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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 HGVS 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.

rs13283004

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:69278152 (GRCh38.p14) 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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.02451 (343/13994, 14KJPN)
G=0.00000 (0/10930, ALFA)
T=0.00000 (0/10930, ALFA) (+ 9 more)
T=0.0475 (317/6676, 8.3KJPN)
T=0.0918 (446/4856, GnomAD)
T=0.1223 (348/2846, KOREAN)
T=0.018 (18/998, GoNL)
T=0.069 (58/840, Korea1K)
T=0.173 (37/214, Qatari)
C=0.49 (38/78, SGDP_PRJ)
C=0.5 (1/2, Siberian)
T=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC124902176 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 10930 C=1.00000 G=0.00000, T=0.00000
European Sub 7030 C=1.0000 G=0.0000, T=0.0000
African Sub 2566 C=1.0000 G=0.0000, T=0.0000
African Others Sub 100 C=1.00 G=0.00, T=0.00
African American Sub 2466 C=1.0000 G=0.0000, T=0.0000
Asian Sub 90 C=1.00 G=0.00, T=0.00
East Asian Sub 68 C=1.00 G=0.00, T=0.00
Other Asian Sub 22 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 138 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 586 C=1.000 G=0.000, T=0.000
South Asian Sub 92 C=1.00 G=0.00, T=0.00
Other Sub 428 C=1.000 G=0.000, T=0.000


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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
14KJPN JAPANESE Study-wide 13994 C=0.97549 T=0.02451
Allele Frequency Aggregator Total Global 10930 C=1.00000 G=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 7030 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2566 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 586 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 428 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 138 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 92 C=1.00 G=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 90 C=1.00 G=0.00, T=0.00
8.3KJPN JAPANESE Study-wide 6676 C=0.9525 T=0.0475
gnomAD - Genomes Global Study-wide 4856 C=0.9082 T=0.0918
gnomAD - Genomes European Sub 3714 C=0.9090 T=0.0910
gnomAD - Genomes African Sub 428 C=0.879 T=0.121
gnomAD - Genomes American Sub 394 C=0.934 T=0.066
gnomAD - Genomes Ashkenazi Jewish Sub 138 C=0.884 T=0.116
gnomAD - Genomes East Asian Sub 130 C=0.923 T=0.077
gnomAD - Genomes Other Sub 52 C=0.92 T=0.08
KOREAN population from KRGDB KOREAN Study-wide 2846 C=0.8777 T=0.1223
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.982 T=0.018
Korean Genome Project KOREAN Study-wide 840 C=0.931 T=0.069
Qatari Global Study-wide 214 C=0.827 T=0.173
SGDP_PRJ Global Study-wide 78 C=0.49 T=0.51
Siberian Global Study-wide 2 C=0.5 T=0.5
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.p14 chr 9 NC_000009.12:g.69278152C>G
GRCh38.p14 chr 9 NC_000009.12:g.69278152C>T
GRCh37.p13 chr 9 NC_000009.11:g.71893068C>G
GRCh37.p13 chr 9 NC_000009.11:g.71893068C>T
Gene: LOC124902176, uncharacterized LOC124902176 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124902176 transcript XR_007061567.1:n. 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

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= G T
GRCh38.p14 chr 9 NC_000009.12:g.69278152= NC_000009.12:g.69278152C>G NC_000009.12:g.69278152C>T
GRCh37.p13 chr 9 NC_000009.11:g.71893068= NC_000009.11:g.71893068C>G NC_000009.11:g.71893068C>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#.

17 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss22782916 Apr 05, 2004 (121)
2 1000GENOMES ss461086641 Sep 17, 2011 (135)
3 EVA-GONL ss986572193 Aug 21, 2014 (142)
4 WEILL_CORNELL_DGM ss1929889359 Feb 12, 2016 (147)
5 USC_VALOUEV ss2153882066 Dec 20, 2016 (150)
6 GRF ss2709744568 Nov 08, 2017 (151)
7 EVA_DECODE ss3723994154 Jul 13, 2019 (153)
8 EVA ss3769214479 Jul 13, 2019 (153)
9 SGDP_PRJ ss3872271024 Apr 26, 2020 (154)
10 KRGDB ss3920054709 Apr 26, 2020 (154)
11 KOGIC ss3965984490 Apr 26, 2020 (154)
12 TOMMO_GENOMICS ss5193561573 Apr 26, 2021 (155)
13 EVA ss5387813561 Oct 16, 2022 (156)
14 TOMMO_GENOMICS ss5737579006 Oct 16, 2022 (156)
15 YY_MCH ss5810666778 Oct 16, 2022 (156)
16 EVA ss5829218351 Oct 16, 2022 (156)
17 EVA ss5976677211 Oct 16, 2022 (156)
18 gnomAD - Genomes NC_000009.12 - 69278152 Apr 26, 2021 (155)
19 Genome of the Netherlands Release 5 NC_000009.11 - 71893068 Apr 26, 2020 (154)
20 KOREAN population from KRGDB NC_000009.11 - 71893068 Apr 26, 2020 (154)
21 Korean Genome Project NC_000009.12 - 69278152 Apr 26, 2020 (154)
22 Qatari NC_000009.11 - 71893068 Apr 26, 2020 (154)
23 SGDP_PRJ NC_000009.11 - 71893068 Apr 26, 2020 (154)
24 Siberian NC_000009.11 - 71893068 Apr 26, 2020 (154)
25 8.3KJPN NC_000009.11 - 71893068 Apr 26, 2021 (155)
26 14KJPN NC_000009.12 - 69278152 Oct 16, 2022 (156)
27 ALFA NC_000009.12 - 69278152 Apr 26, 2021 (155)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
5483214017 NC_000009.12:69278151:C:G NC_000009.12:69278151:C:G (self)
11448261, 27232103, 11931289, 24288004, 6398420, 51530880, ss461086641, ss986572193, ss1929889359, ss2153882066, ss2709744568, ss3769214479, ss3872271024, ss3920054709, ss5193561573, ss5387813561, ss5829218351, ss5976677211 NC_000009.11:71893067:C:T NC_000009.12:69278151:C:T (self)
326566176, 22362491, 71416110, 5483214017, ss3723994154, ss3965984490, ss5737579006, ss5810666778 NC_000009.12:69278151:C:T NC_000009.12:69278151:C:T (self)
ss22782916 NT_023935.16:1057599:C:T NC_000009.12:69278151:C:T (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 rs13283004

Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

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.post761+d5e8e07