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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1524602

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:87190 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.291036 (30862/106042, GnomAD)
A=0.38430 (10689/27814, 14KJPN)
A=0.38523 (6344/16468, 8.3KJPN) (+ 9 more)
A=0.22180 (2631/11862, ALFA)
A=0.3559 (2279/6404, 1000G_30x)
A=0.3960 (1142/2884, KOREAN)
A=0.3935 (713/1812, Korea1K)
G=0.398 (101/254, SGDP_PRJ)
A=0.273 (47/172, Qatari)
A=0.06 (2/34, GENOME_DK)
G=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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 11862 G=0.77820 A=0.22180
European Sub 7618 G=0.8972 A=0.1028
African Sub 2816 G=0.5320 A=0.4680
African Others Sub 108 G=0.454 A=0.546
African American Sub 2708 G=0.5351 A=0.4649
Asian Sub 108 G=0.593 A=0.407
East Asian Sub 84 G=0.58 A=0.42
Other Asian Sub 24 G=0.62 A=0.38
Latin American 1 Sub 146 G=0.781 A=0.219
Latin American 2 Sub 610 G=0.520 A=0.480
South Asian Sub 94 G=0.83 A=0.17
Other Sub 470 G=0.691 A=0.309


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
gnomAD - Genomes Global Study-wide 106042 G=0.708964 A=0.291036
gnomAD - Genomes European Sub 51306 G=0.86035 A=0.13965
gnomAD - Genomes African Sub 37040 G=0.53688 A=0.46312
gnomAD - Genomes American Sub 10898 G=0.57717 A=0.42283
gnomAD - Genomes East Asian Sub 3058 G=0.6272 A=0.3728
gnomAD - Genomes Ashkenazi Jewish Sub 2126 G=0.8678 A=0.1322
gnomAD - Genomes Other Sub 1614 G=0.6815 A=0.3185
14KJPN JAPANESE Study-wide 27814 G=0.61570 A=0.38430
8.3KJPN JAPANESE Study-wide 16468 G=0.61477 A=0.38523
Allele Frequency Aggregator Total Global 11862 G=0.77820 A=0.22180
Allele Frequency Aggregator European Sub 7618 G=0.8972 A=0.1028
Allele Frequency Aggregator African Sub 2816 G=0.5320 A=0.4680
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.520 A=0.480
Allele Frequency Aggregator Other Sub 470 G=0.691 A=0.309
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.781 A=0.219
Allele Frequency Aggregator Asian Sub 108 G=0.593 A=0.407
Allele Frequency Aggregator South Asian Sub 94 G=0.83 A=0.17
1000Genomes_30x Global Study-wide 6404 G=0.6441 A=0.3559
1000Genomes_30x African Sub 1786 G=0.5045 A=0.4955
1000Genomes_30x Europe Sub 1266 G=0.8476 A=0.1524
1000Genomes_30x South Asian Sub 1202 G=0.7263 A=0.2737
1000Genomes_30x East Asian Sub 1170 G=0.6513 A=0.3487
1000Genomes_30x American Sub 980 G=0.527 A=0.473
KOREAN population from KRGDB KOREAN Study-wide 2884 G=0.6040 A=0.3960
Korean Genome Project KOREAN Study-wide 1812 G=0.6065 A=0.3935
SGDP_PRJ Global Study-wide 254 G=0.398 A=0.602
Qatari Global Study-wide 172 G=0.727 A=0.273
The Danish reference pan genome Danish Study-wide 34 G=0.94 A=0.06
Siberian Global Study-wide 4 G=0.5 A=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 1 NC_000001.11:g.87190G>A
GRCh37.p13 chr 1 NC_000001.10:g.87190G>A
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 G= A
GRCh38.p14 chr 1 NC_000001.11:g.87190= NC_000001.11:g.87190G>A
GRCh37.p13 chr 1 NC_000001.10:g.87190= NC_000001.10:g.87190G>A
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#.

38 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2363786 Oct 23, 2000 (88)
2 WI_SSAHASNP ss11344338 Jul 11, 2003 (116)
3 BCM_SSAHASNP ss14252226 Dec 05, 2003 (119)
4 CSHL-HAPMAP ss16425121 Feb 27, 2004 (120)
5 ENSEMBL ss161275062 Dec 01, 2009 (131)
6 BUSHMAN ss197885238 Jul 04, 2010 (132)
7 1000GENOMES ss230395384 Jul 14, 2010 (132)
8 1000GENOMES ss238114931 Jul 15, 2010 (132)
9 GMI ss275679958 May 04, 2012 (137)
10 PJP ss290493643 May 09, 2011 (134)
11 SSMP ss647514904 Apr 25, 2013 (138)
12 EVA-GONL ss974768841 Aug 21, 2014 (142)
13 DDI ss1425684597 Apr 01, 2015 (144)
14 EVA_GENOME_DK ss1573850754 Apr 01, 2015 (144)
15 HAMMER_LAB ss1793705142 Sep 08, 2015 (146)
16 WEILL_CORNELL_DGM ss1917958469 Feb 12, 2016 (147)
17 GENOMED ss1966667272 Jul 19, 2016 (147)
18 USC_VALOUEV ss2147483743 Dec 20, 2016 (150)
19 SYSTEMSBIOZJU ss2624264589 Nov 08, 2017 (151)
20 GRF ss2697373143 Nov 08, 2017 (151)
21 GNOMAD ss2750606797 Nov 08, 2017 (151)
22 SWEGEN ss2986142485 Nov 08, 2017 (151)
23 BIOINF_KMB_FNS_UNIBA ss3023513698 Nov 08, 2017 (151)
24 EVA ss3745720573 Jul 12, 2019 (153)
25 EVA ss3825981351 Apr 25, 2020 (154)
26 SGDP_PRJ ss3847984916 Apr 25, 2020 (154)
27 KRGDB ss3892824692 Apr 25, 2020 (154)
28 KOGIC ss3943623202 Apr 25, 2020 (154)
29 TOMMO_GENOMICS ss5142034492 Apr 25, 2021 (155)
30 EVA ss5316172553 Oct 12, 2022 (156)
31 1000G_HIGH_COVERAGE ss5512476381 Oct 12, 2022 (156)
32 SANFORD_IMAGENETICS ss5624743115 Oct 12, 2022 (156)
33 TOMMO_GENOMICS ss5666167358 Oct 12, 2022 (156)
34 YY_MCH ss5800240763 Oct 12, 2022 (156)
35 EVA ss5831416815 Oct 12, 2022 (156)
36 EVA ss5906703897 Oct 12, 2022 (156)
37 EVA ss5936581857 Oct 12, 2022 (156)
38 EVA ss5979925921 Oct 12, 2022 (156)
39 1000Genomes_30x NC_000001.11 - 87190 Oct 12, 2022 (156)
40 The Danish reference pan genome NC_000001.10 - 87190 Apr 25, 2020 (154)
41 gnomAD - Genomes NC_000001.11 - 87190 Apr 25, 2021 (155)
42 KOREAN population from KRGDB NC_000001.10 - 87190 Apr 25, 2020 (154)
43 Korean Genome Project NC_000001.11 - 87190 Apr 25, 2020 (154)
44 Qatari NC_000001.10 - 87190 Apr 25, 2020 (154)
45 SGDP_PRJ NC_000001.10 - 87190 Apr 25, 2020 (154)
46 Siberian NC_000001.10 - 87190 Apr 25, 2020 (154)
47 8.3KJPN NC_000001.10 - 87190 Apr 25, 2021 (155)
48 14KJPN NC_000001.11 - 87190 Oct 12, 2022 (156)
49 ALFA NC_000001.11 - 87190 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss197885238, ss275679958, ss290493643 NC_000001.9:77052:G:A NC_000001.11:87189:G:A (self)
1357988, 2086, 399, 1896, 97, 3799, ss230395384, ss238114931, ss647514904, ss974768841, ss1425684597, ss1573850754, ss1793705142, ss1917958469, ss1966667272, ss2147483743, ss2624264589, ss2697373143, ss2750606797, ss2986142485, ss3745720573, ss3825981351, ss3847984916, ss3892824692, ss5142034492, ss5316172553, ss5624743115, ss5831416815, ss5936581857, ss5979925921 NC_000001.10:87189:G:A NC_000001.11:87189:G:A (self)
2316, 9886, 1203, 4462, 6144193794, ss3023513698, ss3943623202, ss5512476381, ss5666167358, ss5800240763, ss5906703897 NC_000001.11:87189:G:A NC_000001.11:87189:G:A (self)
ss11344338, ss14252226, ss16425121 NT_077402.1:77052:G:A NC_000001.11:87189:G:A (self)
ss2363786, ss161275062 NT_077402.2:77189:G:A NC_000001.11:87189:G: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 rs1524602

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