Data on Recombination rate and Gene Positions in Humans

Question

I am looking for estimates of per base pair recombination rate in humans and indication on gene positions. The goal is to be a able to plot recombination rate in the y-axis and position (in bp) along all chromosomes in x-axis. Then add the genes on the graph.

I have never had to search for this kind of data. Can you give me some hints of where I could find these data into a simple format like the simple table presented below?

> Gene Positions
from       to
1145146    1147112
1568742    1570012
...

> Recombination rate
from   to       r
1      156787   1.2*1e-9
156788 256888   2*1e-8
....

Answer 1

A good baseline for this type of research in human genetics is Standards and guidelines for the interpretation of sequence variants from ACMG. It is a guideline for clinicians, and it gives a good sense of good variants data, bad variants data and setting up confidence level.

Try to consolidate data from:

Population databases

1. GWAS databases

   • Exome Aggregation Consortium

   • 1000 Genomes Project (there is data in vcf format which is pretty much what you need)

2. SNV databases

   • dbSNP (it is uncurated so you got to be hypercritical)

Disease databases

• ClinVar (be aware "12% of interpreted variants have ≥2 submitters in ClinVar , and 21% are interpreted differently")
• OMIM
• HGMD (it is a gold standard as it is curated, but you could only search for variants but not collect data because you could not download it unless you pay for it)