23andMe SNP data does not correlate with UCSC. What am I doing wrong?
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6.3 years ago
sfcarroll ▴ 80

23andMe provide SNP information via their API, examples below.

 

# Updated: 2014-07-23
# index is a key for the /genomes/ endpoint (2 base pairs per index).
# strand is always +1.
index snp chromosome chromosome_position

316 rs1000219 10 54442734
317 rs1000220 4 16621729
318 rs10002203 4 186504624
319 rs1000221 15 89627396
320 rs1000222 4 140587985

 

When I take one of these SNP entries and cross-check against UCSC, I am getting different coordinates. For example, with hg38:

rs10002203 at chr4:185583220-185583720

How can I cross-reference 23andMe SNPs against an assembly?

23andme UCSC • 1.6k views
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3
Entering edit mode
6.3 years ago
abascalfederico ★ 1.2k

Coordinates chr4:186504624 are for build 37. In build 38 rs10002203 has coordinates: chr4:185583470.

If you click on the SNP within the browser you will be able to see the exact coordinates.

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