What are these chromosomes in the snp138 annotation?

Question

[kindlychung]

Here is some entries from snp138:

chrUn_gl000248     6158        6159        rs2413143     TRUE
chr6_apd_hap1      55127       55128       rs1233627     TRUE
chr6_dbb_hap3      55127       55128       rs1233627     TRUE
chr6_mann_hap4     55127       55128       rs1233627     TRUE
chr6_mcf_hap5      55127       55128       rs1233627     TRUE
chr6_qbl_hap6      55127       55128       rs1233627     TRUE
chr6_ssto_hap7     92586       92587       rs1233627     TRUE
chr6_cox_hap2      274753      274754      rs1233627     TRUE
chr6_mcf_hap5      1104470     1104471     rs9404952     TRUE
chr6_mann_hap4     1104511     1104512     rs9404952     TRUE
chr6_qbl_hap6      1104775     1104776     rs9404952     TRUE
chr6_dbb_hap3      1104814     1104815     rs9404952     TRUE
chr6_ssto_hap7     1141740     1141741     rs9404952     TRUE

The chromosome columns seems cryptic. Could anyone explain what these mean? Thanks!

Answer 1

[Devon Ryan]

chrUn_glXXXX are unplaced contigs. That is, they're believed to belong to the human genome, but it's not clear where they belong (or in some cases they likely have multiple copies in the genome).

All of the *_hap* are haplotype alleles. These are often in the MHC and related loci. A bunch of them are described in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191933/