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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.

rs1962082

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:102624335 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.277358 (73414/264690, TOPMED)
T=0.281689 (42308/150194, ALFA)
T=0.04300 (1215/28258, 14KJPN) (+ 15 more)
T=0.04368 (732/16758, 8.3KJPN)
T=0.2380 (1524/6404, 1000G_30x)
T=0.2362 (1183/5008, 1000G)
T=0.2069 (927/4480, Estonian)
T=0.2888 (1113/3854, ALSPAC)
T=0.2880 (1068/3708, TWINSUK)
T=0.0534 (156/2922, KOREAN)
T=0.2415 (457/1892, HapMap)
T=0.3231 (367/1136, Daghestan)
T=0.325 (324/998, GoNL)
T=0.237 (142/600, NorthernSweden)
C=0.409 (90/220, SGDP_PRJ)
T=0.481 (104/216, Qatari)
T=0.065 (14/216, Vietnamese)
C=0.3 (3/10, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MMP20 : Intron Variant
LOC101928477 : 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 150288 C=0.718248 G=0.000000, T=0.281752
European Sub 131208 C=0.711405 G=0.000000, T=0.288595
African Sub 5296 C=0.7908 G=0.0000, T=0.2092
African Others Sub 196 C=0.806 G=0.000, T=0.194
African American Sub 5100 C=0.7902 G=0.0000, T=0.2098
Asian Sub 624 C=0.965 G=0.000, T=0.035
East Asian Sub 492 C=0.974 G=0.000, T=0.026
Other Asian Sub 132 C=0.932 G=0.000, T=0.068
Latin American 1 Sub 670 C=0.733 G=0.000, T=0.267
Latin American 2 Sub 6066 C=0.7646 G=0.0000, T=0.2354
South Asian Sub 130 C=0.762 G=0.000, T=0.238
Other Sub 6294 C=0.7283 G=0.0000, T=0.2717


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 C=0.722642 T=0.277358
Allele Frequency Aggregator Total Global 150194 C=0.718311 G=0.000000, T=0.281689
Allele Frequency Aggregator European Sub 131132 C=0.711474 G=0.000000, T=0.288526
Allele Frequency Aggregator Other Sub 6276 C=0.7283 G=0.0000, T=0.2717
Allele Frequency Aggregator Latin American 2 Sub 6066 C=0.7646 G=0.0000, T=0.2354
Allele Frequency Aggregator African Sub 5296 C=0.7908 G=0.0000, T=0.2092
Allele Frequency Aggregator Latin American 1 Sub 670 C=0.733 G=0.000, T=0.267
Allele Frequency Aggregator Asian Sub 624 C=0.965 G=0.000, T=0.035
Allele Frequency Aggregator South Asian Sub 130 C=0.762 G=0.000, T=0.238
14KJPN JAPANESE Study-wide 28258 C=0.95700 T=0.04300
8.3KJPN JAPANESE Study-wide 16758 C=0.95632 T=0.04368
1000Genomes_30x Global Study-wide 6404 C=0.7620 T=0.2380
1000Genomes_30x African Sub 1786 C=0.7352 T=0.2648
1000Genomes_30x Europe Sub 1266 C=0.7275 T=0.2725
1000Genomes_30x South Asian Sub 1202 C=0.6739 T=0.3261
1000Genomes_30x East Asian Sub 1170 C=0.9504 T=0.0496
1000Genomes_30x American Sub 980 C=0.739 T=0.261
1000Genomes Global Study-wide 5008 C=0.7638 T=0.2362
1000Genomes African Sub 1322 C=0.7337 T=0.2663
1000Genomes East Asian Sub 1008 C=0.9484 T=0.0516
1000Genomes Europe Sub 1006 C=0.7227 T=0.2773
1000Genomes South Asian Sub 978 C=0.674 T=0.326
1000Genomes American Sub 694 C=0.739 T=0.261
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7931 T=0.2069
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7112 T=0.2888
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7120 T=0.2880
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9466 T=0.0534
HapMap Global Study-wide 1892 C=0.7585 T=0.2415
HapMap American Sub 770 C=0.770 T=0.230
HapMap African Sub 692 C=0.704 T=0.296
HapMap Asian Sub 254 C=0.957 T=0.043
HapMap Europe Sub 176 C=0.636 T=0.364
Genome-wide autozygosity in Daghestan Global Study-wide 1136 C=0.6769 T=0.3231
Genome-wide autozygosity in Daghestan Daghestan Sub 628 C=0.664 T=0.336
Genome-wide autozygosity in Daghestan Near_East Sub 144 C=0.688 T=0.312
Genome-wide autozygosity in Daghestan Central Asia Sub 122 C=0.803 T=0.197
Genome-wide autozygosity in Daghestan Europe Sub 108 C=0.704 T=0.296
Genome-wide autozygosity in Daghestan South Asian Sub 98 C=0.61 T=0.39
Genome-wide autozygosity in Daghestan Caucasus Sub 36 C=0.53 T=0.47
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.675 T=0.325
Northern Sweden ACPOP Study-wide 600 C=0.763 T=0.237
SGDP_PRJ Global Study-wide 220 C=0.409 T=0.591
Qatari Global Study-wide 216 C=0.519 T=0.481
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.935 T=0.065
Siberian Global Study-wide 10 C=0.3 T=0.7
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 11 NC_000011.10:g.102624335C>G
GRCh38.p14 chr 11 NC_000011.10:g.102624335C>T
GRCh37.p13 chr 11 NC_000011.9:g.102495066C>G
GRCh37.p13 chr 11 NC_000011.9:g.102495066C>T
MMP20 RefSeqGene NG_012151.1:g.5998G>C
MMP20 RefSeqGene NG_012151.1:g.5998G>A
Gene: MMP20, matrix metallopeptidase 20 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MMP20 transcript NM_004771.4:c.126+859G>C N/A Intron Variant
Gene: LOC101928477, uncharacterized LOC101928477 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC101928477 transcript variant X4 XR_001748340.2:n. N/A Intron Variant
LOC101928477 transcript variant X5 XR_001748341.2:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X2 XR_007062866.1:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X6 XR_007062867.1:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X1 XR_947957.3:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X3 XR_947958.3:n. N/A Genic Upstream 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 C= G T
GRCh38.p14 chr 11 NC_000011.10:g.102624335= NC_000011.10:g.102624335C>G NC_000011.10:g.102624335C>T
GRCh37.p13 chr 11 NC_000011.9:g.102495066= NC_000011.9:g.102495066C>G NC_000011.9:g.102495066C>T
MMP20 RefSeqGene NG_012151.1:g.5998= NG_012151.1:g.5998G>C NG_012151.1:g.5998G>A
MMP20 transcript NM_004771.3:c.126+859= NM_004771.3:c.126+859G>C NM_004771.3:c.126+859G>A
MMP20 transcript NM_004771.4:c.126+859= NM_004771.4:c.126+859G>C NM_004771.4:c.126+859G>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#.

96 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2865085 Jan 12, 2001 (92)
2 SC_JCM ss3517675 Sep 28, 2001 (123)
3 BCM_SSAHASNP ss10670290 Jul 11, 2003 (123)
4 EGP_SNPS ss28446756 Sep 20, 2004 (123)
5 ABI ss38710291 Mar 14, 2006 (126)
6 EGP_SNPS ss66859658 Nov 29, 2006 (127)
7 ILLUMINA ss75056885 Dec 06, 2007 (129)
8 HGSV ss78628369 Dec 06, 2007 (129)
9 BCMHGSC_JDW ss88750491 Mar 24, 2008 (129)
10 KRIBB_YJKIM ss102645245 Feb 04, 2009 (130)
11 1000GENOMES ss110972846 Jan 25, 2009 (130)
12 ENSEMBL ss132784320 Dec 01, 2009 (131)
13 ILLUMINA ss160482091 Dec 01, 2009 (131)
14 ILLUMINA ss173014481 Jul 04, 2010 (132)
15 BUSHMAN ss203134800 Jul 04, 2010 (132)
16 1000GENOMES ss211187527 Jul 14, 2010 (132)
17 1000GENOMES ss225429077 Jul 14, 2010 (132)
18 1000GENOMES ss235695122 Jul 15, 2010 (132)
19 1000GENOMES ss242298147 Jul 15, 2010 (132)
20 ILLUMINA ss244285891 Jul 04, 2010 (132)
21 ILLUMINA ss480361397 May 04, 2012 (137)
22 ILLUMINA ss480373481 May 04, 2012 (137)
23 ILLUMINA ss481143755 Sep 08, 2015 (146)
24 ILLUMINA ss484978276 May 04, 2012 (137)
25 ILLUMINA ss537015433 Sep 08, 2015 (146)
26 TISHKOFF ss562786819 Apr 25, 2013 (138)
27 SSMP ss658309401 Apr 25, 2013 (138)
28 ILLUMINA ss778848008 Sep 08, 2015 (146)
29 ILLUMINA ss782935443 Sep 08, 2015 (146)
30 ILLUMINA ss783898173 Sep 08, 2015 (146)
31 ILLUMINA ss832190953 Sep 08, 2015 (146)
32 ILLUMINA ss834308627 Sep 08, 2015 (146)
33 EVA-GONL ss988898746 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1077998043 Aug 21, 2014 (142)
35 1000GENOMES ss1342723518 Aug 21, 2014 (142)
36 HAMMER_LAB ss1397615560 Sep 08, 2015 (146)
37 DDI ss1426742624 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1627331085 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1670325118 Apr 01, 2015 (144)
40 EVA_SVP ss1713280231 Apr 01, 2015 (144)
41 ILLUMINA ss1751990955 Sep 08, 2015 (146)
42 HAMMER_LAB ss1806969959 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1932261353 Feb 12, 2016 (147)
44 GENOMED ss1967443185 Jul 19, 2016 (147)
45 JJLAB ss2026875011 Sep 14, 2016 (149)
46 USC_VALOUEV ss2155186794 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2185198744 Dec 20, 2016 (150)
48 ILLUMINA ss2632880255 Nov 08, 2017 (151)
49 GRF ss2699491504 Nov 08, 2017 (151)
50 GNOMAD ss2903770044 Nov 08, 2017 (151)
51 AFFY ss2984954797 Nov 08, 2017 (151)
52 AFFY ss2985597329 Nov 08, 2017 (151)
53 SWEGEN ss3008684256 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3027236172 Nov 08, 2017 (151)
55 CSHL ss3349766712 Nov 08, 2017 (151)
56 ILLUMINA ss3626737408 Oct 12, 2018 (152)
57 ILLUMINA ss3630894905 Oct 12, 2018 (152)
58 ILLUMINA ss3632997460 Oct 12, 2018 (152)
59 ILLUMINA ss3633697351 Oct 12, 2018 (152)
60 ILLUMINA ss3634472478 Oct 12, 2018 (152)
61 ILLUMINA ss3635388680 Oct 12, 2018 (152)
62 ILLUMINA ss3636156597 Oct 12, 2018 (152)
63 ILLUMINA ss3637139578 Oct 12, 2018 (152)
64 ILLUMINA ss3637927098 Oct 12, 2018 (152)
65 ILLUMINA ss3640179815 Oct 12, 2018 (152)
66 ILLUMINA ss3642923880 Oct 12, 2018 (152)
67 ILLUMINA ss3653727399 Oct 12, 2018 (152)
68 EGCUT_WGS ss3676005868 Jul 13, 2019 (153)
69 EVA_DECODE ss3692482342 Jul 13, 2019 (153)
70 ACPOP ss3738488749 Jul 13, 2019 (153)
71 ILLUMINA ss3744773273 Jul 13, 2019 (153)
72 EVA ss3749736700 Jul 13, 2019 (153)
73 ILLUMINA ss3772273059 Jul 13, 2019 (153)
74 PACBIO ss3787050990 Jul 13, 2019 (153)
75 PACBIO ss3792177830 Jul 13, 2019 (153)
76 PACBIO ss3797060328 Jul 13, 2019 (153)
77 KHV_HUMAN_GENOMES ss3815070058 Jul 13, 2019 (153)
78 EVA ss3832808329 Apr 26, 2020 (154)
79 EVA ss3839965762 Apr 26, 2020 (154)
80 EVA ss3845446953 Apr 26, 2020 (154)
81 SGDP_PRJ ss3877014701 Apr 26, 2020 (154)
82 KRGDB ss3925455966 Apr 26, 2020 (154)
83 TOPMED ss4897827177 Apr 26, 2021 (155)
84 TOMMO_GENOMICS ss5203620472 Apr 26, 2021 (155)
85 1000G_HIGH_COVERAGE ss5288692145 Oct 16, 2022 (156)
86 EVA ss5315572791 Oct 16, 2022 (156)
87 HUGCELL_USP ss5483701831 Oct 16, 2022 (156)
88 1000G_HIGH_COVERAGE ss5585069629 Oct 16, 2022 (156)
89 SANFORD_IMAGENETICS ss5651953309 Oct 16, 2022 (156)
90 TOMMO_GENOMICS ss5751990948 Oct 16, 2022 (156)
91 EVA ss5799852756 Oct 16, 2022 (156)
92 YY_MCH ss5812726032 Oct 16, 2022 (156)
93 EVA ss5837146238 Oct 16, 2022 (156)
94 EVA ss5850125260 Oct 16, 2022 (156)
95 EVA ss5921412639 Oct 16, 2022 (156)
96 EVA ss5943275323 Oct 16, 2022 (156)
97 1000Genomes NC_000011.9 - 102495066 Oct 12, 2018 (152)
98 1000Genomes_30x NC_000011.10 - 102624335 Oct 16, 2022 (156)
99 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 102495066 Oct 12, 2018 (152)
100 Genome-wide autozygosity in Daghestan NC_000011.8 - 102000276 Apr 26, 2020 (154)
101 Genetic variation in the Estonian population NC_000011.9 - 102495066 Oct 12, 2018 (152)
102 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 390200996 (NC_000011.10:102624334:C:G 1/132778)
Row 390200997 (NC_000011.10:102624334:C:T 37867/132732)

- Apr 26, 2021 (155)
103 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 390200996 (NC_000011.10:102624334:C:G 1/132778)
Row 390200997 (NC_000011.10:102624334:C:T 37867/132732)

- Apr 26, 2021 (155)
104 Genome of the Netherlands Release 5 NC_000011.9 - 102495066 Apr 26, 2020 (154)
105 HapMap NC_000011.10 - 102624335 Apr 26, 2020 (154)
106 KOREAN population from KRGDB NC_000011.9 - 102495066 Apr 26, 2020 (154)
107 Northern Sweden NC_000011.9 - 102495066 Jul 13, 2019 (153)
108 Qatari NC_000011.9 - 102495066 Apr 26, 2020 (154)
109 SGDP_PRJ NC_000011.9 - 102495066 Apr 26, 2020 (154)
110 Siberian NC_000011.9 - 102495066 Apr 26, 2020 (154)
111 8.3KJPN NC_000011.9 - 102495066 Apr 26, 2021 (155)
112 14KJPN NC_000011.10 - 102624335 Oct 16, 2022 (156)
113 TopMed NC_000011.10 - 102624335 Apr 26, 2021 (155)
114 UK 10K study - Twins NC_000011.9 - 102495066 Oct 12, 2018 (152)
115 A Vietnamese Genetic Variation Database NC_000011.9 - 102495066 Jul 13, 2019 (153)
116 ALFA NC_000011.10 - 102624335 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)
rs2509021 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2903770044 NC_000011.9:102495065:C:G NC_000011.10:102624334:C:G (self)
14274328680 NC_000011.10:102624334:C:G NC_000011.10:102624334:C:G (self)
86676, ss78628369, ss88750491, ss110972846, ss203134800, ss211187527, ss480361397, ss1397615560, ss1713280231, ss3642923880 NC_000011.8:102000275:C:T NC_000011.10:102624334:C:T (self)
55296535, 30687251, 21744116, 13697051, 32633360, 11773614, 14303283, 29031681, 7703148, 61589779, 30687251, 6810612, ss225429077, ss235695122, ss242298147, ss480373481, ss481143755, ss484978276, ss537015433, ss562786819, ss658309401, ss778848008, ss782935443, ss783898173, ss832190953, ss834308627, ss988898746, ss1077998043, ss1342723518, ss1426742624, ss1627331085, ss1670325118, ss1751990955, ss1806969959, ss1932261353, ss1967443185, ss2026875011, ss2155186794, ss2632880255, ss2699491504, ss2903770044, ss2984954797, ss2985597329, ss3008684256, ss3349766712, ss3626737408, ss3630894905, ss3632997460, ss3633697351, ss3634472478, ss3635388680, ss3636156597, ss3637139578, ss3637927098, ss3640179815, ss3653727399, ss3676005868, ss3738488749, ss3744773273, ss3749736700, ss3772273059, ss3787050990, ss3792177830, ss3797060328, ss3832808329, ss3839965762, ss3877014701, ss3925455966, ss5203620472, ss5315572791, ss5651953309, ss5799852756, ss5837146238, ss5943275323 NC_000011.9:102495065:C:T NC_000011.10:102624334:C:T (self)
72595564, 684795, 85828052, 113372833, 14274328680, ss2185198744, ss3027236172, ss3692482342, ss3815070058, ss3845446953, ss4897827177, ss5288692145, ss5483701831, ss5585069629, ss5751990948, ss5812726032, ss5850125260, ss5921412639 NC_000011.10:102624334:C:T NC_000011.10:102624334:C:T (self)
ss10670290 NT_033899.5:6038905:C:T NC_000011.10:102624334:C:T (self)
ss2865085, ss3517675, ss28446756, ss38710291, ss66859658, ss75056885, ss102645245, ss132784320, ss160482091, ss173014481, ss244285891 NT_033899.8:6057481:C:T NC_000011.10:102624334:C: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 rs1962082

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