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".

For any feedback or questions regarding this article (Illumina Knowledge Article #9183), contact Illumina Technical Support [e-mail].