Infinium MethylationEPIC v2.0 Manifest Column Headings
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. A more detailed explanation can be found in the EPIC v2 Manifest Release Notes.
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.
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.
MAPINFO: Chromosomal coordinates of the CpG.
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 SNP_ID: rsids of SNPs located in the probe. Multiple listings of SNP rsids are allowed. dbSNP v153 used as reference.
SNP_DISTANCE SNP_DISTANCE: Distance of SNPs from query base of the probe. Multiple listings of the distance values are associated with rsid.
SNP_MinorAlleleFrequency: 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.
Information in the MethylationEPIC v2.0 manifest references Genome Build 38 unless otherwise stated.
Note: For information on EPICv1 manifest column headings, see article "Infinium MethylationEPIC Manifest Column Headings".
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