# 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](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000001568)".

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