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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.

rs1013498

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:11207551 (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
T>A / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.224228 (59351/264690, TOPMED)
T=0.244839 (34277/139998, GnomAD)
T=0.09583 (2708/28258, 14KJPN) (+ 17 more)
T=0.29788 (5627/18890, ALFA)
T=0.09475 (1588/16760, 8.3KJPN)
T=0.1758 (1126/6404, 1000G_30x)
T=0.1773 (888/5008, 1000G)
T=0.3924 (1758/4480, Estonian)
T=0.3350 (1291/3854, ALSPAC)
T=0.3412 (1265/3708, TWINSUK)
T=0.1041 (305/2930, KOREAN)
T=0.1266 (232/1832, Korea1K)
T=0.332 (331/998, GoNL)
T=0.345 (207/600, NorthernSweden)
T=0.107 (57/534, SGDP_PRJ)
T=0.173 (55/318, HapMap)
T=0.157 (34/216, Qatari)
T=0.199 (43/216, Vietnamese)
T=0.17 (8/46, Siberian)
T=0.40 (16/40, GENOME_DK)
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 T=0.29788 A=0.70212
European Sub 14286 T=0.35405 A=0.64595
African Sub 2946 T=0.0825 A=0.9175
African Others Sub 114 T=0.053 A=0.947
African American Sub 2832 T=0.0837 A=0.9163
Asian Sub 112 T=0.116 A=0.884
East Asian Sub 86 T=0.12 A=0.88
Other Asian Sub 26 T=0.12 A=0.88
Latin American 1 Sub 146 T=0.219 A=0.781
Latin American 2 Sub 610 T=0.170 A=0.830
South Asian Sub 98 T=0.24 A=0.76
Other Sub 692 T=0.221 A=0.779


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 T=0.224228 A=0.775772
gnomAD - Genomes Global Study-wide 139998 T=0.244839 A=0.755161
gnomAD - Genomes European Sub 75808 T=0.34364 A=0.65636
gnomAD - Genomes African Sub 42000 T=0.09267 A=0.90733
gnomAD - Genomes American Sub 13618 T=0.19393 A=0.80607
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.2220 A=0.7780
gnomAD - Genomes East Asian Sub 3100 T=0.1432 A=0.8568
gnomAD - Genomes Other Sub 2152 T=0.2379 A=0.7621
14KJPN JAPANESE Study-wide 28258 T=0.09583 A=0.90417
Allele Frequency Aggregator Total Global 18890 T=0.29788 A=0.70212
Allele Frequency Aggregator European Sub 14286 T=0.35405 A=0.64595
Allele Frequency Aggregator African Sub 2946 T=0.0825 A=0.9175
Allele Frequency Aggregator Other Sub 692 T=0.221 A=0.779
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.170 A=0.830
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.219 A=0.781
Allele Frequency Aggregator Asian Sub 112 T=0.116 A=0.884
Allele Frequency Aggregator South Asian Sub 98 T=0.24 A=0.76
8.3KJPN JAPANESE Study-wide 16760 T=0.09475 A=0.90525
1000Genomes_30x Global Study-wide 6404 T=0.1758 A=0.8242
1000Genomes_30x African Sub 1786 T=0.0487 A=0.9513
1000Genomes_30x Europe Sub 1266 T=0.3428 A=0.6572
1000Genomes_30x South Asian Sub 1202 T=0.2080 A=0.7920
1000Genomes_30x East Asian Sub 1170 T=0.1444 A=0.8556
1000Genomes_30x American Sub 980 T=0.190 A=0.810
1000Genomes Global Study-wide 5008 T=0.1773 A=0.8227
1000Genomes African Sub 1322 T=0.0514 A=0.9486
1000Genomes East Asian Sub 1008 T=0.1419 A=0.8581
1000Genomes Europe Sub 1006 T=0.3410 A=0.6590
1000Genomes South Asian Sub 978 T=0.211 A=0.789
1000Genomes American Sub 694 T=0.184 A=0.816
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.3924 A=0.6076
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.3350 A=0.6650
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.3412 A=0.6588
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.1041 A=0.8959, G=0.0000
Korean Genome Project KOREAN Study-wide 1832 T=0.1266 A=0.8734
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.332 A=0.668
Northern Sweden ACPOP Study-wide 600 T=0.345 A=0.655
SGDP_PRJ Global Study-wide 534 T=0.107 A=0.893
HapMap Global Study-wide 318 T=0.173 A=0.827
HapMap African Sub 120 T=0.058 A=0.942
HapMap American Sub 112 T=0.402 A=0.598
HapMap Asian Sub 86 T=0.03 A=0.97
Qatari Global Study-wide 216 T=0.157 A=0.843
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.199 A=0.801
Siberian Global Study-wide 46 T=0.17 A=0.83
The Danish reference pan genome Danish Study-wide 40 T=0.40 A=0.60
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.11207551T>A
GRCh38.p14 chr 20 NC_000020.11:g.11207551T>G
GRCh37.p13 chr 20 NC_000020.10:g.11188199T>A
GRCh37.p13 chr 20 NC_000020.10:g.11188199T>G
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 T= A G
GRCh38.p14 chr 20 NC_000020.11:g.11207551= NC_000020.11:g.11207551T>A NC_000020.11:g.11207551T>G
GRCh37.p13 chr 20 NC_000020.10:g.11188199= NC_000020.10:g.11188199T>A NC_000020.10:g.11188199T>G
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#.

71 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1476730 Oct 05, 2000 (86)
2 SC_JCM ss5725021 Feb 20, 2003 (111)
3 SC_SNP ss8349290 Apr 21, 2003 (114)
4 BCM_SSAHASNP ss10956254 Jul 11, 2003 (116)
5 CSHL-HAPMAP ss19474195 Feb 27, 2004 (120)
6 CSHL-HAPMAP ss20123486 Feb 27, 2004 (120)
7 ABI ss41439528 Mar 13, 2006 (126)
8 HGSV ss81870751 Dec 15, 2007 (130)
9 BCMHGSC_JDW ss91639459 Mar 24, 2008 (129)
10 BGI ss106179262 Feb 05, 2009 (130)
11 1000GENOMES ss111729890 Jan 25, 2009 (130)
12 1000GENOMES ss113091164 Jan 25, 2009 (130)
13 ILLUMINA-UK ss117486479 Feb 14, 2009 (130)
14 ENSEMBL ss138210798 Dec 01, 2009 (131)
15 GMI ss156170304 Dec 01, 2009 (131)
16 ENSEMBL ss161303969 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss167818389 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss169097781 Jul 04, 2010 (132)
19 BUSHMAN ss203832579 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss208605506 Jul 04, 2010 (132)
21 1000GENOMES ss228259946 Jul 14, 2010 (132)
22 1000GENOMES ss237765200 Jul 15, 2010 (132)
23 1000GENOMES ss243951225 Jul 15, 2010 (132)
24 GMI ss283302303 May 04, 2012 (137)
25 GMI ss287423618 Apr 25, 2013 (138)
26 PJP ss292611781 May 09, 2011 (134)
27 TISHKOFF ss566139594 Apr 25, 2013 (138)
28 SSMP ss662011024 Apr 25, 2013 (138)
29 EVA-GONL ss994545609 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1082078204 Aug 21, 2014 (142)
31 1000GENOMES ss1364088986 Aug 21, 2014 (142)
32 DDI ss1428997577 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1579439672 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1638425897 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1681419930 Apr 01, 2015 (144)
36 EVA_DECODE ss1698601594 Apr 01, 2015 (144)
37 HAMMER_LAB ss1809425194 Sep 08, 2015 (146)
38 WEILL_CORNELL_DGM ss1938055670 Feb 12, 2016 (147)
39 GENOMED ss1969092374 Jul 19, 2016 (147)
40 JJLAB ss2029807452 Sep 14, 2016 (149)
41 USC_VALOUEV ss2158360955 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2241377433 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2629400510 Nov 08, 2017 (151)
44 GRF ss2704034569 Nov 08, 2017 (151)
45 GNOMAD ss2965498699 Nov 08, 2017 (151)
46 SWEGEN ss3017877179 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3028736693 Nov 08, 2017 (151)
48 CSHL ss3352422037 Nov 08, 2017 (151)
49 EGCUT_WGS ss3684594915 Jul 13, 2019 (153)
50 EVA_DECODE ss3706571327 Jul 13, 2019 (153)
51 ACPOP ss3743254136 Jul 13, 2019 (153)
52 EVA ss3758429407 Jul 13, 2019 (153)
53 KHV_HUMAN_GENOMES ss3821602780 Jul 13, 2019 (153)
54 EVA ss3835590904 Apr 27, 2020 (154)
55 EVA ss3841420402 Apr 27, 2020 (154)
56 EVA ss3846928139 Apr 27, 2020 (154)
57 SGDP_PRJ ss3888744370 Apr 27, 2020 (154)
58 KRGDB ss3938934660 Apr 27, 2020 (154)
59 KOGIC ss3981833562 Apr 27, 2020 (154)
60 TOPMED ss5082476369 Apr 26, 2021 (155)
61 TOMMO_GENOMICS ss5228866770 Apr 26, 2021 (155)
62 1000G_HIGH_COVERAGE ss5308106270 Oct 13, 2022 (156)
63 HUGCELL_USP ss5500504874 Oct 13, 2022 (156)
64 1000G_HIGH_COVERAGE ss5614198550 Oct 13, 2022 (156)
65 SANFORD_IMAGENETICS ss5662876986 Oct 13, 2022 (156)
66 TOMMO_GENOMICS ss5787861915 Oct 13, 2022 (156)
67 YY_MCH ss5817821408 Oct 13, 2022 (156)
68 EVA ss5845452691 Oct 13, 2022 (156)
69 EVA ss5853071571 Oct 13, 2022 (156)
70 EVA ss5922699440 Oct 13, 2022 (156)
71 EVA ss5957779269 Oct 13, 2022 (156)
72 1000Genomes NC_000020.10 - 11188199 Oct 12, 2018 (152)
73 1000Genomes_30x NC_000020.11 - 11207551 Oct 13, 2022 (156)
74 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 11188199 Oct 12, 2018 (152)
75 Genetic variation in the Estonian population NC_000020.10 - 11188199 Oct 12, 2018 (152)
76 The Danish reference pan genome NC_000020.10 - 11188199 Apr 27, 2020 (154)
77 gnomAD - Genomes NC_000020.11 - 11207551 Apr 26, 2021 (155)
78 Genome of the Netherlands Release 5 NC_000020.10 - 11188199 Apr 27, 2020 (154)
79 HapMap NC_000020.11 - 11207551 Apr 27, 2020 (154)
80 KOREAN population from KRGDB NC_000020.10 - 11188199 Apr 27, 2020 (154)
81 Korean Genome Project NC_000020.11 - 11207551 Apr 27, 2020 (154)
82 Northern Sweden NC_000020.10 - 11188199 Jul 13, 2019 (153)
83 Qatari NC_000020.10 - 11188199 Apr 27, 2020 (154)
84 SGDP_PRJ NC_000020.10 - 11188199 Apr 27, 2020 (154)
85 Siberian NC_000020.10 - 11188199 Apr 27, 2020 (154)
86 8.3KJPN NC_000020.10 - 11188199 Apr 26, 2021 (155)
87 14KJPN NC_000020.11 - 11207551 Oct 13, 2022 (156)
88 TopMed NC_000020.11 - 11207551 Apr 26, 2021 (155)
89 UK 10K study - Twins NC_000020.10 - 11188199 Oct 12, 2018 (152)
90 A Vietnamese Genetic Variation Database NC_000020.10 - 11188199 Jul 13, 2019 (153)
91 ALFA NC_000020.11 - 11207551 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)
rs58559973 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81870751, ss91639459, ss111729890, ss113091164, ss117486479, ss167818389, ss169097781, ss203832579, ss208605506, ss283302303, ss287423618, ss292611781, ss1698601594 NC_000020.9:11136198:T:A NC_000020.11:11207550:T:A (self)
77529313, 42919671, 30333163, 5604611, 19123614, 46112054, 16539001, 20097592, 40761350, 10877309, 86836077, 42919671, 9475360, ss228259946, ss237765200, ss243951225, ss566139594, ss662011024, ss994545609, ss1082078204, ss1364088986, ss1428997577, ss1579439672, ss1638425897, ss1681419930, ss1809425194, ss1938055670, ss1969092374, ss2029807452, ss2158360955, ss2629400510, ss2704034569, ss2965498699, ss3017877179, ss3352422037, ss3684594915, ss3743254136, ss3758429407, ss3835590904, ss3841420402, ss3888744370, ss3938934660, ss5228866770, ss5662876986, ss5845452691, ss5957779269 NC_000020.10:11188198:T:A NC_000020.11:11207550:T:A (self)
101724485, 546655279, 2072651, 38211563, 121699019, 357585314, 3989631238, ss2241377433, ss3028736693, ss3706571327, ss3821602780, ss3846928139, ss3981833562, ss5082476369, ss5308106270, ss5500504874, ss5614198550, ss5787861915, ss5817821408, ss5853071571, ss5922699440 NC_000020.11:11207550:T:A NC_000020.11:11207550:T:A (self)
ss1476730, ss5725021, ss8349290, ss10956254, ss19474195, ss20123486, ss41439528, ss106179262, ss138210798, ss156170304, ss161303969 NT_011387.8:11128198:T:A NC_000020.11:11207550:T:A (self)
46112054, ss3938934660 NC_000020.10:11188198:T:G NC_000020.11:11207550:T:G (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 rs1013498

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