# Infinium MethylationEPIC Manifest Column Headings

**IlmnID**: Unique identifier from the Illumina CG database. (The probe ID).

**Name**: The IlmnID.

**AddressA\_ID**: For Infinium I beadtypes, this is the Address ID for the probe specific for the A allele. For Infinium II beadtypes, this is 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.

**Infinium\_Design\_Type**: Infinium I (2 probes/locus) or Infinium II (1 probe/locus).

**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.

**Forward\_Sequence**: Plus (+) strand ([HapMap](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717504/)) sequence (5'-3') flanking the CG.

**Genome\_Build**: Genome Build referenced for this manifest.

**CHR**: Chromosome containing the CpG (Build 37).

**MAPINFO**: Chromosomal coordinates of the CpG (Build 37).

**SourceSeq**: The original, genomic sequence used for probe design prior to bisulfite conversion.

**Strand**: The Forward (F) or Reverse (R) designation of the [Design Strand](https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000002837).

* \***Note**: in methylation manifest files, the Forward Strand = the genomic Plus (+) Strand and the Reverse Strand = the genomic Minus (-) Strand. In this context, Forward and Reverse ARE NOT EQUIVALENT to the Forward and Reverse Strand designations originating from [dbSNP](https://www.ncbi.nlm.nih.gov/snp/) or as given in Infinium Genotyping manifests.

**UCSC\_RefGene\_Name**: Target gene names, from the [UCSC database](https://genome.ucsc.edu/). Multiple listings of the same gene name indicate splice variants.

**UCSC\_RefGene\_Accession**: The UCSC accession numbers of the target transcripts. Accession numbers are in the same order as the target gene transcripts.

**UCSC\_RefGene\_Group**: Gene region feature category describing the CpG position, from UCSC. Features are listed in the same order as the target gene transcripts. TSS200 = 0-200 bases upstream of the transcriptional start site (TSS).

* TSS1500 = 200-1500 bases upstream of the TSS.
* 5'UTR = Within the 5' untranslated region, between the TSS and the ATG start site.
* Body = Between the ATG and stop codon; irrespective of the presence of introns, exons, TSS, or promoters.
* 3'UTR = Between the stop codon and poly A signal.

**UCSC\_CpG\_Islands\_Name**: Chromosomal coordinates of the CpG Island from UCSC.

**Relation\_to\_UCSC\_CpG\_Island**: The location of the CpG relative to the CpG island.

* Shore = 0-2 kb from island.
* Shelf = 2-4 kb from island.
* N = Upstream (5’) of CpG island.
* S = Downstream (3’) of CpG island.

**Phantom4\_Enhancers**: Classifications from the Functional Annotation of the Mammalian Genome (FANTOM) consortium as a low- or high-CpG density region associated with [FANTOM4](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688930/pdf/gb-2009-10-4-r39.pdf) promoters.

**Phantom5\_Enhancers:** Chromosomal coordinates from the FANTOM consortium of enhancer regions associated with [FANTOM5](http://fantom.gsc.riken.jp/5/) promoters.

**DMR**: Differentially methylated regions ([experimentally determined](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2958040/pdf/nihms237010.pdf)).

* DMR = Differentially Methylated Region.
* CDMR = Cancer-specific Differentially Methylated Region.
* RDMR = Reprogramming-specific Differentially Methylated Region.

**450k\_Enhancer**: Predicted enhancer elements as annotated in the original 450K design (informatically determined by the [ENCODE Consortium](http://genome.ucsc.edu/ENCODE/)) are marked True.

**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
* Promoter\_Associated\_Cell\_type\_specific
* Unclassified
* Unclassified\_Cell\_type\_specific

**GencodeBasicV12\_NAME**: Target gene names, from the basic GENECODE build. Multiple listings of the same gene name indicate splice variants.

**GencodeBasicV12\_Accession**: The basic GENECODE accession numbers of the target transcripts. Accession numbers are in the same order as the target gene transcripts.

**GencodeBasicV12\_Group**: Gene region feature category describing the CpG position, from basic GENECODE. Features are listed in the same order as the target gene transcripts.

* TSS200 = 0-200 bases upstream of the transcriptional start site (TSS).

**GencodeCompV12\_NAME**: Target gene names, from the complete GENECODE build. Multiple listings of the same gene name indicate splice variants.

**GencodeCompV12\_Accession**: The complete GENECODE accession numbers of the target transcripts. Accession numbers are in the same order as the target gene transcripts.

**GencodeCompV12\_Group**: Gene region feature category describing the CpG position, from complete GENECODE. Features are listed in the same order as the target gene transcripts.

* TSS200 = 0-200 bases upstream of the transcriptional start site (TSS).

**DNase\_Hypersensitivity\_NAME**: Chromosomal coordinates of DNase hypersensitivity regions from ENCODE.

**DNase\_Hypersensitivity\_Evidence\_Count**: Number of experimental sources supporting the identification of each DNase hypersensitivity region from ENCODE.

**OpenChromatin\_NAME**: Chromosomal coordinates of open chromatin regions from ENCODE.

**OpenChromatin\_Evidence\_Count**: Number of experimental sources supporting the identification of each open chromatin region from ENCODE.

**TFBS\_NAME**: Chromosomal coordinates of transcription factor binding sites from ENCODE.

**TFBS\_Evidence\_Count**: Number of experimental sources supporting the identification of each transcription factor binding site from ENCODE.

**DHS**: DNase I Hypersensitivity Site (experimentally determined by the ENCODE project).

**Methyl27\_Loci**: CpG’s carried over from the HumanMethylation27 array (92% carryover) are marked “True”.

**Methyl450\_Loci**: CpGs carried over from the HumanMethylation450 array (94% carryover) are marked True.

**Chromosome\_36**: Chromosome containing the CpG (Build 36).

**Coordinate\_36**: Chromosomal coordinates of the CpG (Build 36).

**SNP\_ID**: rsids of SNPs located in the probe. Multiple listings of SNP rsids are allowed.

**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.

**Random\_Loci**: CpG loci chosen randomly by consortium members during the design process are marked True.

Information in the MethylationEPIC manifest references Genome Build 37 (hg19) unless otherwise stated.

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