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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.

rs2531261

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:61442 (GRCh38.p13) 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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00006 (1/16502, 8.3KJPN)
A=0.02162 (231/10686, ALFA)
A=0.0003 (1/2868, KOREAN) (+ 5 more)
A=0.0000 (0/1800, Korea1K)
A=0.017 (9/520, SGDP_PRJ)
A=0.004 (2/506, NorthernSweden)
A=0.015 (3/206, Qatari)
A=0.00 (0/30, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.p13 chr 1 NC_000001.11:g.61442A>C
GRCh38.p13 chr 1 NC_000001.11:g.61442A>G
GRCh38.p13 chr 1 NC_000001.11:g.61442A>T
GRCh37.p13 chr 1 NC_000001.10:g.61442A>C
GRCh37.p13 chr 1 NC_000001.10:g.61442A>G
GRCh37.p13 chr 1 NC_000001.10:g.61442A>T
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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 10686 A=0.02162 G=0.97838, T=0.00000
European Sub 6962 A=0.0011 G=0.9989, T=0.0000
African Sub 2300 A=0.0896 G=0.9104, T=0.0000
African Others Sub 84 A=0.12 G=0.88, T=0.00
African American Sub 2216 A=0.0884 G=0.9116, T=0.0000
Asian Sub 108 A=0.000 G=1.000, T=0.000
East Asian Sub 84 A=0.00 G=1.00, T=0.00
Other Asian Sub 24 A=0.00 G=1.00, T=0.00
Latin American 1 Sub 146 A=0.027 G=0.973, T=0.000
Latin American 2 Sub 610 A=0.002 G=0.998, T=0.000
South Asian Sub 94 A=0.00 G=1.00, T=0.00
Other Sub 466 A=0.026 G=0.974, 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
8.3KJPN JAPANESE Study-wide 16502 A=0.00006 G=0.99994
KOREAN population from KRGDB KOREAN Study-wide 2868 A=0.0003 C=0.0000, G=0.9997, T=0.0000
Korean Genome Project KOREAN Study-wide 1800 A=0.0000 G=1.0000
SGDP_PRJ Global Study-wide 520 A=0.017 G=0.983
Northern Sweden ACPOP Study-wide 506 A=0.004 G=0.996
Qatari Global Study-wide 206 A=0.015 G=0.985
The Danish reference pan genome Danish Study-wide 30 A=0.00 G=1.00
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 A= C G T
GRCh38.p13 chr 1 NC_000001.11:g.61442= NC_000001.11:g.61442A>C NC_000001.11:g.61442A>G NC_000001.11:g.61442A>T
GRCh37.p13 chr 1 NC_000001.10:g.61442= NC_000001.10:g.61442A>C NC_000001.10:g.61442A>G NC_000001.10:g.61442A>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#.

32 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3548526 Sep 28, 2001 (100)
2 WI_SSAHASNP ss6851649 Feb 20, 2003 (113)
3 WUGSC_SSAHASNP ss14086219 Dec 05, 2003 (124)
4 SSAHASNP ss35430381 May 24, 2005 (125)
5 BCMHGSC_JDW ss87153235 Mar 25, 2008 (144)
6 ILLUMINA-UK ss118438125 Feb 14, 2009 (144)
7 ENSEMBL ss142672872 Dec 01, 2009 (144)
8 GMI ss275679915 May 04, 2012 (144)
9 1000GENOMES ss328356534 May 09, 2011 (144)
10 SSMP ss647514833 Apr 25, 2013 (144)
11 EVA-GONL ss974768757 Aug 21, 2014 (144)
12 DDI ss1425684553 Apr 01, 2015 (144)
13 EVA_GENOME_DK ss1573850721 Apr 01, 2015 (144)
14 HAMMER_LAB ss1793705096 Sep 08, 2015 (146)
15 WEILL_CORNELL_DGM ss1917958257 Feb 12, 2016 (147)
16 JJLAB ss2019497538 Sep 14, 2016 (149)
17 TOPMED ss2321497378 Dec 20, 2016 (150)
18 SYSTEMSBIOZJU ss2624264583 Nov 08, 2017 (151)
19 GRF ss2697373005 Nov 08, 2017 (151)
20 GNOMAD ss2750604192 Nov 08, 2017 (151)
21 SWEGEN ss2986141997 Nov 08, 2017 (151)
22 TOPMED ss3066321909 Nov 08, 2017 (151)
23 TOPMED ss3066321910 Nov 08, 2017 (151)
24 CSHL ss3343271551 Nov 08, 2017 (151)
25 URBANLAB ss3646580387 Oct 11, 2018 (152)
26 ACPOP ss3726715198 Jul 12, 2019 (153)
27 EVA ss3745720532 Jul 12, 2019 (153)
28 EVA ss3825981329 Apr 25, 2020 (154)
29 SGDP_PRJ ss3847984052 Apr 25, 2020 (154)
30 KRGDB ss3892823888 Apr 25, 2020 (154)
31 KOGIC ss3943622644 Apr 25, 2020 (154)
32 TOMMO_GENOMICS ss5142032893 Apr 25, 2021 (155)
33 The Danish reference pan genome NC_000001.10 - 61442 Apr 25, 2020 (154)
34 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 4955 (NC_000001.11:61441:A:G 93304/97174)
Row 4956 (NC_000001.11:61441:A:T 1/97258)

- Apr 25, 2021 (155)
35 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 4955 (NC_000001.11:61441:A:G 93304/97174)
Row 4956 (NC_000001.11:61441:A:T 1/97258)

- Apr 25, 2021 (155)
36 KOREAN population from KRGDB NC_000001.10 - 61442 Apr 25, 2020 (154)
37 Korean Genome Project NC_000001.11 - 61442 Apr 25, 2020 (154)
38 Northern Sweden NC_000001.10 - 61442 Jul 12, 2019 (153)
39 Qatari NC_000001.10 - 61442 Apr 25, 2020 (154)
40 SGDP_PRJ NC_000001.10 - 61442 Apr 25, 2020 (154)
41 8.3KJPN NC_000001.10 - 61442 Apr 25, 2021 (155)
42 ALFA NC_000001.11 - 61442 Apr 25, 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).

Associated ID History Updated (Build)
rs4951877 Mar 31, 2003 (113)
rs10218756 Dec 02, 2004 (124)
rs62637818 Jul 01, 2015 (144)
rs74970982 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
1282, ss3892823888 NC_000001.10:61441:A:C NC_000001.11:61441:A:C (self)
ss35430381 NC_000001.8:51304:A:G NC_000001.11:61441:A:G (self)
ss87153235, ss118438125, ss275679915 NC_000001.9:51304:A:G NC_000001.11:61441:A:G (self)
1357955, 1282, 63, 187, 1032, 2200, ss328356534, ss647514833, ss974768757, ss1425684553, ss1573850721, ss1793705096, ss1917958257, ss2019497538, ss2321497378, ss2624264583, ss2697373005, ss2750604192, ss2986141997, ss3343271551, ss3726715198, ss3745720532, ss3825981329, ss3847984052, ss3892823888, ss5142032893 NC_000001.10:61441:A:G NC_000001.11:61441:A:G (self)
645, 12656232649, ss3066321909, ss3646580387, ss3943622644 NC_000001.11:61441:A:G NC_000001.11:61441:A:G (self)
ss14086219 NT_077402.1:51304:A:G NC_000001.11:61441:A:G (self)
ss3548526, ss6851649, ss142672872 NT_077402.2:51441:A:G NC_000001.11:61441:A:G (self)
1282, ss3892823888 NC_000001.10:61441:A:T NC_000001.11:61441:A:T (self)
12656232649, ss3066321910 NC_000001.11:61441:A:T NC_000001.11:61441:A: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 rs2531261

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.post596+ae089ad