Information about human SNPs in a region or from a list
If a chromosome region was specified, the NCBI eUtils interface to dbSNP will be used to find SNPs within that region. As of April 2010, this search will allow SNPs of Weight 1 or 2. If a region was specified, the search term used during the search will be displayed below.
The NCBI Entrez Neighbor SNP Popup will be used to find neighbor SNPs with Weight=1.
Clicking the "SNP Neighbor Popup" link in the left-hand column of the output display will invoke the NCBI Neighbor SNP Popup which will display neighbor SNPs of Weight=1.
FASTA records for each SNP will not be printed.
FLT records for each SNP will not be printed.
Full XML records for each SNP will not be printed.
Alternate SNP mappings to locations outside the specified target range may be displayed.
SNP IDs will be taken from the input list.
1 unique SNP IDs have been identified, and their detailed records will now be requested from NCBI.
The following table presents a form with checkboxes you can use to de-select SNPs of no interest, and then choose an option below the table for continued processing.
(Please see the notes at the end of this document for assistance interpreting its content.)
Neighbor SNP offset values are relative only to the position of a
SNP on the reference chromosome; stream direction is irrelevant unless
the SNP is being identified within a displayed sequence.
There may be multiple SNPs associated with the same location. As
a result, there may be mulitple neighbor SNPs reported for the
same offset in "Neighbor SNP" lists.
In the table above Neighbor SNP offset locations are
counted differently for Exemplar sequences displayed in "plus" and "minus"
orientations. For example, within an Exemplar sequence displayed in a
plus orientation, positive offset locations are counted from
left to right downstream into a 3' flanking region, and negative offset
locations are counted right to left upstream into the 5' flanking region.
For sequences displayed in a minus orientation, exchange the
words "positive" and "negative" in the preceding sentence.
The orientation of the displayed allele sequences may not match the
orientation of the displayed exemplar sequences with which they are
associated. Also, they may or may not have been recorded with the same
complementarity as the displayed Exemplar sequence.
Neighbor SNPs may map to more than one chromosome; their "weight"
as recorded in dbSNP may be be greater than 2. All SNP neighbor
searches are currently being conducted without regard to the
number of locations to which a neighbor SNP maps.
Here is the table of SNP Function classes:
mrna_acc and protein_acc both null.
coding: synonymy unknown
In gene segment with null mrna and protein. ex. IGLV4-69. geneId=28784
within 3' 0.5kb to a gene.
within 5' 2kb to a gene.
changes to STOP codon.
alters codon to make an altered amino acid in protein product.
indel snp causing frameshift.
3 prime untranslated region
5 prime untranslated region
3 prime acceptor dinucleotide
5 prime donor dinucleotide
Here is the table of Locus Type Codes
Insertion on contig: snp is always represented as one base and this one base in the snp sequence is substituted with more than one bases on the contig sequence in the alignment.
Contig allele is one base long.snp is always represented as one base and this one base in the snp sequence is substituted with exactly one base on the contig.
Deletion on the contig: part of the snp flanking sequence including the snp was absent on the contig sequence in the alignment.
In the alignment, part of the snp flanking sequence including snp is replaced with the contig sequence of longer length.
In the alignment, part of the snp flanking sequence including snp is replaced with the contig sequence of exactly the same length.
In the alignment, part of the snp flanking sequence including snp is replaced with the contig sequence of a shorter length.