PheGenI: Phenotype-Genotype Integrator - National Center for Biotechnology Information

Association Results	Retrieving...	Searched by gene IDs retrieved from gene search.
Genes	1 - 1 of 1	Searched by gene names and/or gene IDs.
SNPs	Retrieving...	Searched by gene symbols retrieved from gene search.
eQTL Data	Retrieving...	Searched by gene IDs retrieved from gene search.
dbGaP Studies	Retrieving...	Searched by traits retrieved from page 1 of association results.
Genome View	Retrieving...

Enter search criteria using the controls below. Use the label or arrow on the left to hide / show any section. Small arrows at the far right side of each section heading to move the section above or below an adjacent section.

Enter the name of any trait or disease and a window will appear with a list of suggestions. Currently, phenotypes are matched to exact MeSH terms; parent, child and synonyms are not indexed. If you wish to narrow your search by category, click on the Browse... button. When more than one trait is selected, the search results will include records that match any of the selected traits. You may also limit the P-value for the Association Results and eQTL data to be less than the specified value.

Select broad trait category to limit the items shown in the trait selection.

Select trait for search. Selection of a trait will limit the trait categories shown above.

Data shown are compiled from both NHGRI GWAS Catalog (Source = NHGRI) and from most significant hits across analyses submitted to dbGaP.

Data shown are selected columns matching search criteria, taken directly from NCBI Gene.

Data shown are selected columns matching search criteria, taken directly from Entrez dbSNP.

Data shown are selected columns matching search criteria, taken directly from NCBI’s GTEx database and browser. This database aims to provide a central resource to archive and display associations between genetic variation and high-throughput molecular-level phenotypes. This effort originated with the NIH GTEx roadmap project; however the scope of this resource will be extended to include any available genotype/molecular phenotype datasets.

Data shown are molecular QTL datasets extracted from the NCBI molQTL resource (coming soon) by matching search criteria.

Data shown are selected dbGaP study information related to the trait information in the Association Results. Each study name is hyperlinked to the corresponding dbGaP study page where the user can apply for authorized access to individual-level data.

The ideogram view is shown for all genomic locations specified in the search which span regions with SNP and Gene Results.

The orientation can be selected as vertical, horizontal, or the default can be used.  The default is horizontal if one chromosome is displayed and vertical otherwise.

The user has the option of including SNPs and or Genes in the display.  If the search criteria include a location it can also be displayed.

The 'Display' option is either the current subset of the SNPs and Genes displayed on the page (e.g., 1 - 50 of 75) or those from all Association Results (e.g., all 75) including those that do not appear in the current page of the Association Results table.  Due to the potential volume of data, the latter option is available only if a phenotype trait was selected in the initial search.

Genetic location may be specified in one of three ways:

Location: chromosome and range (position on chromosome)
Range is specified as two numbers in multiple formats by a space, hyphen, or comma. The following examples are equivalent:
1000000:10000000
1M-10M
1000K 10000K
Gene: One or more gene symbols or NCBI Gene IDs separated by spaces, commas, or on separate lines.
SNP: One or more dbSNP rs numbers separated by spaces, commas, or on separate lines. The 'rs' prefix is optional.

You may optionally select one or more SNP functional classes. If none are selected, then all functional classes are included including 'intergenic.'
This entire section is optional if a category and/or trait are selected in the phenotype selection.

Genes

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#

Symbol

Description

Location

OMIM

1

LOC107980440

ABL breakpoint recombination region

9

: 130,710,129 - 130,854,140

Aliases:

none

Summary:

This region is known to undergo mitotic DNA recombination with other recombination regions found within the BCR, RhoGEF and GTPase activating protein (BCR) gene, including the major-, minor-, micro-, p195, p225, and p230 breakpoint cluster regions, located on the q arm of chromosome 22. Recombination between these regions results in t(9;22)(q34;q11) translocations, and can produce different gene fusions involving the BCR, RhoGEF and GTPase activating protein (BCR) gene and the ABL proto-oncogene 1, non-receptor tyrosine kinase (ABL1) gene, depending on the location of the recombination region within BCR. The smaller derivative chromosome resulting from this translocation is commonly known as the Philadelphia (Ph) chromosome. Translocations resulting from recombination events produce different chimeric transcripts. Recombination with the major-breakpoint cluster region produces e13a2 and e14a2 transcripts, recombination with the minor-breakpoint cluster region produces the e1a2 transcript, and recombination with the micro-breakpoint cluster region produces the e19a2 transcript, the e6a2, e8a2, e15a2, and e18a2 are produced as a result of recombination with the p195, p200, e15a2 and e18a2 breakpoint recombination regions, respectively. The abnormal tyrosine kinase activity of the chimeric proteins can result in leukemias such as chronic myelogenous leukemia (CML), acute lymphoblastic leukemia (ALL), and acute myelogenous leukemia (AML). It has been noted that this region contains a palindromic sequence with 243 nucleotides of perfect reverse complementarity, separated by about 2 kb. Analysis of recombination breakpoints is consistent with recombination occurring through a non-homologous end joining (NHEJ) pathway. A mechanism to explain this recombination event has yet to be determined, but it has been noted that BCR and ABL tend to be in close physical proximity during cell division in hematopoietic stem cells. This close proximity could provide opportunities for aberrant recombination in the event of double strand break formation. [provided by RefSeq, May 2016]

{ "section": "GENE", "summary": "1 - 1 of 1", "retstart": 0, "pageSize": 100, "count": 1, "SEQ": { "chr": [ ["9", 130710129, 130854140] ], "markers": { "9": [ ["LOC107980440", "NC_000009.12", 130710129, 130854140, "ABL breakpoint recombination region", "", 107980440] ] }, "unmapped": [ ] } }