in the Infinium MethylationEPIC v2.0 Manifest File (CSV).
The associated product files can be accessed from the Infinium MethylationEPIC v2.0 Product Files page.
The sections below describe each manifest column heading and the corresponding information provided to support data analysis, annotation, and interpretation.
IlmnID
Unique identifier extended with the following design strand designations
Illumina strand (T/B)
Assay Strand (C / O)
Infinium Design Type (1/2)
Rep_Num
Name
Unique identifier from the Illumina CG database
AddressA_ID
For Infinium I beadtypes this is the Address ID for the probe specific for the A allele. For Infinium II beadtypes thisis the Address ID for the probe used for both A and B alleles (in this case AddressB_ID and AlleleB_ProbeSeq columns will be empty).
AlleleA_ProbeSeq
The sequence of the probe identified in the AddressA_ID column
AddressB_ID
For Infinium I beadtypes the address ID for the probe specific for the B allele.
AlleleB_ProbeSeq
For Infinium I beadtypes the sequence of the probe identified in the AddressB_ID column.
Next_Base
For Infinium I probes the nucleotide immediately following the CpG. Blank for Infinium II.
Color_Channel
For Infinium I probes the color channel of the Next_Base signal (Red/Green).
col
For Infinium I probes the color channel of the Next_Base signal (R/G).
Probe_Type
Probe type: cg=CpG, nv=nucleotide variant, rs=dbSNP rsID, ch=Cp<nonG base>.
Strand_FR
The Forward (F) or Reverse (R) designation of the Design Strand. F is eq to ref or + strand.
Strand_TB
The Illumina TOP (T) or Bottom (B) designation of the Design strand.
Strand_CO
The assay Converted (C) or Opposite (O) designation of the Design strand.
Infinium_Design
Infinium Design (1) - 2 probes or (2)- 1probe.
Infinium_Design_Type
Infinium I (2 probes/locus) or Infinium II (1 probe/locus).
CHR
Chromosome containing the CpG (GRCh38).
MAPINFO
Chromosomal coordinates of the CpG (GRCh38).
Species
Species which the assays were designed for (Homo sapiens)
Genome_Build
Genome Build referenced for this manifest.
Source_Seq
The original genomic sequence used for probe design prior to bisulfite conversion.
Forward_Sequence
Plus (+) strand sequence (5'-3') flanking the CG.
Top_Sequence
Top strand sequence (5'-3') flanking the CG.
Rep_Num
Reflects the replicate number if the Name has replicate designs.
UCSC_RefGene_Group
NCBI RefSeq Gene region
5UTR=5' untranslated region between the TSS and ATG start site
3UTR=3' untranslated region between stop codon and poly A signal
exon_#
TSS200=1-200 bp 5' the TSS
TS1500=200-1500 bp 5' of the TSS
UCSC_RefGene_Name
NCBI RefSeq Gene Name: Target gene names from the RefSeq database. Multiple listings of the same gene name indicate splice variants.
UCSC_RefGene_Accession
NCBI RefSeq Transcript ID: The RefSeq accession numbers of the target transcripts. Accession numbers are in the same order as the target gene transcripts.
UCSC_CpG_Islands_Name
Chromosomal coordinates of the CpG Island from UCSC.
Relation_to_UCSC_CpG_Island
Island=within boundaries of a CpG Island
N_Shore=0-2kb 5' of Island
N_Shelf=2kb-4kb 5' of Island
S_Shore=0-2kb 3' of Island
S_Shelf=2kb-4kb 3' of Island.
GencodeV41_Group
Gencode v41 Gene region
5UTR=5' untranslated region between the TSS and ATG start site
3UTR=3'untranslated region between stop codon and poly A signal
exon_#
TSS200=1-200 bp 5' the TSS
TS1500=200-1500 bp 5' of the TSS
GencodeV41_Name
Gencode v41 Gene Name: Target gene names from the RefSeq database. Multiple listings of the same gene name indicate splice variants.
GencodeV41_Accession
Gencode v41 Transcript ID: The RefSeq accession numbers of the target transcripts. Accession numbers are in the same order as the target gene transcripts.
Phantom5_Enhancers
Chromosomal coordinates from the FANTOM consortium of enhancer regions associated with FANTOM5 promoters.
HMM_Island
Hidden Markov Model Islands. Chromosomal map coordinates of computationally predicted CpG islands.
Regulatory_Feature_Name
Chromosomal map coordinates of the regulatory feature (informatically determined by the ENCODE Consortium).
Regulatory_Feature_Group
Description of the regulatory feature referenced in Regulatory_Feature_Name as provided by the Methylation Consortium - Gene_Associated, Gene_Associated _Cell_type_specific, nonGene_Associated, Promoter_Associated_Cell_type_specific, Unclassified, Unclassified_Cell_type_specific.
450k_Enhancer
Predicted enhancer elements as annotated in the original 450K design (informatically determined by the ENCODE Consortium) are marked True.
DMR
Differentially methylated regions (experimentally determined). CDMR = Cancer-specific Differentially Methylated Region.
DNase_Hypersensitivity_NAME
Name of the DNase Hypersensitivity site as defined in Encode v5.
Encode_CisReg_Site
Name and classification of the CisRegulatory Region as defined in Encode v5.
Encode_CisReg_Site_Evid
Evidence for each CisReg Region/Classification based on 87 studies in Encode v5 based on AllData-Full classification.
OpenChromatin_NAME
Classification of Open Chromatin sites based on 1600+ studies in Encode v5.
OpenChromatin_Evidence_Count
Evidence for each Open Chromatin site classification based on 1600+ studies in Encode v5.
Methyl450_Loci
Locus Name in Infinium Methyl450 Manifest.
Methyl27_Loci
Locus Name in Infinium Methyl27 Manifest.
EPICv1_Loci
Locus Name in Infinium EPICv1 Manifest.
Manifest_probe_match
Indicates if the AlleleA_ProbeSeq matches for Methyl450K and EPIC v1 is also a probe sequence match.
SNP_ID
rsids of SNPs located in the probe. Multiple listings of SNP rsids are allowed. dbSNP v153 used as reference.
SNP_DISTANCE
Distance of SNPs from query base of the probe. Multiple listings of the distance values are associated with rsid.
SNP_MinorAlleleFrequency
Minor allele frequency of SNPs. Multiple listings of the minor allele frequencies are associated with rsid.
CHR_37
Chromosome containing the CpG from GRCh37.
MAPINFO_37
Chromosomal coordinates of the CpG GRCh37.
References:
For any feedback or questions regarding this article (Illumina Knowledge Article #9183), contact Illumina Technical Support techsupport@illumina.com.
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