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) 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.

*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 dbSNPor as given in Infinium Genotyping manifests.

UCSC_RefGene_Name: Target gene names, from the UCSC database. 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 FANTOM 4promoters. 

Phantom5_Enhancers: Chromosomal coordinates from the FANTOM consortium of enhancer regions associated with FANTOM5promoters.  

DMR: Differentially methylated regions (experimentally determined).

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) 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.