Search Reference Sequence for Markers


This search form allows you to explore for markers (SNP’s or CpG’s) of a certain type within a particular region of interest (for ex. a Gene or Chromosome position). See the criteria for which SNP’s are stored in the database here. CpG sites are from the Illumina 450K or 27K arrays.

ASM-confirmed SNP’s have been published in the literature as being suspected of Allele-Specific Methylation.

ASM-candidate SNP’s match the following criteria:

  • The SNP forms a CpG site with at least one of its alleles.

Interrogable SNP’s match the following criteria:

  • At least 1 enzyme cuts in the region 50 b.p. before the SNP from this list: HpyCH4IV, AciI, HhaI, HpaI



Query for markers of type:

Interrogable SNP ASM-confirmed SNP ASM-candidate SNP CpG-450K CpG-27K CpG-Genomic
Filtering by SNP Minor Allele Frequency (MAF) where: ≤ MAF ≤
Filtering by HapMap SNP’s and where sample size ≥

Within

(a) Genes ‐ one per line

Returning only markers within: kb upstream downstream (exclusive) of the genes
Adding ± kb to the region

(b) Chromosome

From: to:

(c) Between the first and last markers from a list

(d) Nearest (up- and downstream) to each marker in a list

(e) From this list of markers

Using reference marker type as: SNP CpG (450K or 27K, genomic)
List of markers (one rs or cg # per line, genomic cpg in format 5cg1234)
Adding ± kb to the region ‐ for (c) only