How to extract the gap region in human genome?

Just notice that I should avoid the gap region, esp. when we generate a random background as your null distribution using tools such as bedtools shuffle.

Short answer: go below UCSC Table Browser link and choose to save as a bed file
 http://genome.ucsc.edu/cgi-bin/hgTables?clade=mammal&org=Human&db=hg19&hgta_group=allTables&hgta_track=hg19&hgta_table=gap&hgta_regionType=genome&hgta_outputType=primaryTable

As below table shown, 8.28% of hg19 assembly are simply gap.

Gap (gap) Summary Statistics

	item count 457 item bases 239,845,127 (8.28%) item total 239,845,127 (8.28%) smallest item 47 average item 524,825 biggest item 30,000,000