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Supplemental Material Supplemental Figure 1. PheGenI search order strategy. Phenotype searches are linked to the association results from dbGaP and the GWAS catalog. The rs numbers, and genes mapped to those rs numbers, are subsequently used to query dbSNP, NCBI Gene, and GTEx in a series of parallel searches. Similar searches can be performed for chromosomal location, gene, or SNP, and results are filtered accordingly. Supplemental Figure 2. Association results returned by PheGenI after executing a search for celiac disease trait and limiting p-value to 1 X 10-8. These data can be downloaded as tab delimited text. For better viewing, only the first 25 of 33 association results are shown. Supplemental Text. Linking to PheGenI Records. To link to PheGenI, the base URL is http://www.ncbi.nlm.nih.gov/gap/PheGenI and is case sensitive. A link to a particular search requires a query string to be appended to the URL and this begins with a question mark (?) followed by name=value pairs used as search parameters and separated with an ampersand (&). The name=value pairs may contain some nonalphanumeric characters replaced by a percent sign (%) followed by two hexadecimal digits representing the ASCII code of the original character. The following two encoded characters are used in the provided examples: %20 - 20 hex, 32 decimal, ASCII space %0A - 0A hex, 10 decimal, new line or line feed This overview is for constructing the most basic parameters and it is shown in three sections: Phenotype search, Location search, and Other parameters. The minimum requirement is to specify at least one trait (phenoTrait) or one of the three location specifications. Both a trait and a location can be specified. A parameter named tab must be specified in order for any search to be performed. This determines which, if any location search is to be performed. Following are the three options for the tab parameter tab=0 - location search tab=1 - gene search tab=2 - SNP search This also determines which tab will be displayed in the form on the web page. If no genotype search is to be specified, then tab=0 is recommended. If the tab parameter is omitted, then the other parameters will be used to fill in the search form, but no search will be performed until the user clicks on the "Search" button. Phenotype search Parameter: phenoTrait Value: the exact name of a trait. This is case sensitive and more than 1 trait can be specified, but with a separate phenoTrait parameter for each. Following is an example with two traits specified: http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=0&phenoTrait=Celiac%20Disease&phenoTrait= Arthritis,%20Rheumatoid Location search The location search has three options, Chromosome location, Gene Search, or SNP Search. Only one of these options can be implemented. Chromosome location Parameter: tab Value: 0 - for chromosome location. Parameter: chr - chromosome Value: an integer from 1 to 22 or X, Y, or MT Parameter: from Value: integer, the minimum number location in base pairs within the specified chromosome. This is required if not searching for a phenotype trait. Parameter: to Value: integer, the maximum number location in base pairs within the specified chromosome. This is required if not searching for a phenotype trait and must be greater than the “from” parameter. Here are two examples. The first is a search by location on chr. 6 and 20-40 Mbp, and the second is a phenotype and location search for "Diabetes Mellitus, Type 1" on chromosome 6. http://www.ncbi.nlm.nih.gov/gap/PheGenI?chr=6&from=30000000&to=40000000&tab=0 http://www.ncbi.nlm.nih.gov/gap/PheGenI?chr=6&phenoTrait=Diabetes%20Mellitus,%20Type %201&tab=0 Gene search Parameter: tab Value: 1 for gene search Parameter: gene Value: one or more gene symbols or IDs separated by non-alphanumeric characters, i.e. spaces, commas, etc. Unlike the phenoTrait parameter, there should only be one gene parameter specified but the value can contain multiple genes. Following are some examples with more than one gene specified: http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=1&gene=ABO%20DMD http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=1&gene=28%201756 SNP search Parameter: tab Value: 2 for SNP search Parameter: rs Value: one or more rs numbers separated by non-numeric characters. The rs numbers can optionally be prefixed with “rs.” For example searching for "328" or "rs328" are equivalent. Like the "gene" parameter specified above, only one rs parameter can be specified but the value can contain multiple rs numbers. Following is an example with three rs numbers: http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=2&rs=rs579459%0A507666%0A10521971 Other parameters: Parameter: pv – integer, p-value exponent Value: a positive integer that represents the minimum acceptable P-value for association and eQTL results. For example, if pv=10, then the minimum p-value is 1 x 10-10. The value specified is positive but represent the negative power of 10. The following example is a modified example of the SNP example search with a p-value specified: http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=2&rs=rs579459%0A507666%0A10521971&pv =10 Parameter: fxn Value: one of the following: exon, intron, neargene, UTR. This is case sensitive. This parameter specifies the SNP function class and more than one can be specified but the parameter name must be specified for each value. For example fxn=exon&fxn=intron is valid, but fxn=exon%20intron is not because two values are specified for one parameter. Following is an example which searches for "Diabetes Mellitus, Type 1" on chr 6 but only with SNPs that have a function class: http://www.ncbi.nlm.nih.gov/gap/PheGenI?tab=0&chr=6&phenoTrait=Diabetes%20Mellitus,%2 0Type%201&fxn=exon&fxn=neargene&fxn=UTR&fxn=intron