Name: rs2292731
Published: September 21, 2022
License: Open Access

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.

rs2292731

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:102625674 (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=0.156440 (41408/264690, TOPMED)
T=0.155340 (21752/140028, GnomAD)
T=0.35332 (9984/28258, 14KJPN) (+ 17 more)
T=0.14722 (2781/18890, ALFA)
T=0.35535 (5955/16758, 8.3KJPN)
T=0.1794 (1149/6404, 1000G_30x)
T=0.1801 (902/5008, 1000G)
T=0.1754 (786/4480, Estonian)
T=0.1303 (502/3854, ALSPAC)
T=0.1400 (519/3708, TWINSUK)
T=0.3737 (1095/2930, KOREAN)
T=0.3745 (686/1832, Korea1K)
T=0.117 (117/998, GoNL)
T=0.125 (75/600, NorthernSweden)
T=0.079 (17/216, Qatari)
T=0.356 (77/216, Vietnamese)
C=0.403 (75/186, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.50 (12/24, Siberian)
T=0.50 (12/24, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MMP20 : 2KB Upstream 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	18890	C=0.85278	T=0.14722
European	Sub	14286	C=0.85391	T=0.14609
African	Sub	2946	C=0.8503	T=0.1497
African Others	Sub	114	C=0.886	T=0.114
African American	Sub	2832	C=0.8489	T=0.1511
Asian	Sub	112	C=0.679	T=0.321
East Asian	Sub	86	C=0.65	T=0.35
Other Asian	Sub	26	C=0.77	T=0.23
Latin American 1	Sub	146	C=0.863	T=0.137
Latin American 2	Sub	610	C=0.815	T=0.185
South Asian	Sub	98	C=0.95	T=0.05
Other	Sub	692	C=0.886	T=0.114

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.843560	T=0.156440
gnomAD - Genomes	Global	Study-wide	140028	C=0.844660	T=0.155340
gnomAD - Genomes	European	Sub	75862	C=0.85282	T=0.14718
gnomAD - Genomes	African	Sub	41930	C=0.84321	T=0.15679
gnomAD - Genomes	American	Sub	13634	C=0.82617	T=0.17383
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9149	T=0.0851
gnomAD - Genomes	East Asian	Sub	3126	C=0.6718	T=0.3282
gnomAD - Genomes	Other	Sub	2152	C=0.8448	T=0.1552
14KJPN	JAPANESE	Study-wide	28258	C=0.64668	T=0.35332
Allele Frequency Aggregator	Total	Global	18890	C=0.85278	T=0.14722
Allele Frequency Aggregator	European	Sub	14286	C=0.85391	T=0.14609
Allele Frequency Aggregator	African	Sub	2946	C=0.8503	T=0.1497
Allele Frequency Aggregator	Other	Sub	692	C=0.886	T=0.114
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.815	T=0.185
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.863	T=0.137
Allele Frequency Aggregator	Asian	Sub	112	C=0.679	T=0.321
Allele Frequency Aggregator	South Asian	Sub	98	C=0.95	T=0.05
8.3KJPN	JAPANESE	Study-wide	16758	C=0.64465	T=0.35535
1000Genomes_30x	Global	Study-wide	6404	C=0.8206	T=0.1794
1000Genomes_30x	African	Sub	1786	C=0.8219	T=0.1781
1000Genomes_30x	Europe	Sub	1266	C=0.8602	T=0.1398
1000Genomes_30x	South Asian	Sub	1202	C=0.9168	T=0.0832
1000Genomes_30x	East Asian	Sub	1170	C=0.6812	T=0.3188
1000Genomes_30x	American	Sub	980	C=0.815	T=0.185
1000Genomes	Global	Study-wide	5008	C=0.8199	T=0.1801
1000Genomes	African	Sub	1322	C=0.8230	T=0.1770
1000Genomes	East Asian	Sub	1008	C=0.6855	T=0.3145
1000Genomes	Europe	Sub	1006	C=0.8598	T=0.1402
1000Genomes	South Asian	Sub	978	C=0.919	T=0.081
1000Genomes	American	Sub	694	C=0.811	T=0.189
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8246	T=0.1754
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8697	T=0.1303
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8600	T=0.1400
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.6263	G=0.0000, T=0.3737
Korean Genome Project	KOREAN	Study-wide	1832	C=0.6255	T=0.3745
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.883	T=0.117
Northern Sweden	ACPOP	Study-wide	600	C=0.875	T=0.125
Qatari	Global	Study-wide	216	C=0.921	T=0.079
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.644	T=0.356
SGDP_PRJ	Global	Study-wide	186	C=0.403	T=0.597
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
Siberian	Global	Study-wide	24	C=0.50	T=0.50

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.102625674C>G
GRCh38.p14 chr 11	NC_000011.10:g.102625674C>T
GRCh37.p13 chr 11	NC_000011.9:g.102496405C>G
GRCh37.p13 chr 11	NC_000011.9:g.102496405C>T
MMP20 RefSeqGene	NG_012151.1:g.4659G>C
MMP20 RefSeqGene	NG_012151.1:g.4659G>A

Gene: MMP20, matrix metallopeptidase 20 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
MMP20 transcript	NM_004771.4:c.	N/A	Upstream Transcript 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

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

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.102625674=	NC_000011.10:g.102625674C>G	NC_000011.10:g.102625674C>T
GRCh37.p13 chr 11	NC_000011.9:g.102496405=	NC_000011.9:g.102496405C>G	NC_000011.9:g.102496405C>T
MMP20 RefSeqGene	NG_012151.1:g.4659=	NG_012151.1:g.4659G>C	NG_012151.1:g.4659G>A

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#.

64 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss3235517	Sep 28, 2001 (100)
2	SC_JCM	ss5932472	Feb 20, 2003 (111)
3	BCM_SSAHASNP	ss10700881	Jul 11, 2003 (116)
4	SC_SNP	ss16009079	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss16546332	Feb 27, 2004 (120)
6	SSAHASNP	ss20856249	Apr 05, 2004 (121)
7	EGP_SNPS	ss28446748	Sep 20, 2004 (123)
8	ABI	ss38731203	Mar 15, 2006 (126)
9	HUMANGENOME_JCVI	ss97506036	Feb 06, 2009 (130)
10	BGI	ss106766202	Feb 06, 2009 (130)
11	1000GENOMES	ss115083342	Jan 25, 2009 (130)
12	ENSEMBL	ss137876620	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss170778548	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss175261035	Jul 04, 2010 (132)
15	BUSHMAN	ss203134824	Jul 04, 2010 (132)
16	1000GENOMES	ss225429084	Jul 14, 2010 (132)
17	1000GENOMES	ss235695128	Jul 15, 2010 (132)
18	1000GENOMES	ss242298153	Jul 15, 2010 (132)
19	GMI	ss281148045	May 04, 2012 (137)
20	PJP	ss291126745	May 09, 2011 (134)
21	TISHKOFF	ss562786826	Apr 25, 2013 (138)
22	SSMP	ss658309418	Apr 25, 2013 (138)
23	EVA-GONL	ss988898760	Aug 21, 2014 (142)
24	JMKIDD_LAB	ss1077998053	Aug 21, 2014 (142)
25	1000GENOMES	ss1342723566	Aug 21, 2014 (142)
26	EVA_GENOME_DK	ss1575916076	Apr 01, 2015 (144)
27	EVA_DECODE	ss1598562906	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1627331113	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1670325146	Apr 01, 2015 (144)
30	HAMMER_LAB	ss1806969966	Sep 08, 2015 (146)
31	WEILL_CORNELL_DGM	ss1932261364	Feb 12, 2016 (147)
32	GENOMED	ss1967443190	Jul 19, 2016 (147)
33	JJLAB	ss2026875020	Sep 14, 2016 (149)
34	USC_VALOUEV	ss2155186804	Dec 20, 2016 (150)
35	HUMAN_LONGEVITY	ss2185198836	Dec 20, 2016 (150)
36	SYSTEMSBIOZJU	ss2627910722	Nov 08, 2017 (151)
37	GRF	ss2699491514	Nov 08, 2017 (151)
38	GNOMAD	ss2903770159	Nov 08, 2017 (151)
39	SWEGEN	ss3008684269	Nov 08, 2017 (151)
40	BIOINF_KMB_FNS_UNIBA	ss3027236178	Nov 08, 2017 (151)
41	CSHL	ss3349766718	Nov 08, 2017 (151)
42	URBANLAB	ss3649690763	Oct 12, 2018 (152)
43	EGCUT_WGS	ss3676005886	Jul 13, 2019 (153)
44	EVA_DECODE	ss3692482361	Jul 13, 2019 (153)
45	ACPOP	ss3738488759	Jul 13, 2019 (153)
46	EVA	ss3749736722	Jul 13, 2019 (153)
47	KHV_HUMAN_GENOMES	ss3815070073	Jul 13, 2019 (153)
48	EVA	ss3832808336	Apr 26, 2020 (154)
49	SGDP_PRJ	ss3877014727	Apr 26, 2020 (154)
50	KRGDB	ss3925455989	Apr 26, 2020 (154)
51	KOGIC	ss3970631482	Apr 26, 2020 (154)
52	TOPMED	ss4897827546	Apr 26, 2021 (155)
53	TOMMO_GENOMICS	ss5203620529	Apr 26, 2021 (155)
54	1000G_HIGH_COVERAGE	ss5288692183	Oct 16, 2022 (156)
55	EVA	ss5401859664	Oct 16, 2022 (156)
56	HUGCELL_USP	ss5483701857	Oct 16, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5585069688	Oct 16, 2022 (156)
58	SANFORD_IMAGENETICS	ss5651953328	Oct 16, 2022 (156)
59	TOMMO_GENOMICS	ss5751991012	Oct 16, 2022 (156)
60	YY_MCH	ss5812726044	Oct 16, 2022 (156)
61	EVA	ss5837146255	Oct 16, 2022 (156)
62	EVA	ss5850125268	Oct 16, 2022 (156)
63	EVA	ss5921412691	Oct 16, 2022 (156)
64	EVA	ss5943275344	Oct 16, 2022 (156)
65	1000Genomes	NC_000011.9 - 102496405	Oct 12, 2018 (152)
66	1000Genomes_30x	NC_000011.10 - 102625674	Oct 16, 2022 (156)
67	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 102496405	Oct 12, 2018 (152)
68	Genetic variation in the Estonian population	NC_000011.9 - 102496405	Oct 12, 2018 (152)
69	The Danish reference pan genome	NC_000011.9 - 102496405	Apr 26, 2020 (154)
70	gnomAD - Genomes	NC_000011.10 - 102625674	Apr 26, 2021 (155)
71	Genome of the Netherlands Release 5	NC_000011.9 - 102496405	Apr 26, 2020 (154)
72	KOREAN population from KRGDB	NC_000011.9 - 102496405	Apr 26, 2020 (154)
73	Korean Genome Project	NC_000011.10 - 102625674	Apr 26, 2020 (154)
74	Northern Sweden	NC_000011.9 - 102496405	Jul 13, 2019 (153)
75	Qatari	NC_000011.9 - 102496405	Apr 26, 2020 (154)
76	SGDP_PRJ	NC_000011.9 - 102496405	Apr 26, 2020 (154)
77	Siberian	NC_000011.9 - 102496405	Apr 26, 2020 (154)
78	8.3KJPN	NC_000011.9 - 102496405	Apr 26, 2021 (155)
79	14KJPN	NC_000011.10 - 102625674	Oct 16, 2022 (156)
80	TopMed	NC_000011.10 - 102625674	Apr 26, 2021 (155)
81	UK 10K study - Twins	NC_000011.9 - 102496405	Oct 12, 2018 (152)
82	A Vietnamese Genetic Variation Database	NC_000011.9 - 102496405	Jul 13, 2019 (153)
83	ALFA	NC_000011.10 - 102625674	Apr 26, 2021 (155)

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)
rs17174345	Oct 08, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
32633383, ss3925455989	NC_000011.9:102496404:C:G	NC_000011.10:102625673:C:G	(self)
ss115083342, ss170778548, ss175261035, ss203134824, ss281148045, ss291126745, ss1598562906	NC_000011.8:102001614:C:T	NC_000011.10:102625673:C:T	(self)
55296584, 30687283, 21744134, 2710458, 13697065, 32633383, 11773624, 14303294, 29031707, 7703158, 61589836, 30687283, 6810621, ss225429084, ss235695128, ss242298153, ss562786826, ss658309418, ss988898760, ss1077998053, ss1342723566, ss1575916076, ss1627331113, ss1670325146, ss1806969966, ss1932261364, ss1967443190, ss2026875020, ss2155186804, ss2627910722, ss2699491514, ss2903770159, ss3008684269, ss3349766718, ss3676005886, ss3738488759, ss3749736722, ss3832808336, ss3877014727, ss3925455989, ss5203620529, ss5401859664, ss5651953328, ss5837146255, ss5943275344	NC_000011.9:102496404:C:T	NC_000011.10:102625673:C:T	(self)
72595623, 390201323, 27009483, 85828116, 113373202, 12372053725, ss2185198836, ss3027236178, ss3649690763, ss3692482361, ss3815070073, ss3970631482, ss4897827546, ss5288692183, ss5483701857, ss5585069688, ss5751991012, ss5812726044, ss5850125268, ss5921412691	NC_000011.10:102625673:C:T	NC_000011.10:102625673:C:T	(self)
ss10700881	NT_033899.5:6040244:C:T	NC_000011.10:102625673:C:T	(self)
ss16009079, ss16546332, ss20856249	NT_033899.6:6040256:C:T	NC_000011.10:102625673:C:T	(self)
ss3235517, ss5932472, ss28446748, ss38731203, ss97506036, ss106766202, ss137876620	NT_033899.8:6058820:C:T	NC_000011.10:102625673:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs2292731

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2292731