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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.

rs113490123

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:13643097 (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=0.129238 (34208/264690, TOPMED)
A=0.121926 (17087/140142, GnomAD)
A=0.06929 (1958/28258, 14KJPN) (+ 15 more)
A=0.10397 (1964/18890, ALFA)
A=0.06683 (1120/16760, 8.3KJPN)
A=0.1346 (862/6404, 1000G_30x)
A=0.1310 (656/5008, 1000G)
A=0.0906 (406/4480, Estonian)
A=0.0736 (215/2922, KOREAN)
A=0.0830 (152/1832, Korea1K)
A=0.071 (71/998, GoNL)
A=0.073 (44/600, NorthernSweden)
A=0.028 (15/534, MGP)
A=0.065 (14/216, Qatari)
A=0.051 (11/216, Vietnamese)
G=0.418 (46/110, SGDP_PRJ)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, 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 18890 G=0.89603 A=0.10397
European Sub 14286 G=0.92069 A=0.07931
African Sub 2946 G=0.8041 A=0.1959
African Others Sub 114 G=0.763 A=0.237
African American Sub 2832 G=0.8058 A=0.1942
Asian Sub 112 G=0.911 A=0.089
East Asian Sub 86 G=0.92 A=0.08
Other Asian Sub 26 G=0.88 A=0.12
Latin American 1 Sub 146 G=0.911 A=0.089
Latin American 2 Sub 610 G=0.774 A=0.226
South Asian Sub 98 G=0.92 A=0.08
Other Sub 692 G=0.877 A=0.123


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
TopMed Global Study-wide 264690 G=0.870762 A=0.129238
gnomAD - Genomes Global Study-wide 140142 G=0.878074 A=0.121926
gnomAD - Genomes European Sub 75902 G=0.92048 A=0.07952
gnomAD - Genomes African Sub 41998 G=0.81247 A=0.18753
gnomAD - Genomes American Sub 13638 G=0.80921 A=0.19079
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9455 A=0.0545
gnomAD - Genomes East Asian Sub 3132 G=0.9464 A=0.0536
gnomAD - Genomes Other Sub 2148 G=0.8957 A=0.1043
14KJPN JAPANESE Study-wide 28258 G=0.93071 A=0.06929
Allele Frequency Aggregator Total Global 18890 G=0.89603 A=0.10397
Allele Frequency Aggregator European Sub 14286 G=0.92069 A=0.07931
Allele Frequency Aggregator African Sub 2946 G=0.8041 A=0.1959
Allele Frequency Aggregator Other Sub 692 G=0.877 A=0.123
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.774 A=0.226
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.911 A=0.089
Allele Frequency Aggregator Asian Sub 112 G=0.911 A=0.089
Allele Frequency Aggregator South Asian Sub 98 G=0.92 A=0.08
8.3KJPN JAPANESE Study-wide 16760 G=0.93317 A=0.06683
1000Genomes_30x Global Study-wide 6404 G=0.8654 A=0.1346
1000Genomes_30x African Sub 1786 G=0.7872 A=0.2128
1000Genomes_30x Europe Sub 1266 G=0.9297 A=0.0703
1000Genomes_30x South Asian Sub 1202 G=0.9359 A=0.0641
1000Genomes_30x East Asian Sub 1170 G=0.9453 A=0.0547
1000Genomes_30x American Sub 980 G=0.743 A=0.257
1000Genomes Global Study-wide 5008 G=0.8690 A=0.1310
1000Genomes African Sub 1322 G=0.7859 A=0.2141
1000Genomes East Asian Sub 1008 G=0.9425 A=0.0575
1000Genomes Europe Sub 1006 G=0.9264 A=0.0736
1000Genomes South Asian Sub 978 G=0.938 A=0.062
1000Genomes American Sub 694 G=0.741 A=0.259
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9094 A=0.0906
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9264 A=0.0736
Korean Genome Project KOREAN Study-wide 1832 G=0.9170 A=0.0830
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.929 A=0.071
Northern Sweden ACPOP Study-wide 600 G=0.927 A=0.073
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.972 A=0.028
Qatari Global Study-wide 216 G=0.935 A=0.065
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.949 A=0.051
SGDP_PRJ Global Study-wide 110 G=0.418 A=0.582
Siberian Global Study-wide 2 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.13643097G>A
GRCh37.p13 chr 1 NC_000001.10:g.13969592G>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.13643097= NC_000001.11:g.13643097G>A
GRCh37.p13 chr 1 NC_000001.10:g.13969592= NC_000001.10:g.13969592G>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#.

48 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 BUSHMAN ss198039944 Jul 04, 2010 (132)
2 1000GENOMES ss218243626 Jul 14, 2010 (132)
3 1000GENOMES ss230431738 Jul 14, 2010 (132)
4 1000GENOMES ss238146299 Jul 15, 2010 (132)
5 GMI ss475581221 May 04, 2012 (137)
6 TISHKOFF ss553812694 Apr 25, 2013 (138)
7 SSMP ss647587433 Apr 25, 2013 (138)
8 EVA-GONL ss974871414 Aug 21, 2014 (142)
9 JMKIDD_LAB ss1067679874 Aug 21, 2014 (142)
10 1000GENOMES ss1289746490 Aug 21, 2014 (142)
11 DDI ss1425717780 Apr 01, 2015 (144)
12 EVA_DECODE ss1584228591 Apr 01, 2015 (144)
13 EVA_MGP ss1710889576 Apr 01, 2015 (144)
14 HAMMER_LAB ss1793928264 Sep 08, 2015 (146)
15 WEILL_CORNELL_DGM ss1918074038 Feb 12, 2016 (147)
16 GENOMED ss1966687486 Jul 19, 2016 (147)
17 JJLAB ss2019550483 Sep 14, 2016 (149)
18 USC_VALOUEV ss2147548743 Dec 20, 2016 (150)
19 HUMAN_LONGEVITY ss2160165563 Dec 20, 2016 (150)
20 GRF ss2697449460 Nov 08, 2017 (151)
21 GNOMAD ss2751822966 Nov 08, 2017 (151)
22 SWEGEN ss2986333614 Nov 08, 2017 (151)
23 BIOINF_KMB_FNS_UNIBA ss3023538667 Nov 08, 2017 (151)
24 CSHL ss3343326502 Nov 08, 2017 (151)
25 EGCUT_WGS ss3654420013 Jul 12, 2019 (153)
26 EVA_DECODE ss3686197698 Jul 12, 2019 (153)
27 ACPOP ss3726804889 Jul 12, 2019 (153)
28 EVA ss3745848340 Jul 12, 2019 (153)
29 KHV_HUMAN_GENOMES ss3798869665 Jul 12, 2019 (153)
30 EVA ss3826030791 Apr 25, 2020 (154)
31 SGDP_PRJ ss3848242604 Apr 25, 2020 (154)
32 KRGDB ss3893133181 Apr 25, 2020 (154)
33 KOGIC ss3943866209 Apr 25, 2020 (154)
34 TOPMED ss4439765596 Apr 25, 2021 (155)
35 TOMMO_GENOMICS ss5142570513 Apr 25, 2021 (155)
36 1000G_HIGH_COVERAGE ss5241246585 Oct 12, 2022 (156)
37 EVA ss5316865359 Oct 12, 2022 (156)
38 HUGCELL_USP ss5442431238 Oct 12, 2022 (156)
39 EVA ss5505768831 Oct 12, 2022 (156)
40 1000G_HIGH_COVERAGE ss5513034282 Oct 12, 2022 (156)
41 SANFORD_IMAGENETICS ss5624963326 Oct 12, 2022 (156)
42 TOMMO_GENOMICS ss5666907995 Oct 12, 2022 (156)
43 YY_MCH ss5800342726 Oct 12, 2022 (156)
44 EVA ss5831563150 Oct 12, 2022 (156)
45 EVA ss5848790483 Oct 12, 2022 (156)
46 EVA ss5907106750 Oct 12, 2022 (156)
47 EVA ss5936782254 Oct 12, 2022 (156)
48 EVA ss5979934696 Oct 12, 2022 (156)
49 1000Genomes NC_000001.10 - 13969592 Oct 11, 2018 (152)
50 1000Genomes_30x NC_000001.11 - 13643097 Oct 12, 2022 (156)
51 Genetic variation in the Estonian population NC_000001.10 - 13969592 Oct 11, 2018 (152)
52 gnomAD - Genomes NC_000001.11 - 13643097 Apr 25, 2021 (155)
53 Genome of the Netherlands Release 5 NC_000001.10 - 13969592 Apr 25, 2020 (154)
54 KOREAN population from KRGDB NC_000001.10 - 13969592 Apr 25, 2020 (154)
55 Korean Genome Project NC_000001.11 - 13643097 Apr 25, 2020 (154)
56 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 13969592 Apr 25, 2020 (154)
57 Northern Sweden NC_000001.10 - 13969592 Jul 12, 2019 (153)
58 Qatari NC_000001.10 - 13969592 Apr 25, 2020 (154)
59 SGDP_PRJ NC_000001.10 - 13969592 Apr 25, 2020 (154)
60 Siberian NC_000001.10 - 13969592 Apr 25, 2020 (154)
61 8.3KJPN NC_000001.10 - 13969592 Apr 25, 2021 (155)
62 14KJPN NC_000001.11 - 13643097 Oct 12, 2022 (156)
63 TopMed NC_000001.11 - 13643097 Apr 25, 2021 (155)
64 A Vietnamese Genetic Variation Database NC_000001.10 - 13969592 Jul 12, 2019 (153)
65 ALFA NC_000001.11 - 13643097 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
ss198039944, ss475581221, ss1584228591 NC_000001.9:13842178:G:A NC_000001.11:13643096:G:A (self)
424610, 158261, 94488, 310575, 6328, 89754, 115968, 259584, 65097, 539820, 45863, ss218243626, ss230431738, ss238146299, ss553812694, ss647587433, ss974871414, ss1067679874, ss1289746490, ss1425717780, ss1710889576, ss1793928264, ss1918074038, ss1966687486, ss2019550483, ss2147548743, ss2697449460, ss2751822966, ss2986333614, ss3343326502, ss3654420013, ss3726804889, ss3745848340, ss3826030791, ss3848242604, ss3893133181, ss5142570513, ss5316865359, ss5505768831, ss5624963326, ss5831563150, ss5936782254, ss5979934696 NC_000001.10:13969591:G:A NC_000001.11:13643096:G:A (self)
560217, 2994321, 244210, 745099, 3371931, 3268463746, ss2160165563, ss3023538667, ss3686197698, ss3798869665, ss3943866209, ss4439765596, ss5241246585, ss5442431238, ss5513034282, ss5666907995, ss5800342726, ss5848790483, ss5907106750 NC_000001.11:13643096:G:A NC_000001.11:13643096: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 rs113490123

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