PLINK: Whole genome data analysis toolset plink...
Last original PLINK release is v1.07 (10-Oct-2009); PLINK 1.9 is now available for beta-testing

Whole genome association analysis toolset

Introduction | Basics | Download | Reference | Formats | Data management | Summary stats | Filters | Stratification | IBS/IBD | Association | Family-based | Permutation | LD calcualtions | Haplotypes | Conditional tests | Proxy association | Imputation | Dosage data | Meta-analysis | Result annotation | Clumping | Gene Report | Epistasis | Rare CNVs | Common CNPs | R-plugins | SNP annotation | Simulation | Profiles | ID helper | Resources | Flow chart | Misc. | FAQ | gPLINK

1. Introduction

2. Basic information

3. Download and general notes

4. Command reference table

5. Basic usage/data formats 6. Data management

7. Summary stats 8. Inclusion thresholds 9. Population stratification 10. IBS/IBD estimation 11. Association 12. Family-based association 13. Permutation procedures 14. LD calculations 15. Multimarker tests 16. Conditional haplotype tests 17. Proxy association 18. Imputation (beta) 19. Dosage data 20. Meta-analysis 21. Annotation 22. LD-based results clumping 23. Gene-based report 24. Epistasis 25. Rare CNVs 26. Common CNPs 27. R-plugins 28. Annotation web-lookup 29. Simulation tools 30. Profile scoring 31. ID helper 32. Resources 33. Flow-chart 34. Miscellaneous 35. FAQ & Hints

36. gPLINK

SNP annotation database lookup

This page describes PLINK's ability to output basic annotation information on SNPs on common WGAS genotyping platforms, via a web-based lookup function.

The SNP annotation data were compiled by Patrick Sullivan's lab; the original data files are available here.

NOTE All gene names must be HUGO standard gene names . For example, the serotonin transporter is SLC6A4 (not HTT or SERT).

If you use these annotations in a publication, include the following sentence and corresponding references:
     Using the PLINK retrieval interface, SNP annotations were created using 
     the TAMAL database (1) based chiefly on UCSC genome browser files (2), 
     HapMap (3), and dbSNP (4).
  1. Hemminger BM, Saelim B, Sullivan PF. TAMAL: An integrated approach to choosing SNPs for genetic studies of human complex traits. Bioinformatics 2006;22:626-7.
  2. Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ. The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 2006;34:D590-8.
  3. Altshuler D, Brooks LD, Chakravarti A, Collins FS, Daly MJ, Donnelly P. A haplotype map of the human genome. Nature 2005;437:1299-320.
  4. Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Helmberg W, Kapustin Y, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2006;34:D173-80.

Basic usage for SNP lookup function

The basic command is, for example,

plink --lookup rs1475515

which outputs to the LOG file the following information
PLINK-SNP (WGAS SNP annotation courtesy of Patrick Sullivan)
Connecting to web... 

SNP ID                          : rs1475515
Affy ID                         :
Affy 5.0                        : no
Affy 6.0                        : no
Perlegen ID                     :
Perlgen 600                     : no
Illumina 650                    : yes
Illumina 550                    : no
Non-syn SNP                     : no
SNP Error                       : no
SNP Pos Duplication             : no
Chromosome                      : 1
Strand                          : -
HG17 Position (bp)              : 228459232
HG18 Position (bp)              : 230219120
Pseudo-autosomal region?        : N/A
NCBI reference allele           : T
UCSC reference allele           : A
Observed alleles                : C/T
Human alleles                   : C/T
Predominant human allele        : A
Chimp allele                    : T
Macaque allele                  : T
dbSNP MAF                       : 0.038
HapMap CEU MAF                  : 0
HapMap ASI MAF                  : 0
HapMap YRI MAF                  : 0.15
HapMap CEU Strand               : -
HapMap CEU Allele               : C
HapMap ASI Allele               : C
HapMap YRI Allele               : C
In gene transcript              :
In gene coding region           :
Nearby Genes(KB distance)       :
Segmental duplication?          : no
Copy Number Variant?            : no
Conservation >95% pctile?       : no
Conservation >99% pctile?       : no
Disease-causing region?         : no
miRNA target? (TargetScan)      : no
miRNA target? (PicTAR)          : no
Regulatory potential?           : yes
Promotor region? (Stanford)     : no
Promotor region? (firstEF)      : no
Transfactor binding site        : no
Enhancer?                       : no
Exon?                           : no
Consensus splice site?          : no
5' UTR?                         : no
3' UTR?                         : no

To perform a lookup query on a batch of SNPs rather than 1 at a time, use the command

plink --lookup-list hits.list

where hits.list is just a list of SNP IDs (RS numbers); this will generate a file
containing multiple reports of the above kind. There is a limit to the number of SNPs that can be submitted at one time (currently 200).

Gene-based SNP lookup

It is possible to dump all SNPs in a gene with the command
plink --lookup-gene DISC1

which does two things: writes some gene-centric informationto the LOG file, and lists all the SNPs that feature on common WGAS platforms to the file
By default, SNPs within 20kb upstream and downstream of the gene are recorded. To change this, add the command
     --lookup-gene-kb 0
     --lookup-gene-kb 100
for example.

In the information written to the LOG file, there is a strong bias towards neuropsychiatrically-relevant information, reflecting the research interests of the creator. For example, the output for DISC1 is: (note: there are a few relatively redundant or uninformative fields currently that will be removed in future releases)
  Looking up gene information (and SNPs +/- 20 kb)
  Connecting to web... Writing SNP details to [ plink.snp.list ]

  Gene Name                               : DISC1
  Product                                 : disrupted in schizophrenia 1 isoform Es
  Entry                                   : 1
  CCDS Name                               : CCDS31056.1
  KG ID                                   : uc001hux.1
  SwissProt ID                            : Q9NRI5-4
  Hugo ID                                 : 2888
  Hugo alias                              :
  Hugo old gene names                     :
  Has gene name?                          : no
  HG18 strand                             : +
  HG18 chrom                              : 1
  HG18 TX Start                           : 229829236
  HG18 TX End                             : 229924970
  HG18 CDS Start                          : 229829236
  HG18 CDS End                            : 229924970
  HG18 TX Length                          : 95734
  HG18 TX Length Percentile               : 96
  HG17 strand                             : -
  HG17 chrom                              : 0
  HG17 TX Start                           : 0
  HG17 TX End                             : 0
  HG17 CDS Start                          : 0
  HG17 CDS End                            : 0
  HG17 TX Length                          : 0
  Has HG17 pos                            : no
  mRNA accession numbers                  : NM_001012958.1 ENST00000317586 OTTHUMT00000092355
  Protein accession numbers               : NP_001012976.1 ENSP00000320784 OTTHUMP00000035959
  Pseudoautosomal HG18                    : no
  Pseudoautosomal HG17                    : no
  Brain expressed 50th percentile         : yes
  Brain expressed 75th percentile         : yes
  Correlated cortex expression            : NA
  Correlated lymphoblastoid expression    : yes
  Number association studies from SZGene  : 20
  Annotation from SLEP database           : ? Schizophrenia [PMID=16033310]/{Schizoaffective 
                                          : disorder, susceptibility to}, 181500 (3) [OMIM=605210]
                                          : /{Schizophrenia, susceptibility to}, 604906 (3) [OMIM=605210]
  Association studies from GAD database   : psych (16)
It is possible to supply a list of genes to lookup, with the command
plink --lookup-gene-list mygenes.txt

that will dump the SNPs from multple genes in a SET file format, e.g. where the file
is something like
These could then be subsequently extracted with the command
     --extract plink.snp.list
as the END comments and gene names will just be ignored if these are not SNP IDs in the MAP file.

Description of the annotation information

For a detailed description of the annotation fields and how they were compiled, please see Patrick Sullivan's PDF
This document last modified Wednesday, 25-Jan-2017 11:52:28 EST