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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the Aliases tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs17059487

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr8:28821579 (GRCh38.p12) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
C>A
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
INTS9 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p12 chr 8 NC_000008.11:g.28821579C>A
GRCh37.p13 chr 8 NC_000008.10:g.28679096C>A
INTS9 RefSeqGene NG_016981.2:g.73603G>T
INTS9 RefSeqGene NG_016981.1:g.73603G>T
Gene: INTS9, integrator complex subunit 9 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
INTS9 transcript variant 2 NM_001145159.2:c. N/A Intron Variant
INTS9 transcript variant 4 NM_001172562.1:c. N/A Intron Variant
INTS9 transcript variant 5 NM_001363038.2:c. N/A Intron Variant
INTS9 transcript variant 1 NM_018250.4:c. N/A Intron Variant
INTS9 transcript variant 3 NR_026826.2:n. N/A Intron Variant
INTS9 transcript variant X5 XM_006716357.4:c. N/A Intron Variant
INTS9 transcript variant X2 XM_011544573.1:c. N/A Intron Variant
INTS9 transcript variant X3 XM_011544574.1:c. N/A Intron Variant
INTS9 transcript variant X4 XM_011544575.2:c. N/A Intron Variant
INTS9 transcript variant X6 XM_011544576.2:c. N/A Intron Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Not Reported in ClinVar
Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

None
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement C= A Note
GRCh38.p12 chr 8 NC_000008.11:g.28821579= NC_000008.11:g.28821579C>A
GRCh37.p13 chr 8 NC_000008.10:g.28679096= NC_000008.10:g.28679096C>A
INTS9 RefSeqGene NG_016981.2:g.73603= NG_016981.2:g.73603G>T
INTS9 RefSeqGene NG_016981.1:g.73603= NG_016981.1:g.73603G>T
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

47 SubSNP submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24092738 Sep 20, 2004 (123)
2 ILLUMINA ss67172106 Nov 30, 2006 (127)
3 ILLUMINA ss67528176 Nov 30, 2006 (127)
4 ILLUMINA ss68171810 Dec 12, 2006 (127)
5 ILLUMINA ss70652137 May 25, 2008 (130)
6 ILLUMINA ss71210013 May 17, 2007 (127)
7 ILLUMINA ss75781311 Dec 07, 2007 (129)
8 KRIBB_YJKIM ss85356529 Dec 15, 2007 (130)
9 ILLUMINA ss153612734 Dec 01, 2009 (131)
10 GMI ss156200777 Dec 01, 2009 (131)
11 ILLUMINA ss159305588 Dec 01, 2009 (131)
12 ILLUMINA ss160417524 Dec 01, 2009 (131)
13 ILLUMINA ss172726835 Jul 04, 2010 (132)
14 GMI ss279751538 May 04, 2012 (137)
15 ILLUMINA ss480163569 May 04, 2012 (137)
16 ILLUMINA ss480173170 May 04, 2012 (137)
17 ILLUMINA ss480886509 Sep 08, 2015 (146)
18 ILLUMINA ss484879804 May 04, 2012 (137)
19 ILLUMINA ss536940359 Sep 08, 2015 (146)
20 ILLUMINA ss778826996 Sep 08, 2015 (146)
21 ILLUMINA ss782886294 Sep 08, 2015 (146)
22 ILLUMINA ss783849950 Sep 08, 2015 (146)
23 ILLUMINA ss832140742 Sep 08, 2015 (146)
24 ILLUMINA ss832817662 Jul 13, 2019 (153)
25 ILLUMINA ss834287403 Sep 08, 2015 (146)
26 EVA_SVP ss1713027018 Apr 01, 2015 (144)
27 ILLUMINA ss1752727868 Sep 08, 2015 (146)
28 USC_VALOUEV ss2153242832 Dec 20, 2016 (150)
29 ILLUMINA ss2634730885 Nov 08, 2017 (151)
30 ILLUMINA ss2635182046 Nov 08, 2017 (151)
31 TOPMED ss3557647897 Nov 08, 2017 (151)
32 ILLUMINA ss3630030927 Oct 12, 2018 (152)
33 ILLUMINA ss3632630868 Oct 12, 2018 (152)
34 ILLUMINA ss3633496629 Oct 12, 2018 (152)
35 ILLUMINA ss3634223233 Oct 12, 2018 (152)
36 ILLUMINA ss3635166217 Oct 12, 2018 (152)
37 ILLUMINA ss3635902122 Oct 12, 2018 (152)
38 ILLUMINA ss3636903382 Oct 12, 2018 (152)
39 ILLUMINA ss3637655275 Oct 12, 2018 (152)
40 ILLUMINA ss3638752741 Oct 12, 2018 (152)
41 ILLUMINA ss3639379102 Oct 12, 2018 (152)
42 ILLUMINA ss3639984141 Oct 12, 2018 (152)
43 ILLUMINA ss3640873507 Oct 12, 2018 (152)
44 ILLUMINA ss3643684183 Oct 12, 2018 (152)
45 ILLUMINA ss3644027658 Oct 12, 2018 (152)
46 ILLUMINA ss3745466033 Jul 13, 2019 (153)
47 ILLUMINA ss3772958550 Jul 13, 2019 (153)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs59742530 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss279751538, ss480163569, ss1713027018, ss2635182046, ss3639379102, ss3639984141, ss3643684183, ss3644027658 NC_000008.9:28735014:C:A NC_000008.11:28821578:C:A (self)
ss480173170, ss480886509, ss484879804, ss536940359, ss778826996, ss782886294, ss783849950, ss832140742, ss832817662, ss834287403, ss1752727868, ss2153242832, ss2634730885, ss3630030927, ss3632630868, ss3633496629, ss3634223233, ss3635166217, ss3635902122, ss3636903382, ss3637655275, ss3638752741, ss3640873507, ss3745466033, ss3772958550 NC_000008.10:28679095:C:A NC_000008.11:28821578:C:A (self)
ss3557647897 NC_000008.11:28821578:C:A NC_000008.11:28821578:C:A (self)
ss24092738, ss67172106, ss67528176, ss68171810, ss70652137, ss71210013, ss75781311, ss85356529, ss153612734, ss156200777, ss159305588, ss160417524, ss172726835 NT_167187.1:16537241:C:A NC_000008.11:28821578:C:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs17059487

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post308+0fe9b3b