# Infinium Methylation Screening Array Manifest Column Headings The Infinium Methylation Screening Array Manifest Column Headings PDF file is available for download from the [Infinium Methylation Screening Array Manifest Files page](https://support.illumina.com/downloads/infinium-methylation-screening-manifest-files.html). Below are the detailed descriptions of the Infinium Methylation Screening Array Manifest file columns. **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 on the table below.\ **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 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 this is 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:** Color\_Channel: For Infinium I probes the color channel of the Next\_Base signal (R/G). Used for Bioconductor methylation array analysis software tools\ **Probe\_Type:** Probe type: cg=CpG, rs=dbSNP rsID, ch=Cp\ **Strand\_FR:** The Forward (F) or Reverse (R) designation of the Design Strand. F is equal to reference, + 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)- 1 probe. Used for Bioconductor methylation array analysis software tools\ **Infinium\_Design\_Type:** Infinium I (2 probes/locus) or Infinium II (1 probe/locus)\ **Rep\_Num:** Reflects the replicate number if the Name has replicate designs\ **CHR:** Chromosome containing the CpG (GRCh38)\ **MAPINFO:** Chromosomal coordinates of the CpG (GRCh38)\ **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\ **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. Intronic regions included\ **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. Intronic regions included\ **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 original ENCODE Consortium)\ **Regulatory\_Feature\_Group:** Description of the regulatory feature referenced in Regulatory\_Feature\_Name as provided by the original ENCODE Consortium - Gene\_Associated, Gene\_Associated \_Cell\_type\_specific, nonGene\_Associated, Promoter\_Associated\_Cell\_type\_specific, Unclassified, Unclassified\_Cell\_type\_specific\ **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\ **EPICv2\_Locus\_Match:** Locus Name (IlmnID) in Infinium MethylationEPICv2.0 Manifest\ **EPICv1\_Locus\_Match:** Locus Name (IlmnID) in Infinium MethylationEPICv1.0 Manifest\ **Methyl450\_Locus\_Match:** Locus Name (IlmnID) in Infinium Methylation450K Manifest\ **EPICv2\_ProbeSeq\_Match:** Indicates if the AlleleA\_ProbeSeq matches for EPIC v2\ **EPICv1\_ProbeSeq\_Match:** Indicates if the AlleleA\_ProbeSeq matches for EPIC v1\ **Methyl450\_ProbeSeq\_Match:** Indicates if the AlleleA\_ProbeSeq matches for Methylation450K\ **SNP\_ID:** rsIDs of SNPs located in the probe. Multiple listings of SNP rsIDs are allowed. dbSNP v155 used as reference\ **SNP\_DISTANCE:** Distance of SNPs from query base of the probe. Multiple listings of the distance values are associated with rsid. dbSNP v155 used as reference\ **SNP\_MinorAlleleFrequency:** Minor allele frequency of SNPs. Multiple listings of the minor allele frequencies are associated with rsid. dbSNP v155 used as reference\ **CHR\_GRCh37:** Chromosome containing the CpG (GRCh37)\ **MAPINFO\_GRCh37:** Chromosomal coordinates of the CpG (GRCh37) The logic for how the IlmnID is determined is shown below in the leftmost table column and other relevant information on how the IlmnID is generated is given in the remaining columns: | **IlmnID** | **Name** | **Strand\_TB** | **Strand\_CO** | **Infinium\_Design\_Type** | **The specific synthetic oligonucleotide probe replicate** | | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | |

The IlmnID is a
composite of multiple
information fields: the
name of the probe,
whether the probe
targets the top or
bottom strand, whether
the probe targets the
bisulfite converted
strand or
complementary strand
after amplification, the
Infinium probe design
type, and the number of
times the probe was
synthesized for array
representation.
Example of IlmnID:
cg12345678\_TC13
This probe would be a
CG probe with an eight
digit code that relates
to the probe sequence.
The following "T"
indicates that the probe
targets the top strand.
The adjacent "C"
indicates that the probe
targets the strand that
is initially bisulfite
converted. The "1"
indicates that the probe
has a Type I Infinium
design. The "3"
indicates that the probe
was synthesized three
times for representation
on the array The
multiple fields that
comprise the IlmnID
are provided in the
table columns to the
right.

|

The name of the
probe is
determined by
combining the
locus target
identifier, which
designates the
function of a given
probe, with an
eight digit code
that relates to the
probe sequence.
In situations where
the eight digit code
has not yet been
generated,
standard genomic
coordinates are
used. Example of
probe name:
cg12345678
Examples of locus
target identifiers:
cg= CpG
interrogating
ch= CpH
interrogating
rs = SNP
interrogating

|

Strand\_TB relates to
whether the probe is
designed to target
the top or bottom
strands of a given
locus as defined by
Illumina's standard
designation for
ambiguous SNP
probes. Examples of
top/bottom strand
designations: Top
strand = T
Bottom strand = B

|

Strand\_CO refers to
whether the probe is
designed to target the
originally bisulfite
converted DNA
strand, or the strand
resulting from
amplification of the
originally converted
DNA strand.
Examples of
converted/unconverted
designations:
Converted strand = C
Opposite strand = O

|

Infinium\_Design\_ Type
refers to whether the probe
utilizes a Type I design that
uses two attempted bead
types to probe a single
locus, or a Type II design
that uses one attempted
bead type to probe a single
locus. Examples of Infinium
design type designations:
Infinium Type I design = 1
Infinium Type II design = 2

|

This value depends on how many times a probe was
synthesized for representation on the array. For instance, if
the probe was synthesized three separate times, the probe
generated by the first synthesis would be denoted as "1",
while the probe generated from the second synthesis would
be denoted as "2", and the probe generated from the third
synthesis would be denoted as "3".

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