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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.

rs2031713

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:21403457 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.128195 (33932/264690, TOPMED)
A=0.135734 (18936/139508, GnomAD)
A=0.01458 (412/28258, 14KJPN) (+ 16 more)
A=0.01468 (246/16760, 8.3KJPN)
A=0.18506 (2744/14828, ALFA)
A=0.0792 (507/6404, 1000G_30x)
A=0.0773 (387/5008, 1000G)
A=0.2038 (913/4480, Estonian)
A=0.1871 (721/3854, ALSPAC)
A=0.1634 (606/3708, TWINSUK)
A=0.0133 (39/2930, KOREAN)
A=0.0153 (28/1832, Korea1K)
A=0.197 (197/998, GoNL)
A=0.203 (122/600, NorthernSweden)
A=0.104 (57/550, SGDP_PRJ)
A=0.064 (21/328, HapMap)
A=0.106 (23/216, Qatari)
A=0.13 (7/52, Siberian)
A=0.15 (6/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105372558 : 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 14828 A=0.18506 G=0.81494, T=0.00000
European Sub 12538 A=0.20171 G=0.79829, T=0.00000
African Sub 1458 A=0.0535 G=0.9465, T=0.0000
African Others Sub 62 A=0.00 G=1.00, T=0.00
African American Sub 1396 A=0.0559 G=0.9441, T=0.0000
Asian Sub 20 A=0.00 G=1.00, T=0.00
East Asian Sub 14 A=0.00 G=1.00, T=0.00
Other Asian Sub 6 A=0.0 G=1.0, T=0.0
Latin American 1 Sub 316 A=0.168 G=0.832, T=0.000
Latin American 2 Sub 38 A=0.53 G=0.47, T=0.00
South Asian Sub 36 A=0.06 G=0.94, T=0.00
Other Sub 422 A=0.147 G=0.853, 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
TopMed Global Study-wide 264690 A=0.128195 G=0.871805
gnomAD - Genomes Global Study-wide 139508 A=0.135734 G=0.864266
gnomAD - Genomes European Sub 75456 A=0.18713 G=0.81287
gnomAD - Genomes African Sub 41866 A=0.05205 G=0.94795
gnomAD - Genomes American Sub 13602 A=0.14836 G=0.85164
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.0895 G=0.9105
gnomAD - Genomes East Asian Sub 3126 A=0.0147 G=0.9853
gnomAD - Genomes Other Sub 2138 A=0.1291 G=0.8709
14KJPN JAPANESE Study-wide 28258 A=0.01458 G=0.98542
8.3KJPN JAPANESE Study-wide 16760 A=0.01468 G=0.98532
Allele Frequency Aggregator Total Global 14828 A=0.18506 G=0.81494, T=0.00000
Allele Frequency Aggregator European Sub 12538 A=0.20171 G=0.79829, T=0.00000
Allele Frequency Aggregator African Sub 1458 A=0.0535 G=0.9465, T=0.0000
Allele Frequency Aggregator Other Sub 422 A=0.147 G=0.853, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 316 A=0.168 G=0.832, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 38 A=0.53 G=0.47, T=0.00
Allele Frequency Aggregator South Asian Sub 36 A=0.06 G=0.94, T=0.00
Allele Frequency Aggregator Asian Sub 20 A=0.00 G=1.00, T=0.00
1000Genomes_30x Global Study-wide 6404 A=0.0792 G=0.9208
1000Genomes_30x African Sub 1786 A=0.0308 G=0.9692
1000Genomes_30x Europe Sub 1266 A=0.1738 G=0.8262
1000Genomes_30x South Asian Sub 1202 A=0.0699 G=0.9301
1000Genomes_30x East Asian Sub 1170 A=0.0145 G=0.9855
1000Genomes_30x American Sub 980 A=0.134 G=0.866
1000Genomes Global Study-wide 5008 A=0.0773 G=0.9227
1000Genomes African Sub 1322 A=0.0340 G=0.9660
1000Genomes East Asian Sub 1008 A=0.0159 G=0.9841
1000Genomes Europe Sub 1006 A=0.1740 G=0.8260
1000Genomes South Asian Sub 978 A=0.062 G=0.938
1000Genomes American Sub 694 A=0.130 G=0.870
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.2038 G=0.7962
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.1871 G=0.8129
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.1634 G=0.8366
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0133 G=0.9867
Korean Genome Project KOREAN Study-wide 1832 A=0.0153 G=0.9847
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.197 G=0.803
Northern Sweden ACPOP Study-wide 600 A=0.203 G=0.797
SGDP_PRJ Global Study-wide 550 A=0.104 G=0.896
HapMap Global Study-wide 328 A=0.064 G=0.936
HapMap African Sub 120 A=0.008 G=0.992
HapMap American Sub 120 A=0.158 G=0.842
HapMap Asian Sub 88 A=0.01 G=0.99
Qatari Global Study-wide 216 A=0.106 G=0.894
Siberian Global Study-wide 52 A=0.13 G=0.87
The Danish reference pan genome Danish Study-wide 40 A=0.15 G=0.85
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 20 NC_000020.11:g.21403457A>G
GRCh38.p14 chr 20 NC_000020.11:g.21403457A>T
GRCh37.p13 chr 20 NC_000020.10:g.21384095A>G
GRCh37.p13 chr 20 NC_000020.10:g.21384095A>T
Gene: LOC105372558, uncharacterized LOC105372558 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105372558 transcript variant X1 XR_001754526.1:n. N/A Intron Variant
LOC105372558 transcript variant X2 XR_001754528.1:n. N/A Intron Variant
LOC105372558 transcript variant X3 XR_001754530.1:n. N/A Intron Variant
LOC105372558 transcript variant X7 XR_001754527.3:n. N/A Genic Downstream Transcript Variant
LOC105372558 transcript variant X8 XR_001754531.3:n. N/A Genic Downstream Transcript Variant
LOC105372558 transcript variant X4 XR_001754532.1:n. N/A Genic Downstream Transcript Variant
LOC105372558 transcript variant X5 XR_007067725.1:n. N/A Genic Downstream Transcript Variant
LOC105372558 transcript variant X6 XR_937325.4:n. N/A Genic Downstream Transcript Variant
LOC105372558 transcript variant X9 XR_937329.4:n. N/A Genic Downstream Transcript Variant
LOC105372558 transcript variant X10 XR_937330.4:n. N/A Genic Downstream Transcript 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 A= G T
GRCh38.p14 chr 20 NC_000020.11:g.21403457= NC_000020.11:g.21403457A>G NC_000020.11:g.21403457A>T
GRCh37.p13 chr 20 NC_000020.10:g.21384095= NC_000020.10:g.21384095A>G NC_000020.10:g.21384095A>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#.

73 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2940586 Apr 12, 2001 (94)
2 SC_JCM ss5852401 Feb 20, 2003 (111)
3 SC_SNP ss8358599 Apr 21, 2003 (114)
4 WI_SSAHASNP ss12478802 Jul 11, 2003 (116)
5 CSHL-HAPMAP ss17689785 Feb 27, 2004 (120)
6 SSAHASNP ss21788763 Apr 05, 2004 (121)
7 HGSV ss78521414 Dec 07, 2007 (129)
8 HGSV ss81102479 Dec 16, 2007 (130)
9 HGSV ss81658740 Dec 16, 2007 (130)
10 HGSV ss81716377 Dec 16, 2007 (130)
11 HGSV ss84241440 Dec 16, 2007 (130)
12 BCMHGSC_JDW ss91665919 Mar 24, 2008 (129)
13 1000GENOMES ss111856754 Jan 25, 2009 (130)
14 ILLUMINA-UK ss117511881 Dec 01, 2009 (131)
15 ENSEMBL ss133023513 Dec 01, 2009 (131)
16 ENSEMBL ss138223430 Dec 01, 2009 (131)
17 GMI ss156265597 Dec 01, 2009 (131)
18 ILLUMINA ss160491011 Dec 01, 2009 (131)
19 1000GENOMES ss212010229 Jul 14, 2010 (132)
20 1000GENOMES ss228301936 Jul 14, 2010 (132)
21 1000GENOMES ss237796997 Jul 15, 2010 (132)
22 1000GENOMES ss243976243 Jul 15, 2010 (132)
23 GMI ss283332328 May 04, 2012 (137)
24 GMI ss287437234 Apr 25, 2013 (138)
25 PJP ss292629866 May 09, 2011 (134)
26 ILLUMINA ss481179393 Sep 08, 2015 (146)
27 SSMP ss662063618 Apr 25, 2013 (138)
28 EVA-GONL ss994626075 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1082138113 Aug 21, 2014 (142)
30 1000GENOMES ss1364380491 Aug 21, 2014 (142)
31 DDI ss1429021793 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1579472548 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1638585243 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1681579276 Apr 01, 2015 (144)
35 EVA_DECODE ss1698684961 Apr 01, 2015 (144)
36 WEILL_CORNELL_DGM ss1938133026 Feb 12, 2016 (147)
37 GENOMED ss1969112598 Jul 19, 2016 (147)
38 JJLAB ss2029851779 Sep 14, 2016 (149)
39 USC_VALOUEV ss2158404602 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2241985226 Dec 20, 2016 (150)
41 GRF ss2704080569 Nov 08, 2017 (151)
42 GNOMAD ss2966314800 Nov 08, 2017 (151)
43 SWEGEN ss3017995311 Nov 08, 2017 (151)
44 CSHL ss3352458201 Nov 08, 2017 (151)
45 ILLUMINA ss3636521897 Oct 12, 2018 (152)
46 URBANLAB ss3650989680 Oct 12, 2018 (152)
47 EGCUT_WGS ss3684720409 Jul 13, 2019 (153)
48 EVA_DECODE ss3706717475 Jul 13, 2019 (153)
49 ACPOP ss3743319941 Jul 13, 2019 (153)
50 EVA ss3758524299 Jul 13, 2019 (153)
51 PACBIO ss3788621383 Jul 13, 2019 (153)
52 PACBIO ss3793518555 Jul 13, 2019 (153)
53 PACBIO ss3798405734 Jul 13, 2019 (153)
54 KHV_HUMAN_GENOMES ss3821692751 Jul 13, 2019 (153)
55 EVA ss3835629969 Apr 27, 2020 (154)
56 EVA ss3846949363 Apr 27, 2020 (154)
57 SGDP_PRJ ss3888897772 Apr 27, 2020 (154)
58 KRGDB ss3939102707 Apr 27, 2020 (154)
59 KOGIC ss3981969985 Apr 27, 2020 (154)
60 TOPMED ss5085024347 Apr 26, 2021 (155)
61 TOMMO_GENOMICS ss5229192605 Apr 26, 2021 (155)
62 1000G_HIGH_COVERAGE ss5308358233 Oct 13, 2022 (156)
63 EVA ss5436770375 Oct 13, 2022 (156)
64 HUGCELL_USP ss5500736180 Oct 13, 2022 (156)
65 EVA ss5512183006 Oct 13, 2022 (156)
66 1000G_HIGH_COVERAGE ss5614579484 Oct 13, 2022 (156)
67 SANFORD_IMAGENETICS ss5663022476 Oct 13, 2022 (156)
68 TOMMO_GENOMICS ss5788279034 Oct 13, 2022 (156)
69 YY_MCH ss5817886696 Oct 13, 2022 (156)
70 EVA ss5845555648 Oct 13, 2022 (156)
71 EVA ss5853104181 Oct 13, 2022 (156)
72 EVA ss5922995086 Oct 13, 2022 (156)
73 EVA ss5957936566 Oct 13, 2022 (156)
74 1000Genomes NC_000020.10 - 21384095 Oct 12, 2018 (152)
75 1000Genomes_30x NC_000020.11 - 21403457 Oct 13, 2022 (156)
76 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 21384095 Oct 12, 2018 (152)
77 Genetic variation in the Estonian population NC_000020.10 - 21384095 Oct 12, 2018 (152)
78 The Danish reference pan genome NC_000020.10 - 21384095 Apr 27, 2020 (154)
79 gnomAD - Genomes NC_000020.11 - 21403457 Apr 26, 2021 (155)
80 Genome of the Netherlands Release 5 NC_000020.10 - 21384095 Apr 27, 2020 (154)
81 HapMap NC_000020.11 - 21403457 Apr 27, 2020 (154)
82 KOREAN population from KRGDB NC_000020.10 - 21384095 Apr 27, 2020 (154)
83 Korean Genome Project NC_000020.11 - 21403457 Apr 27, 2020 (154)
84 Northern Sweden NC_000020.10 - 21384095 Jul 13, 2019 (153)
85 Qatari NC_000020.10 - 21384095 Apr 27, 2020 (154)
86 SGDP_PRJ NC_000020.10 - 21384095 Apr 27, 2020 (154)
87 Siberian NC_000020.10 - 21384095 Apr 27, 2020 (154)
88 8.3KJPN NC_000020.10 - 21384095 Apr 26, 2021 (155)
89 14KJPN NC_000020.11 - 21403457 Oct 13, 2022 (156)
90 TopMed NC_000020.11 - 21403457 Apr 26, 2021 (155)
91 UK 10K study - Twins NC_000020.10 - 21384095 Oct 12, 2018 (152)
92 ALFA NC_000020.11 - 21403457 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).

Associated ID History Updated (Build)
rs61258291 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78521414, ss81102479, ss81658740, ss81716377, ss84241440, ss91665919, ss111856754, ss117511881, ss160491011, ss212010229, ss283332328, ss287437234, ss292629866, ss1698684961 NC_000020.9:21332094:A:G NC_000020.11:21403456:A:G (self)
77831175, 43094292, 30458657, 5637487, 19202586, 46280101, 16604806, 20174948, 40914752, 10920956, 87161912, 43094292, ss228301936, ss237796997, ss243976243, ss481179393, ss662063618, ss994626075, ss1082138113, ss1364380491, ss1429021793, ss1579472548, ss1638585243, ss1681579276, ss1938133026, ss1969112598, ss2029851779, ss2158404602, ss2704080569, ss2966314800, ss3017995311, ss3352458201, ss3636521897, ss3684720409, ss3743319941, ss3758524299, ss3788621383, ss3793518555, ss3798405734, ss3835629969, ss3888897772, ss3939102707, ss5229192605, ss5436770375, ss5512183006, ss5663022476, ss5845555648, ss5957936566 NC_000020.10:21384094:A:G NC_000020.11:21403456:A:G (self)
102105419, 548731810, 2096282, 38347986, 122116138, 360133292, 2103006186, ss2241985226, ss3650989680, ss3706717475, ss3821692751, ss3846949363, ss3981969985, ss5085024347, ss5308358233, ss5500736180, ss5614579484, ss5788279034, ss5817886696, ss5853104181, ss5922995086 NC_000020.11:21403456:A:G NC_000020.11:21403456:A:G (self)
ss2940586, ss5852401, ss8358599, ss12478802, ss17689785, ss21788763, ss133023513, ss138223430, ss156265597 NT_011387.8:21324094:A:G NC_000020.11:21403456:A:G (self)
2103006186 NC_000020.11:21403456:A:T NC_000020.11:21403456: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 rs2031713

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