The variants which are in the Finrisk dataset also have a visualization in SISu. This visualization is different for common variants (>=75 samples) and rare variants (< 75 samples). It is based on the county of residence of the sampled persons and shows the minor allele frequency for each county for both common and rare variants. For rare variants it also shows the locations of individual samples on the map. The minor allele frequencies for each county have been calculated using this formula (where the Ns are the amounts of samples of that respective county):
(Nhet + 2*Nalt hom) / ((Nref hom + Nhet + Nalt hom)*2)
For both visualizations, hovering your mouse over a county will show a tooltip containing detailed information of the allele frequency and N:s (ref hom, het, alt hom) of that county. Take in account that in Finland, the population density is not the same throughout the country. Refer to the population density map below (source: Wikipedia 2016) to find out how the population is spread around the country.
Common variant visualization
For common variants (>=75), the visualization shows a colored map of Finland. In the colored map, a white area with dashed borders means that no Finrisk samples have exist for that county. For counties from which samples have been gathered, a color is shown between white and blue (#0095A9), with grey borders. The color reflects the minor allele frequency of that county: the bluer, the larger the allele frequency is. The value is linearly normalized between the counties with the biggest allele frequency (#0095A9 blue) and zero (white). Because of this, visualizations of different variants can not be directly compared with each other.
Rare variant visualization
For rare variants (<75), the visualization shows a greyscale map of Finland with black dots scattered around the map. Also in this visualization, a white county with dashed borders means that no samples have been gathered from that county. For counties from which samples have been gathered, a color is shown between white and grey (#DBDBDB). The color reflects the minor allele frequency of that county: the darker the larger the allele frequency is. As in the common variant visualization, in the rare variant visualization the value is linearly normalized between the biggest allele frequency and zero. Thus, different variants' visualizations cannot be directly compared with each other.
In the rare variant visualization the black dots show the birthplaces of the individual sample persons. In the database, these datapoints contain location info on a municipal level. Because of this, the visualization slightly randomizes the sample locations to enable the showing of all individual samples on the map. Do not take the locations as exact coordinates, but as guidelines on the general location of the sample. It is also possible that one individual appears in the dataset several times and thus is also shown on the map multiple times. Hence, always compare the values shown on map to the SISu reference data and be especially careful if the numbers of homo- or heterozygous individuals are bigger on the map than in the aggregated SISu reference data.