Name: rs1940046
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.

rs1940046

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:102627051 (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: C=0.254940 (67480/264690, TOPMED)
C=0.256591 (35912/139958, GnomAD)
C=0.08960 (2532/28258, 14KJPN) (+ 16 more)
C=0.25359 (4516/17808, ALFA)
C=0.09124 (1529/16758, 8.3KJPN)
C=0.2445 (1566/6404, 1000G_30x)
C=0.2402 (1203/5008, 1000G)
C=0.2464 (1104/4480, Estonian)
C=0.2252 (868/3854, ALSPAC)
C=0.2206 (818/3708, TWINSUK)
C=0.0959 (281/2930, KOREAN)
C=0.1015 (186/1832, Korea1K)
C=0.228 (228/998, GoNL)
C=0.243 (146/600, NorthernSweden)
C=0.124 (66/532, SGDP_PRJ)
C=0.241 (52/216, Qatari)
C=0.014 (3/216, Vietnamese)
C=0.07 (4/56, Siberian)
C=0.33 (13/40, GENOME_DK)

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	17808	C=0.25359	G=0.74641, T=0.00000
European	Sub	13666	C=0.23855	G=0.76145, T=0.00000
African	Sub	2488	C=0.3348	G=0.6652, T=0.0000
African Others	Sub	96	C=0.35	G=0.65, T=0.00
African American	Sub	2392	C=0.3340	G=0.6660, T=0.0000
Asian	Sub	112	C=0.080	G=0.920, T=0.000
East Asian	Sub	86	C=0.10	G=0.90, T=0.00
Other Asian	Sub	26	C=0.00	G=1.00, T=0.00
Latin American 1	Sub	146	C=0.247	G=0.753, T=0.000
Latin American 2	Sub	610	C=0.266	G=0.734, T=0.000
South Asian	Sub	98	C=0.17	G=0.83, T=0.00
Other	Sub	688	C=0.289	G=0.711, T=0.000

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=0.254940	G=0.745060
gnomAD - Genomes	Global	Study-wide	139958	C=0.256591	G=0.743409
gnomAD - Genomes	European	Sub	75818	C=0.22466	G=0.77534
gnomAD - Genomes	African	Sub	41900	C=0.32780	G=0.67220
gnomAD - Genomes	American	Sub	13642	C=0.24476	G=0.75524
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.3100	G=0.6900
gnomAD - Genomes	East Asian	Sub	3134	C=0.0801	G=0.9199
gnomAD - Genomes	Other	Sub	2148	C=0.2449	G=0.7551
14KJPN	JAPANESE	Study-wide	28258	C=0.08960	G=0.91040
Allele Frequency Aggregator	Total	Global	17808	C=0.25359	G=0.74641, T=0.00000
Allele Frequency Aggregator	European	Sub	13666	C=0.23855	G=0.76145, T=0.00000
Allele Frequency Aggregator	African	Sub	2488	C=0.3348	G=0.6652, T=0.0000
Allele Frequency Aggregator	Other	Sub	688	C=0.289	G=0.711, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.266	G=0.734, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.247	G=0.753, T=0.000
Allele Frequency Aggregator	Asian	Sub	112	C=0.080	G=0.920, T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.17	G=0.83, T=0.00
8.3KJPN	JAPANESE	Study-wide	16758	C=0.09124	G=0.90876
1000Genomes_30x	Global	Study-wide	6404	C=0.2445	G=0.7555
1000Genomes_30x	African	Sub	1786	C=0.3634	G=0.6366
1000Genomes_30x	Europe	Sub	1266	C=0.2441	G=0.7559
1000Genomes_30x	South Asian	Sub	1202	C=0.2121	G=0.7879
1000Genomes_30x	East Asian	Sub	1170	C=0.0974	G=0.9026
1000Genomes_30x	American	Sub	980	C=0.244	G=0.756
1000Genomes	Global	Study-wide	5008	C=0.2402	G=0.7598
1000Genomes	African	Sub	1322	C=0.3616	G=0.6384
1000Genomes	East Asian	Sub	1008	C=0.0962	G=0.9038
1000Genomes	Europe	Sub	1006	C=0.2425	G=0.7575
1000Genomes	South Asian	Sub	978	C=0.215	G=0.785
1000Genomes	American	Sub	694	C=0.251	G=0.749
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.2464	G=0.7536
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.2252	G=0.7748
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.2206	G=0.7794
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0959	G=0.9041, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	C=0.1015	G=0.8985
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.228	G=0.772
Northern Sweden	ACPOP	Study-wide	600	C=0.243	G=0.757
SGDP_PRJ	Global	Study-wide	532	C=0.124	G=0.876
Qatari	Global	Study-wide	216	C=0.241	G=0.759
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.014	G=0.986
Siberian	Global	Study-wide	56	C=0.07	G=0.93
The Danish reference pan genome	Danish	Study-wide	40	C=0.33	G=0.68

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.102627051C>G
GRCh38.p14 chr 11	NC_000011.10:g.102627051C>T
GRCh37.p13 chr 11	NC_000011.9:g.102497782C>G
GRCh37.p13 chr 11	NC_000011.9:g.102497782C>T
MMP20 RefSeqGene	NG_012151.1:g.3282G>C
MMP20 RefSeqGene	NG_012151.1:g.3282G>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 X3	XR_947958.3: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

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.102627051=	NC_000011.10:g.102627051C>G	NC_000011.10:g.102627051C>T
GRCh37.p13 chr 11	NC_000011.9:g.102497782=	NC_000011.9:g.102497782C>G	NC_000011.9:g.102497782C>T
MMP20 RefSeqGene	NG_012151.1:g.3282=	NG_012151.1:g.3282G>C	NG_012151.1:g.3282G>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#.

77 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2830758	Jan 12, 2001 (92)
2	SC_JCM	ss3818719	Sep 28, 2001 (100)
3	BCM_SSAHASNP	ss10649667	Jul 11, 2003 (116)
4	SC_SNP	ss16216946	Feb 27, 2004 (120)
5	EGP_SNPS	ss28446732	Sep 20, 2004 (123)
6	ABI	ss38744365	Mar 15, 2006 (126)
7	EGP_SNPS	ss66859656	Dec 01, 2006 (127)
8	HGSV	ss77214594	Dec 06, 2007 (129)
9	BCMHGSC_JDW	ss88750546	Mar 24, 2008 (129)
10	HUMANGENOME_JCVI	ss97506044	Feb 04, 2009 (130)
11	BGI	ss106766212	Feb 04, 2009 (130)
12	1000GENOMES	ss110972962	Jan 25, 2009 (130)
13	1000GENOMES	ss115083421	Jan 25, 2009 (130)
14	ENSEMBL	ss132784376	Dec 01, 2009 (131)
15	ENSEMBL	ss142849730	Dec 01, 2009 (131)
16	GMI	ss156720726	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss168721488	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss170778656	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss175261058	Jul 04, 2010 (132)
20	BUSHMAN	ss203134864	Jul 04, 2010 (132)
21	BCM-HGSC-SUB	ss207635439	Jul 04, 2010 (132)
22	1000GENOMES	ss225429096	Jul 14, 2010 (132)
23	1000GENOMES	ss235695138	Jul 15, 2010 (132)
24	1000GENOMES	ss242298163	Jul 15, 2010 (132)
25	BL	ss255361461	May 09, 2011 (134)
26	GMI	ss281148057	May 04, 2012 (137)
27	GMI	ss286445470	Apr 25, 2013 (138)
28	PJP	ss291126755	May 09, 2011 (134)
29	TISHKOFF	ss562786839	Apr 25, 2013 (138)
30	SSMP	ss658309428	Apr 25, 2013 (138)
31	EVA-GONL	ss988898773	Aug 21, 2014 (142)
32	1000GENOMES	ss1342723610	Aug 21, 2014 (142)
33	DDI	ss1426742639	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1575916097	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1627331140	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1670325173	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1806969977	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1932261378	Feb 12, 2016 (147)
39	GENOMED	ss1967443201	Jul 19, 2016 (147)
40	JJLAB	ss2026875031	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2155186818	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2185198929	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2627910734	Nov 08, 2017 (151)
44	GRF	ss2699491526	Nov 08, 2017 (151)
45	GNOMAD	ss2903770288	Nov 08, 2017 (151)
46	SWEGEN	ss3008684288	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3027236188	Nov 08, 2017 (151)
48	CSHL	ss3349766728	Nov 08, 2017 (151)
49	URBANLAB	ss3649690774	Oct 12, 2018 (152)
50	EGCUT_WGS	ss3676005907	Jul 13, 2019 (153)
51	EVA_DECODE	ss3692482389	Jul 13, 2019 (153)
52	ACPOP	ss3738488775	Jul 13, 2019 (153)
53	EVA	ss3749736739	Jul 13, 2019 (153)
54	PACBIO	ss3787051009	Jul 13, 2019 (153)
55	PACBIO	ss3792177848	Jul 13, 2019 (153)
56	PACBIO	ss3797060346	Jul 13, 2019 (153)
57	KHV_HUMAN_GENOMES	ss3815070094	Jul 13, 2019 (153)
58	EVA	ss3832808347	Apr 26, 2020 (154)
59	EVA	ss3839965779	Apr 26, 2020 (154)
60	EVA	ss3845446970	Apr 26, 2020 (154)
61	SGDP_PRJ	ss3877014748	Apr 26, 2020 (154)
62	KRGDB	ss3925456009	Apr 26, 2020 (154)
63	KOGIC	ss3970631502	Apr 26, 2020 (154)
64	TOPMED	ss4897827931	Apr 26, 2021 (155)
65	TOMMO_GENOMICS	ss5203620575	Apr 26, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5288692225	Oct 16, 2022 (156)
67	EVA	ss5401859737	Oct 16, 2022 (156)
68	HUGCELL_USP	ss5483701900	Oct 16, 2022 (156)
69	EVA	ss5510496308	Oct 16, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5585069746	Oct 16, 2022 (156)
71	SANFORD_IMAGENETICS	ss5651953355	Oct 16, 2022 (156)
72	TOMMO_GENOMICS	ss5751991063	Oct 16, 2022 (156)
73	YY_MCH	ss5812726061	Oct 16, 2022 (156)
74	EVA	ss5837146269	Oct 16, 2022 (156)
75	EVA	ss5850125279	Oct 16, 2022 (156)
76	EVA	ss5921412743	Oct 16, 2022 (156)
77	EVA	ss5943275371	Oct 16, 2022 (156)
78	1000Genomes	NC_000011.9 - 102497782	Oct 12, 2018 (152)
79	1000Genomes_30x	NC_000011.10 - 102627051	Oct 16, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 102497782	Oct 12, 2018 (152)
81	Genetic variation in the Estonian population	NC_000011.9 - 102497782	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000011.9 - 102497782	Apr 26, 2020 (154)
83	gnomAD - Genomes	NC_000011.10 - 102627051	Apr 26, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000011.9 - 102497782	Apr 26, 2020 (154)
85	KOREAN population from KRGDB	NC_000011.9 - 102497782	Apr 26, 2020 (154)
86	Korean Genome Project	NC_000011.10 - 102627051	Apr 26, 2020 (154)
87	Northern Sweden	NC_000011.9 - 102497782	Jul 13, 2019 (153)
88	Qatari	NC_000011.9 - 102497782	Apr 26, 2020 (154)
89	SGDP_PRJ	NC_000011.9 - 102497782	Apr 26, 2020 (154)
90	Siberian	NC_000011.9 - 102497782	Apr 26, 2020 (154)
91	8.3KJPN	NC_000011.9 - 102497782	Apr 26, 2021 (155)
92	14KJPN	NC_000011.10 - 102627051	Oct 16, 2022 (156)
93	TopMed	NC_000011.10 - 102627051	Apr 26, 2021 (155)
94	UK 10K study - Twins	NC_000011.9 - 102497782	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000011.9 - 102497782	Jul 13, 2019 (153)
96	ALFA	NC_000011.10 - 102627051	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77214594, ss88750546, ss110972962, ss115083421, ss168721488, ss170778656, ss175261058, ss203134864, ss207635439, ss255361461, ss281148057, ss286445470, ss291126755	NC_000011.8:102002991:C:G	NC_000011.10:102627050:C:G	(self)
55296633, 30687311, 21744155, 2710468, 13697078, 32633403, 11773640, 14303308, 29031728, 7703172, 61589882, 30687311, 6810634, ss225429096, ss235695138, ss242298163, ss562786839, ss658309428, ss988898773, ss1342723610, ss1426742639, ss1575916097, ss1627331140, ss1670325173, ss1806969977, ss1932261378, ss1967443201, ss2026875031, ss2155186818, ss2627910734, ss2699491526, ss2903770288, ss3008684288, ss3349766728, ss3676005907, ss3738488775, ss3749736739, ss3787051009, ss3792177848, ss3797060346, ss3832808347, ss3839965779, ss3877014748, ss3925456009, ss5203620575, ss5401859737, ss5510496308, ss5651953355, ss5837146269, ss5943275371	NC_000011.9:102497781:C:G	NC_000011.10:102627050:C:G	(self)
72595681, 390201625, 27009503, 85828167, 113373587, 6852628919, ss2185198929, ss3027236188, ss3649690774, ss3692482389, ss3815070094, ss3845446970, ss3970631502, ss4897827931, ss5288692225, ss5483701900, ss5585069746, ss5751991063, ss5812726061, ss5850125279, ss5921412743	NC_000011.10:102627050:C:G	NC_000011.10:102627050:C:G	(self)
ss10649667	NT_033899.5:6041621:C:G	NC_000011.10:102627050:C:G	(self)
ss16216946	NT_033899.6:6041633:C:G	NC_000011.10:102627050:C:G	(self)
ss2830758, ss3818719, ss28446732, ss38744365, ss66859656, ss97506044, ss106766212, ss132784376, ss142849730, ss156720726	NT_033899.8:6060197:C:G	NC_000011.10:102627050:C:G	(self)
32633403, ss3925456009	NC_000011.9:102497781:C:T	NC_000011.10:102627050:C:T	(self)
6852628919	NC_000011.10:102627050:C:T	NC_000011.10:102627050: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 rs1940046

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

rs1940046