dbSNP 142 and 1000 Genomes Phase 3


Due to a somewhat catastrophic hardware failure during our production cycle for Ensembl release 79, we have only been able to release human dbSNP 142 incorporating 1000 Genomes phase 3 data on our GRCh37-based services (Web: grch37.ensembl.org, REST API: grch37.rest.ensembl.org, MySQL: anonymous@ensembldb.ensembl.org:3337, VEP: grch37.ensembl.org/vep). We hope to have these data on GRCh38 for Ensembl release 80; our GRCh38 database is based on dbSNP 138 until then.

VEP and GRCh38

For users of the Variant Effect Predictor (VEP) living in the brave new GRCh38 world, we have made available a VCF file which can be used to incorporate IDs and allele frequencies from the 1000 Genomes phase 3 data into your results. See this handy guide for details.

Viewing phase 3 data on the web

Using the same VCF as above, you can attach this as a custom data file to your Ensembl browser; this will allow you to see the genomic locations of the variants and their consequence types on our Region in Detail view.

Attach the following URL as a VCF (indexed): ftp://ftp.ensembl.org/pub/release-79/variation/VEP/1KG.phase3.GRCh38.vcf.gz

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You can then see the data alongside the tracks from our database:

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