Name: rs2221013
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.

rs2221013

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99269418 (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: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.270452 (71586/264690, TOPMED)
A=0.257857 (36086/139946, GnomAD)
G=0.17492 (4943/28258, 14KJPN) (+ 13 more)
A=0.25238 (4674/18520, ALFA)
G=0.17291 (2898/16760, 8.3KJPN)
A=0.3865 (2475/6404, 1000G_30x)
A=0.4004 (2005/5008, 1000G)
A=0.2319 (1039/4480, Estonian)
G=0.2010 (589/2930, KOREAN)
G=0.1889 (346/1832, Korea1K)
A=0.236 (236/998, GoNL)
A=0.192 (115/600, NorthernSweden)
G=0.349 (99/284, SGDP_PRJ)
A=0.264 (57/216, Qatari)
G=0.182 (39/214, Vietnamese)
G=0.40 (8/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC100507053 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	18520	G=0.74762	A=0.25238	0.557883	0.062635	0.379482	0
European	Sub	14152	G=0.75855	A=0.24145	0.571085	0.053985	0.374929	3
African	Sub	2898	G=0.7219	A=0.2781	0.518288	0.074534	0.407177	0
African Others	Sub	114	G=0.754	A=0.246	0.596491	0.087719	0.315789	1
African American	Sub	2784	G=0.7205	A=0.2795	0.515086	0.073994	0.41092	0
Asian	Sub	112	G=0.170	A=0.830	0.017857	0.678571	0.303571	0
East Asian	Sub	86	G=0.16	A=0.84	0.0	0.674419	0.325581	1
Other Asian	Sub	26	G=0.19	A=0.81	0.076923	0.692308	0.230769	1
Latin American 1	Sub	146	G=0.705	A=0.295	0.520548	0.109589	0.369863	1
Latin American 2	Sub	610	G=0.808	A=0.192	0.652459	0.036066	0.311475	0
South Asian	Sub	98	G=0.51	A=0.49	0.22449	0.204082	0.571429	1
Other	Sub	504	G=0.702	A=0.298	0.496032	0.09127	0.412698	0

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	G=0.729548	A=0.270452
gnomAD - Genomes	Global	Study-wide	139946	G=0.742143	A=0.257857
gnomAD - Genomes	European	Sub	75822	G=0.76801	A=0.23199
gnomAD - Genomes	African	Sub	41902	G=0.71722	A=0.28278
gnomAD - Genomes	American	Sub	13628	G=0.80092	A=0.19908
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.7512	A=0.2488
gnomAD - Genomes	East Asian	Sub	3128	G=0.1966	A=0.8034
gnomAD - Genomes	Other	Sub	2146	G=0.7227	A=0.2773
14KJPN	JAPANESE	Study-wide	28258	G=0.17492	A=0.82508
Allele Frequency Aggregator	Total	Global	18520	G=0.74762	A=0.25238
Allele Frequency Aggregator	European	Sub	14152	G=0.75855	A=0.24145
Allele Frequency Aggregator	African	Sub	2898	G=0.7219	A=0.2781
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.808	A=0.192
Allele Frequency Aggregator	Other	Sub	504	G=0.702	A=0.298
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.705	A=0.295
Allele Frequency Aggregator	Asian	Sub	112	G=0.170	A=0.830
Allele Frequency Aggregator	South Asian	Sub	98	G=0.51	A=0.49
8.3KJPN	JAPANESE	Study-wide	16760	G=0.17291	A=0.82709
1000Genomes_30x	Global	Study-wide	6404	G=0.6135	A=0.3865
1000Genomes_30x	African	Sub	1786	G=0.7503	A=0.2497
1000Genomes_30x	Europe	Sub	1266	G=0.7362	A=0.2638
1000Genomes_30x	South Asian	Sub	1202	G=0.5000	A=0.5000
1000Genomes_30x	East Asian	Sub	1170	G=0.2068	A=0.7932
1000Genomes_30x	American	Sub	980	G=0.831	A=0.169
1000Genomes	Global	Study-wide	5008	G=0.5996	A=0.4004
1000Genomes	African	Sub	1322	G=0.7504	A=0.2496
1000Genomes	East Asian	Sub	1008	G=0.2014	A=0.7986
1000Genomes	Europe	Sub	1006	G=0.7445	A=0.2555
1000Genomes	South Asian	Sub	978	G=0.501	A=0.499
1000Genomes	American	Sub	694	G=0.820	A=0.180
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7681	A=0.2319
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.2010	A=0.7990
Korean Genome Project	KOREAN	Study-wide	1832	G=0.1889	A=0.8111
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.764	A=0.236
Northern Sweden	ACPOP	Study-wide	600	G=0.808	A=0.192
SGDP_PRJ	Global	Study-wide	284	G=0.349	A=0.651
Qatari	Global	Study-wide	216	G=0.736	A=0.264
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.182	A=0.818
Siberian	Global	Study-wide	20	G=0.40	A=0.60

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 4	NC_000004.12:g.99269418G>A
GRCh37.p13 chr 4	NC_000004.11:g.100190575G>A

Gene: LOC100507053, uncharacterized LOC100507053 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC100507053 transcript	NR_037884.1:n.	N/A	Intron 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	G=	A
GRCh38.p14 chr 4	NC_000004.12:g.99269418=	NC_000004.12:g.99269418G>A
GRCh37.p13 chr 4	NC_000004.11:g.100190575=	NC_000004.11:g.100190575G>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#.

42 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCMHGSC_JDW	ss92703324	Mar 24, 2008 (129)
2	BUSHMAN	ss198921285	Jul 04, 2010 (144)
3	GMI	ss277844454	May 04, 2012 (144)
4	GMI	ss284967894	Apr 25, 2013 (144)
5	PJP	ss293147533	May 09, 2011 (144)
6	1000GENOMES	ss331832219	May 09, 2011 (144)
7	SSMP	ss651525781	Apr 25, 2013 (144)
8	EVA-GONL	ss980450325	Aug 21, 2014 (144)
9	1000GENOMES	ss1310980531	Aug 21, 2014 (144)
10	EVA_DECODE	ss1589954353	Apr 01, 2015 (144)
11	WEILL_CORNELL_DGM	ss1923690358	Feb 12, 2016 (147)
12	JJLAB	ss2022431145	Sep 14, 2016 (149)
13	USC_VALOUEV	ss2150560319	Dec 20, 2016 (150)
14	HUMAN_LONGEVITY	ss2265426747	Dec 20, 2016 (150)
15	SYSTEMSBIOZJU	ss2625714511	Nov 08, 2017 (151)
16	GRF	ss2706037152	Nov 08, 2017 (151)
17	GNOMAD	ss2812856598	Nov 08, 2017 (151)
18	SWEGEN	ss2995210809	Nov 08, 2017 (151)
19	CSHL	ss3345861897	Nov 08, 2017 (151)
20	URBANLAB	ss3647802684	Oct 12, 2018 (152)
21	EGCUT_WGS	ss3663106659	Jul 13, 2019 (153)
22	EVA_DECODE	ss3712657183	Jul 13, 2019 (153)
23	ACPOP	ss3731421977	Jul 13, 2019 (153)
24	EVA	ss3762167255	Jul 13, 2019 (153)
25	KHV_HUMAN_GENOMES	ss3805315683	Jul 13, 2019 (153)
26	EVA	ss3828703643	Apr 26, 2020 (154)
27	SGDP_PRJ	ss3859610992	Apr 26, 2020 (154)
28	KRGDB	ss3905888545	Apr 26, 2020 (154)
29	KOGIC	ss3954742591	Apr 26, 2020 (154)
30	TOPMED	ss4624647076	Apr 26, 2021 (155)
31	TOMMO_GENOMICS	ss5167079214	Apr 26, 2021 (155)
32	1000G_HIGH_COVERAGE	ss5260289104	Oct 13, 2022 (156)
33	EVA	ss5350977482	Oct 13, 2022 (156)
34	HUGCELL_USP	ss5458931488	Oct 13, 2022 (156)
35	EVA	ss5507641576	Oct 13, 2022 (156)
36	1000G_HIGH_COVERAGE	ss5541957333	Oct 13, 2022 (156)
37	SANFORD_IMAGENETICS	ss5635665958	Oct 13, 2022 (156)
38	TOMMO_GENOMICS	ss5701810687	Oct 13, 2022 (156)
39	YY_MCH	ss5805354136	Oct 13, 2022 (156)
40	EVA	ss5844424489	Oct 13, 2022 (156)
41	EVA	ss5864677782	Oct 13, 2022 (156)
42	EVA	ss5964056677	Oct 13, 2022 (156)
43	1000Genomes	NC_000004.11 - 100190575	Oct 12, 2018 (152)
44	1000Genomes_30x	NC_000004.12 - 99269418	Oct 13, 2022 (156)
45	Genetic variation in the Estonian population	NC_000004.11 - 100190575	Oct 12, 2018 (152)
46	gnomAD - Genomes	NC_000004.12 - 99269418	Apr 26, 2021 (155)
47	Genome of the Netherlands Release 5	NC_000004.11 - 100190575	Apr 26, 2020 (154)
48	KOREAN population from KRGDB	NC_000004.11 - 100190575	Apr 26, 2020 (154)
49	Korean Genome Project	NC_000004.12 - 99269418	Apr 26, 2020 (154)
50	Northern Sweden	NC_000004.11 - 100190575	Jul 13, 2019 (153)
51	Qatari	NC_000004.11 - 100190575	Apr 26, 2020 (154)
52	SGDP_PRJ	NC_000004.11 - 100190575	Apr 26, 2020 (154)
53	Siberian	NC_000004.11 - 100190575	Apr 26, 2020 (154)
54	8.3KJPN	NC_000004.11 - 100190575	Apr 26, 2021 (155)
55	14KJPN	NC_000004.12 - 99269418	Oct 13, 2022 (156)
56	TopMed	NC_000004.12 - 99269418	Apr 26, 2021 (155)
57	A Vietnamese Genetic Variation Database	NC_000004.11 - 100190575	Jul 13, 2019 (153)
58	ALFA	NC_000004.12 - 99269418	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)
rs4566658	Oct 16, 2006 (127)
rs113673572	Jul 01, 2015 (144)
rs144700914	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss92703324, ss198921285, ss277844454, ss284967894, ss293147533, ss1589954353	NC_000004.10:100409597:G:A	NC_000004.12:99269417:G:A	(self)
22422751, 8844907, 5513807, 13065939, 4706842, 5732288, 11627972, 3076673, 25048521, 2744413, ss331832219, ss651525781, ss980450325, ss1310980531, ss1923690358, ss2022431145, ss2150560319, ss2625714511, ss2706037152, ss2812856598, ss2995210809, ss3345861897, ss3663106659, ss3731421977, ss3762167255, ss3828703643, ss3859610992, ss3905888545, ss5167079214, ss5350977482, ss5507641576, ss5635665958, ss5844424489, ss5964056677	NC_000004.11:100190574:G:A	NC_000004.12:99269417:G:A	(self)
29483268, 158839155, 11120592, 35647791, 462024632, 11002399794, ss2265426747, ss3647802684, ss3712657183, ss3805315683, ss3954742591, ss4624647076, ss5260289104, ss5458931488, ss5541957333, ss5701810687, ss5805354136, ss5864677782	NC_000004.12:99269417:G:A	NC_000004.12:99269417:G:A	(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 rs2221013

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2221013