How to collect SNP dataset from databases for SNP analysis?

Question

[arr234]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449402/ - In this study, it is mentioned that human APOE gene has 183 validated SNPs out of which 31 are missense, 21 are synonymous, 2 are nonsense, 98 are intronic, 7 are 5′ UTR, 6 are 3′ UTR, 7 are downstream, 8 are upstream, 1 is splice donor and 2 are splice acceptor variants. This data is collected using dbSNP. I would like to know how to collect these validated SNP dataset from dbSNP.

[maryamtavasoli71]

ExSNP database (http://www.exsnp.org/DZeQTL)

Answer 1

[Kevin Blighe]

The link provided by maryamtavasoli71 relates to eQTL studies, which is not what you want.

If you are not comfortable using the command line and in working with the dbSNP data locally, then you can just use the Ensembl Genome Browser to look up all variants in a particular gene. HERE is a search configured for APOE:

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Click on the Excel® sheet icon (at right) in order to download the data as CSV:

The data contains scores from in silico predictors, like SIFT, PolyPhen, MutationAssessor, CADD, etc. I did my own quick filtering and more or less identified ~200 'damaging' variants in the gene.

Kevin

Answer 2

[Pierre Lindenbaum]

using mysq ucsc

$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -P 3306 -D hg38 -e 'select func,valid,count(*) from snp142 where chrom="chr19" and chromStart>=44905749 and chromEnd<=44909395 group by func,valid'
+----------------------------+--------------------------------------------------------+----------+
| func                       | valid                                                  | count(*) |
+----------------------------+--------------------------------------------------------+----------+
| coding-synon               | unknown                                                |       13 |
| coding-synon               | by-frequency                                           |        1 |
| coding-synon               | by-1000genomes                                         |        3 |
| coding-synon               | by-cluster,by-1000genomes                              |        2 |
| coding-synon               | by-frequency,by-1000genomes                            |        2 |
| intron                     | unknown                                                |       25 |
| intron                     | by-cluster                                             |        4 |
| intron                     | by-1000genomes                                         |       33 |
| intron                     | by-cluster,by-1000genomes                              |        3 |
| intron                     | by-frequency,by-1000genomes                            |       24 |
| intron                     | by-cluster,by-frequency,by-1000genomes                 |       11 |
| near-gene-5                | by-cluster,by-frequency,by-1000genomes                 |        1 |
| nonsense                   | unknown                                                |        2 |
| missense                   | unknown                                                |       28 |
| missense                   | by-cluster                                             |        8 |
| missense                   | by-1000genomes                                         |       11 |
| missense                   | by-frequency,by-1000genomes                            |        7 |
| missense                   | by-cluster,by-frequency,by-1000genomes                 |        1 |
| missense                   | by-cluster,by-frequency,by-2hit-2allele,by-1000genomes |        2 |
| missense                   | by-frequency,by-hapmap,by-1000genomes                  |        1 |
| intron,missense            | by-1000genomes                                         |        1 |
| intron,missense            | by-frequency,by-1000genomes                            |        1 |
| intron,missense            | by-cluster,by-frequency,by-hapmap,by-1000genomes       |        1 |
| frameshift                 | unknown                                                |        1 |
| cds-indel                  | unknown                                                |        2 |
| untranslated-3             | unknown                                                |        2 |
| untranslated-3             | by-1000genomes                                         |        1 |
| untranslated-3             | by-frequency,by-1000genomes                            |        3 |
| untranslated-5             | by-1000genomes                                         |        3 |
| intron,untranslated-5      | by-1000genomes                                         |        1 |
| intron,untranslated-5      | by-frequency,by-1000genomes                            |        1 |
| near-gene-5,untranslated-5 | by-1000genomes                                         |        1 |
| splice-3                   | unknown                                                |        1 |
| splice-3                   | by-cluster                                             |        1 |
| splice-5                   | by-cluster                                             |        1 |
+----------------------------+--------------------------------------------------------+----------+