## Description

This track shows allele frequencies for the four HapMap populations in the ten ENCODE regions that have been resequenced for variation. The data for each population is shown in a separate subtrack:

- HapMap Allele Frequencies (CEU): Utah residents with ancestry from northern and western Europe
- HapMap Allele Frequencies (CHB): Han Chinese in Beijing, China
- HapMap Allele Frequencies (JPT): Japanese in Tokyo, Japan
- HapMap Allele Frequencies (YRI): Yoruba in Ibadan, Nigeria

The ENCODE regions targeted in this annotation include:

- ENr112 (chr2)
- ENr131 (chr2)
- ENr113 (chr4)
- ENm010 (chr7)
- ENm013 (chr7)
- ENm014 (chr7)
- ENr321 (chr8)
- ENr232 (chr9)
- ENr123 (chr12)
- ENr213 (chr18)

See the Methods section for a discussion of the scoring method used in this annotation.

The data set combines SNPs from the HapMap resequencing project, in addition to SNPs discovered previously.

## Display Conventions and Configuration

The complete list of subtracks available in this annotation is shown at the top of the track description page. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide.

Allele locations are indicated by tickmarks using a grayscale coloring scheme based on score, where darker shading indicates a higher score. A lower score indicates little or no variation; a higher score indicates a split between the reference and variant observations in the population. The track details page for an individual allele displays the variant and reference sequences, the allele frequencies, the origination of the data, and the total sample count.

## Methods

See the International HapMap Project website for information about how these data were collected and analyzed.

The score calculation in this annotation is a function of the minor allele frequency (maf), which varies from 0.0 to 0.5. The score has been normalized to a range of 500 to 1000 using the formula `score = 500 + (maf * 1000)`. Thus, a score of 500 indicates no variation; a score of 1000 indicates an even split between reference and variant observations in the population.

## Credits

These data were obtained from HapMap public release 16c.1. Thanks to the International HapMap Project for making this information available.