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Table 1 Archaic SNPs in the LWK population (1000 genome project). The table indicates the average number of block SNPs and singletons in the archaic linkage blocks of LWK and summarizes the distribution of the archaic alleles in structurally defined genomic sub-regions as well as in regions defined by ChIP-seq tracks. Numbers indicate the absolute count of archaic SNPs detected in the region; numbers in brackets indicate the percentage in reference to the total amount of the respective SNP type

From: Analysis of archaic human haplotypes suggests that 5hmC acts as an epigenetic guide for NCO recombination

Type of archaic SNP Average number of SNPs per linkage block* Distribution of archaic SNPs
Complete genome Genic region HLA genes (MHC I and II) CpG Island (CGI) Open chromatin (DNase I)a Recomb. hotspot (DCM1)b H3K4me3/H3K27me3 (bivalent)a 5mC tracksc 5hmC tracksd
Block SNP 4.30 1021071 379447 5278 9105 178314 10424 33888 776586 11914
(53.81) (37.16) (0.52) (0.89) (17.46) (1.02) (3.32) (88.60) (1.17)
Singleton 3.69 876329 353376 3025 15175 196934 56698 49900 656974 22400
(46.19) (40.32) (0.35) (1.73) (22.47) (6.47) (5.69) (86.90) (2.56)
Total 8.00 1897400 732823 8303 24280 375248 67122 83788 1433560 34314
(100.00) (38.62) (0.44) (1.28) (19.78) (3.54) (4.42) (87.81) (1.81)
  1. *237,312 linkage blocks (2–500 SNPs, average size: 20.3 kb)
  2. aENCODE-tracks [18, 19]
  3. bHuman testis [20]
  4. cH1 stem cells, partial coverage [1]
  5. dH1 stem cells [21]