# Infinium Methylation450K manifest column headings

Detailed descriptions of the Infinium HumanMethylation450K manifest file column headings are listed.

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

**Name**: The IlmnID.

**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](http://hapmap.ncbi.nlm.nih.gov/)) sequence (5'-3') flanking the CG.

**Genome\_Build**: Genome Build referenced by the 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 before bisulfite conversion.

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

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

**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](http://www.ncbi.nlm.nih.gov/projects/SNP/) or as given in Infinium Genotyping manifests.

**Probe\_SNPs**: rsid(s) of SNP(s) located 10­-50 bases from the target CpG.

**Probe\_SNPs\_10**: rsid(s) of SNP(s) located ≤ 10 bases from the target CpG.

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

**Methyl27\_Loci**: CpG’s carried over from the HumanMethylation27 array (95% carryover) are marked True.

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

**UCSC\_RefGene\_Accession**: The UCSC accession number(s) of the target transcript(s). Accession numbers are given in the same order as the target gene transcripts.

**UCSC\_RefGene\_Group**: Gene region feature category describing the CpG position, from UCSC. Features 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.

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

**Enhancer**: Predicted enhancer elements (determined by the [ENCODE Consortium](http://genome.ucsc.edu/ENCODE/) using informatics) 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 (determined by the [ENCODE Consortium](http://genome.ucsc.edu/ENCODE/) using informatics).

**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

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

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

\
\
\ <br>

|                                                                                                                                                                                                                                                                                                                                                                   |
| :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
| *For any feedback or questions regarding this article (Illumina Knowledge Article #1567), contact Illumina Technical Support* [*techsupport@illumina.com*](mailto:techsupport@illumina.com?subject=Question%2FFeedback%20Regarding%20Illumina%20Knowledge%20Article%20#000001567%20-%20Microarray%20\&body=Dear%20Illumina%20Technical%20Support,%0D%0A%0D%0A)*.* |


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://knowledge.illumina.com/microarray/general/microarray-general-reference_material-list/000001567.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.