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) 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 dbSNP or 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 FANTOM4 promoters.
Phantom5_Enhancers: Chromosomal coordinates from the FANTOM consortium of enhancer regions associated with FANTOM5 promoters.
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.
For any feedback or questions regarding this article (Illumina Knowledge Article #1568), contact Illumina Technical Support techsupport@illumina.com. |
Last updated