Genetic positions of SNPs in Homo sapiens

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Mubita, Mwangana

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Sep 5, 2022, 4:13:34 PM9/5/22
to gen...@soe.ucsc.edu

Dear genome browser team,

 

Warm greetings.

Could you please guide me on where I can find the most recent human genetic map based on genome build hg38? I would like to retrieve genetic positions of SNPs listed below:

 

SNP Name

Chromosome

Genetic position

Physical position

Ref. allele

Alt. allele

rs3889348

7

5298844

A

G

rs2289669

17

19560030

G

A

rs12943590

17

19716685

G

A

rs34834489

17

19716951

G

A

rs758427

17

19717164

A

G

rs272893

5

132327369

T

C

rs12208357

6

160122116

C

T

rs2282143 

6

160136611

C

T

rs34130495

6

160139792

G

A

rs72552763

6

160139849

G

T

rs622342

6

160151834

C

A

rs34059508

6

160154805

G

A

rs316019

6

16024925

A

C

rs145450955

6

160250619

G

A

rs201919874

6

160250625

G

A

rs7757336

6

160268526

T

G

rs2481030

6

160335403

A

G

rs520685

6

160346817

G

A

rs520829

6

160346873

T

G

rs2292334

6

160437156

G

A

rs8187722

6

160443726

A

G

 

I have found a genetic map on https://github.com/joepickrell/1000-genomes-genetic-maps but it is based on genome build hg19 and the genetic positions may not be the same for hg38.

 

Please feel to point towards someone who might be of help.

 

Kind regards,

Mubita

 

 

 

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Mwangana Mubita
Acting HOD: Department of Pharmacology & Therapeutics
Hage Geingob Campus: School of Pharmacy
University of Namibia
Tel: +264612065057
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Luis Nassar

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Sep 8, 2022, 5:05:40 PM9/8/22
to Mubita, Mwangana, gen...@soe.ucsc.edu
Hello, Mubita.

Thank you for your interest in the Genome Browser.

The genetic maps are generated by the data providers, such as the one you linked to from 1000G on hg19. We are not aware of any for hg38 on our site.

There are some others out there, e.g. https://www.biostars.org/p/9517179/#9517225. That one linked (https://alkesgroup.broadinstitute.org/Eagle/downloads/tables/) was generated by using our hg19 to hg38 liftOver chain file on the same 1000G file you linked to. Since these data are outside of the scope of the Genome Browser, I only mention them in hopes they may help but we do not offer support for that file or any other external data.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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Mubita, Mwangana

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Sep 8, 2022, 6:55:15 PM9/8/22
to Luis Nassar, gen...@soe.ucsc.edu

Dear Luis,

Thanks for your response.

I will have a look the links you have highlighted.

CAUTION -EXTERNAL SENDER: Please be careful when opening links and attachments. UNAM Directorate: Information & Communication Technology Services (DICTS)

 

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