GRCh37 / hg19

• Basic manifest with mapping information (EPICv2, EPIC, HM450)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  address_A

  address_B

  target

  nextBase

  channel

  Probe_ID

  mapFlag_A

  mapChrm_A

  mapPos_A

  mapQ_A

  mapCigar_A

  AlleleA_ProbeSeq

  mapNM_A

  mapAS_A

  mapYD_A

  mapFlag_B

  mapChrm_B

  mapPos_B

  mapQ_B

  mapCigar_B

  AlleleB_ProbeSeq

  mapNM_B

  mapAS_B

  mapYD_B

  type

• Basic annotation with suggested overall masking (EPIC, HM450, HM27)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  probe_strand

  Probe_ID

  address_A

  address_B

  channel

  designType

  nextBase

  nextBaseRef

  probeType

  orientation

  probeCpGcnt

  context35

  probeBeg

  probeEnd

  ProbeSeq_A

  ProbeSeq_B

  gene

  gene_HGNC

  chrm_A

  beg_A

  flag_A

  mapQ_A

  cigar_A

  NM_A

  chrm_B

  beg_B

  flag_B

  mapQ_B

  cigar_B

  NM_B

  wDecoy_chrm_A

  wDecoy_beg_A

  wDecoy_mapQ_A

  wDecoy_cigar_A

  wDecoy_NM_A

  wDecoy_chrm_B

  wDecoy_beg_B

  wDecoy_mapQ_B

  wDecoy_cigar_B

  wDecoy_NM_B

  posMatch

• Gene association, promoters (GENCODEv26, lifted to hg19) (EPICv2, EPIC, HM450, HM27)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  probe_strand

  Probe_ID

  genesUniq

  geneNames

  transcriptTypes

  transcriptIDs

  distToTSS

Previous versions:
GENCODEv19 (EPICv2 )

• Converting SNP probes to VCF format - rs probes (EPIC)
  Column header: (header description)

  chrm

  beg

  end

  rs

  designType

  U

  REF

  ALT

• Converting SNP probes to VCF format - channel-switching Infinium-I probes (EPIC)
  Column header: (header description)

  chrm

  beg

  end

  strand

  cg

  designType

  In-band

  REF

  ALT

  rs

• Population-specific masking GRCh37/hg19 (EPIC, HM450, HM27)
  

  CpG_chrm

  CpG_beg

  CpG_end

  probeID

  MASK_general_AFR

  MASK_snp5_AFR

  MASK_general_EAS

  MASK_snp5_EAS

  MASK_general_EUR

  MASK_snp5_EUR

  ...

  MASK_snp5_ASW

• Roadmap Epigenomics Mapping Consortium, 15 chromHMM states, 127 samples (EPIC, HM450, HM27)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  probeID

  E001

  E002

  E003

  E004

  E005

  E006

  E007

  E008

  E009

  E010

  E011

  E012

  E013

  E014

  E015

  E016

  E017

  E018

  ...

  E129

• ENCODE chromHMM states, 15 chromHMM states, 9 samples (EPIC, HM450, HM27)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  probeID

  Gm12878

  H1hesc

  Hepg2

  Hmec

  Hsmm

  Huvec

  K562

  Nhek

  Nhlf

• Imprinted differentially methylated loci, based on Court et al. 2014 Genome Research, PMID 24402520 (EPIC, HM450, HM27)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  probeID

  ICR

  PaternalOrMaternal

• ENCODE Transcription Factor Binding Sites, 171 TFs and 91 samples from ENCODE project, include distance to summit (EPIC, HM450, HM27)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  probeID

  TFBS_location

  TFBS_summit

  sample

  TF

  loc_summit

• CTCF binding sites, based on Wang et al. 2012 Genome Research, PMID 22955990 (EPIC, HM450, HM27)
  Column header: (header description)

  CpG_chrm

  CpG_beg

  CpG_end

  probeID

  CTCF

  distance