Name: rs2099884
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.

rs2099884

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:141842417 (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 / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.143501 (20099/140062, GnomAD)
A=0.143757 (19538/135910, ALFA)
A=0.46090 (13024/28258, 14KJPN) (+ 19 more)
A=0.46414 (7779/16760, 8.3KJPN)
A=0.2211 (1416/6404, 1000G_30x)
A=0.2274 (1139/5008, 1000G)
A=0.1426 (639/4480, Estonian)
A=0.1448 (558/3854, ALSPAC)
A=0.1413 (524/3708, TWINSUK)
A=0.4659 (1365/2930, KOREAN)
A=0.2008 (380/1892, HapMap)
A=0.4618 (846/1832, Korea1K)
A=0.150 (150/998, GoNL)
A=0.477 (375/786, PRJEB37584)
A=0.407 (255/626, Chileans)
A=0.100 (60/600, NorthernSweden)
G=0.383 (85/222, SGDP_PRJ)
A=0.106 (23/216, Qatari)
G=0.500 (107/214, Vietnamese)
A=0.500 (107/214, Vietnamese)
A=0.15 (6/40, GENOME_DK)
G=0.46 (13/28, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
Publications: 1 citation
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	135910	G=0.856243	A=0.143757, T=0.000000
European	Sub	114790	G=0.865380	A=0.134620, T=0.000000
African	Sub	5332	G=0.9501	A=0.0499, T=0.0000
African Others	Sub	194	G=0.964	A=0.036, T=0.000
African American	Sub	5138	G=0.9496	A=0.0504, T=0.0000
Asian	Sub	308	G=0.565	A=0.435, T=0.000
East Asian	Sub	198	G=0.551	A=0.449, T=0.000
Other Asian	Sub	110	G=0.591	A=0.409, T=0.000
Latin American 1	Sub	810	G=0.848	A=0.152, T=0.000
Latin American 2	Sub	7912	G=0.6934	A=0.3066, T=0.0000
South Asian	Sub	146	G=0.904	A=0.096, T=0.000
Other	Sub	6612	G=0.8303	A=0.1697, T=0.0000

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
gnomAD - Genomes	Global	Study-wide	140062	G=0.856499	A=0.143501
gnomAD - Genomes	European	Sub	75862	G=0.85816	A=0.14184
gnomAD - Genomes	African	Sub	41994	G=0.91044	A=0.08956
gnomAD - Genomes	American	Sub	13618	G=0.75349	A=0.24651
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.8919	A=0.1081
gnomAD - Genomes	East Asian	Sub	3116	G=0.5138	A=0.4862
gnomAD - Genomes	Other	Sub	2150	G=0.8386	A=0.1614
Allele Frequency Aggregator	Total	Global	135910	G=0.856243	A=0.143757, T=0.000000
Allele Frequency Aggregator	European	Sub	114790	G=0.865380	A=0.134620, T=0.000000
Allele Frequency Aggregator	Latin American 2	Sub	7912	G=0.6934	A=0.3066, T=0.0000
Allele Frequency Aggregator	Other	Sub	6612	G=0.8303	A=0.1697, T=0.0000
Allele Frequency Aggregator	African	Sub	5332	G=0.9501	A=0.0499, T=0.0000
Allele Frequency Aggregator	Latin American 1	Sub	810	G=0.848	A=0.152, T=0.000
Allele Frequency Aggregator	Asian	Sub	308	G=0.565	A=0.435, T=0.000
Allele Frequency Aggregator	South Asian	Sub	146	G=0.904	A=0.096, T=0.000
14KJPN	JAPANESE	Study-wide	28258	G=0.53910	A=0.46090
8.3KJPN	JAPANESE	Study-wide	16760	G=0.53586	A=0.46414
1000Genomes_30x	Global	Study-wide	6404	G=0.7789	A=0.2211
1000Genomes_30x	African	Sub	1786	G=0.9345	A=0.0655
1000Genomes_30x	Europe	Sub	1266	G=0.8436	A=0.1564
1000Genomes_30x	South Asian	Sub	1202	G=0.8161	A=0.1839
1000Genomes_30x	East Asian	Sub	1170	G=0.4889	A=0.5111
1000Genomes_30x	American	Sub	980	G=0.712	A=0.288
1000Genomes	Global	Study-wide	5008	G=0.7726	A=0.2274
1000Genomes	African	Sub	1322	G=0.9312	A=0.0688
1000Genomes	East Asian	Sub	1008	G=0.4960	A=0.5040
1000Genomes	Europe	Sub	1006	G=0.8509	A=0.1491
1000Genomes	South Asian	Sub	978	G=0.819	A=0.181
1000Genomes	American	Sub	694	G=0.693	A=0.307
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8574	A=0.1426
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8552	A=0.1448
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8587	A=0.1413
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.5341	A=0.4659
HapMap	Global	Study-wide	1892	G=0.7992	A=0.2008
HapMap	American	Sub	770	G=0.719	A=0.281
HapMap	African	Sub	692	G=0.945	A=0.055
HapMap	Asian	Sub	254	G=0.579	A=0.421
HapMap	Europe	Sub	176	G=0.892	A=0.108
Korean Genome Project	KOREAN	Study-wide	1832	G=0.5382	A=0.4618
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.850	A=0.150
CNV burdens in cranial meningiomas	Global	Study-wide	786	G=0.523	A=0.477
CNV burdens in cranial meningiomas	CRM	Sub	786	G=0.523	A=0.477
Chileans	Chilean	Study-wide	626	G=0.593	A=0.407
Northern Sweden	ACPOP	Study-wide	600	G=0.900	A=0.100
SGDP_PRJ	Global	Study-wide	222	G=0.383	A=0.617
Qatari	Global	Study-wide	216	G=0.894	A=0.106
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.500	A=0.500
The Danish reference pan genome	Danish	Study-wide	40	G=0.85	A=0.15
Siberian	Global	Study-wide	28	G=0.46	A=0.54

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.141842417G>A
GRCh38.p14 chr 4	NC_000004.12:g.141842417G>T
GRCh37.p13 chr 4	NC_000004.11:g.142763570G>A
GRCh37.p13 chr 4	NC_000004.11:g.142763570G>T

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	T
GRCh38.p14 chr 4	NC_000004.12:g.141842417=	NC_000004.12:g.141842417G>A	NC_000004.12:g.141842417G>T
GRCh37.p13 chr 4	NC_000004.11:g.142763570=	NC_000004.11:g.142763570G>A	NC_000004.11:g.142763570G>T

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#.

95 SubSNP, 23 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3017915	Jun 15, 2001 (96)
2	TSC-CSHL	ss5199691	Oct 08, 2002 (108)
3	SC_SNP	ss14789912	Dec 05, 2003 (119)
4	ABI	ss42331027	Mar 13, 2006 (126)
5	AFFY	ss66248422	Dec 03, 2006 (127)
6	AFFY	ss76393935	Dec 06, 2007 (129)
7	HGSV	ss81397550	Dec 15, 2007 (130)
8	KRIBB_YJKIM	ss81687377	Dec 14, 2007 (130)
9	HGSV	ss82580740	Dec 15, 2007 (130)
10	BCMHGSC_JDW	ss92807378	Mar 24, 2008 (129)
11	BGI	ss104125769	Dec 01, 2009 (131)
12	1000GENOMES	ss108410347	Jan 23, 2009 (130)
13	ILLUMINA-UK	ss117218311	Feb 14, 2009 (130)
14	ENSEMBL	ss139928041	Dec 01, 2009 (131)
15	GMI	ss157996887	Dec 01, 2009 (131)
16	ILLUMINA	ss160501749	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss167240187	Jul 04, 2010 (132)
18	AFFY	ss173462369	Jul 04, 2010 (132)
19	1000GENOMES	ss221259209	Jul 14, 2010 (132)
20	1000GENOMES	ss232633511	Jul 14, 2010 (132)
21	1000GENOMES	ss239873234	Jul 15, 2010 (132)
22	BL	ss253580956	May 09, 2011 (134)
23	GMI	ss277967053	May 04, 2012 (137)
24	PJP	ss293204992	May 09, 2011 (134)
25	ILLUMINA	ss480422662	May 04, 2012 (137)
26	ILLUMINA	ss480436138	May 04, 2012 (137)
27	ILLUMINA	ss481221559	Sep 08, 2015 (146)
28	ILLUMINA	ss485008806	May 04, 2012 (137)
29	ILLUMINA	ss537038427	Sep 08, 2015 (146)
30	SSMP	ss651726489	Apr 25, 2013 (138)
31	ILLUMINA	ss778480923	Sep 08, 2015 (146)
32	ILLUMINA	ss782950709	Sep 08, 2015 (146)
33	ILLUMINA	ss783912973	Sep 08, 2015 (146)
34	ILLUMINA	ss832206638	Sep 08, 2015 (146)
35	ILLUMINA	ss833936802	Sep 08, 2015 (146)
36	EVA-GONL	ss980769512	Aug 21, 2014 (142)
37	JMKIDD_LAB	ss1072026634	Aug 21, 2014 (142)
38	1000GENOMES	ss1312154628	Aug 21, 2014 (142)
39	DDI	ss1430077359	Apr 01, 2015 (144)
40	EVA_GENOME_DK	ss1580813683	Apr 01, 2015 (144)
41	EVA_DECODE	ss1590281781	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1611350730	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1654344763	Apr 01, 2015 (144)
44	EVA_SVP	ss1712712165	Apr 01, 2015 (144)
45	ILLUMINA	ss1752500809	Sep 08, 2015 (146)
46	WEILL_CORNELL_DGM	ss1924011188	Feb 12, 2016 (147)
47	GENOMED	ss1969892197	Jul 19, 2016 (147)
48	JJLAB	ss2022592794	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2150724292	Dec 20, 2016 (150)
50	HUMAN_LONGEVITY	ss2267847496	Dec 20, 2016 (150)
51	SYSTEMSBIOZJU	ss2625792979	Nov 08, 2017 (151)
52	ILLUMINA	ss2634187566	Nov 08, 2017 (151)
53	GRF	ss2706216303	Nov 08, 2017 (151)
54	GNOMAD	ss2816230841	Nov 08, 2017 (151)
55	SWEGEN	ss2995694898	Nov 08, 2017 (151)
56	BIOINF_KMB_FNS_UNIBA	ss3025073726	Nov 08, 2017 (151)
57	CSHL	ss3346002640	Nov 08, 2017 (151)
58	ILLUMINA	ss3629082094	Oct 12, 2018 (152)
59	ILLUMINA	ss3632119748	Oct 12, 2018 (152)
60	ILLUMINA	ss3633351416	Oct 12, 2018 (152)
61	ILLUMINA	ss3634071026	Oct 12, 2018 (152)
62	ILLUMINA	ss3634973606	Oct 12, 2018 (152)
63	ILLUMINA	ss3635753569	Oct 12, 2018 (152)
64	ILLUMINA	ss3636680555	Oct 12, 2018 (152)
65	ILLUMINA	ss3637506130	Oct 12, 2018 (152)
66	ILLUMINA	ss3640680900	Oct 12, 2018 (152)
67	EGCUT_WGS	ss3663603932	Jul 13, 2019 (153)
68	EVA_DECODE	ss3713226966	Jul 13, 2019 (153)
69	ACPOP	ss3731684664	Jul 13, 2019 (153)
70	ILLUMINA	ss3745273836	Jul 13, 2019 (153)
71	EVA	ss3762515675	Jul 13, 2019 (153)
72	ILLUMINA	ss3772768300	Jul 13, 2019 (153)
73	KHV_HUMAN_GENOMES	ss3805676600	Jul 13, 2019 (153)
74	EVA	ss3828853861	Apr 26, 2020 (154)
75	SGDP_PRJ	ss3860236695	Apr 26, 2020 (154)
76	KRGDB	ss3906565168	Apr 26, 2020 (154)
77	KOGIC	ss3955281042	Apr 26, 2020 (154)
78	EVA	ss3984536192	Apr 26, 2021 (155)
79	TOPMED	ss4634960212	Apr 26, 2021 (155)
80	TOPMED	ss4634960213	Apr 26, 2021 (155)
81	TOMMO_GENOMICS	ss5168389360	Apr 26, 2021 (155)
82	1000G_HIGH_COVERAGE	ss5261319959	Oct 17, 2022 (156)
83	EVA	ss5314996481	Oct 17, 2022 (156)
84	EVA	ss5352839465	Oct 17, 2022 (156)
85	HUGCELL_USP	ss5459847416	Oct 17, 2022 (156)
86	EVA	ss5507763759	Oct 17, 2022 (156)
87	1000G_HIGH_COVERAGE	ss5543571810	Oct 17, 2022 (156)
88	SANFORD_IMAGENETICS	ss5636270037	Oct 17, 2022 (156)
89	TOMMO_GENOMICS	ss5703486791	Oct 17, 2022 (156)
90	EVA	ss5799629125	Oct 17, 2022 (156)
91	YY_MCH	ss5805612593	Oct 17, 2022 (156)
92	EVA	ss5844830802	Oct 17, 2022 (156)
93	EVA	ss5854482597	Oct 17, 2022 (156)
94	EVA	ss5865844252	Oct 17, 2022 (156)
95	EVA	ss5964673701	Oct 17, 2022 (156)
96	1000Genomes	NC_000004.11 - 142763570	Oct 12, 2018 (152)
97	1000Genomes_30x	NC_000004.12 - 141842417	Oct 17, 2022 (156)
98	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 142763570	Oct 12, 2018 (152)
99	Chileans	NC_000004.11 - 142763570	Apr 26, 2020 (154)
100	Genetic variation in the Estonian population	NC_000004.11 - 142763570	Oct 12, 2018 (152)
101	The Danish reference pan genome	NC_000004.11 - 142763570	Apr 26, 2020 (154)
102	gnomAD - Genomes	NC_000004.12 - 141842417	Apr 26, 2021 (155)
103	Genome of the Netherlands Release 5	NC_000004.11 - 142763570	Apr 26, 2020 (154)
104	HapMap	NC_000004.12 - 141842417	Apr 26, 2020 (154)
105	KOREAN population from KRGDB	NC_000004.11 - 142763570	Apr 26, 2020 (154)
106	Korean Genome Project	NC_000004.12 - 141842417	Apr 26, 2020 (154)
107	Northern Sweden	NC_000004.11 - 142763570	Jul 13, 2019 (153)
108	CNV burdens in cranial meningiomas	NC_000004.11 - 142763570	Apr 26, 2021 (155)
109	Qatari	NC_000004.11 - 142763570	Apr 26, 2020 (154)
110	SGDP_PRJ	NC_000004.11 - 142763570	Apr 26, 2020 (154)
111	Siberian	NC_000004.11 - 142763570	Apr 26, 2020 (154)
112	8.3KJPN	NC_000004.11 - 142763570	Apr 26, 2021 (155)
113	14KJPN	NC_000004.12 - 141842417	Oct 17, 2022 (156)
114	TopMed Submission ignored due to conflicting rows: Row 472337768 (NC_000004.12:141842416:G:A 42816/264690) Row 472337769 (NC_000004.12:141842416:G:T 1/264690)	-	Apr 26, 2021 (155)
115	TopMed Submission ignored due to conflicting rows: Row 472337768 (NC_000004.12:141842416:G:A 42816/264690) Row 472337769 (NC_000004.12:141842416:G:T 1/264690)	-	Apr 26, 2021 (155)
116	UK 10K study - Twins	NC_000004.11 - 142763570	Oct 12, 2018 (152)
117	A Vietnamese Genetic Variation Database	NC_000004.11 - 142763570	Jul 13, 2019 (153)
118	ALFA	NC_000004.12 - 141842417	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)
rs56848060	Feb 27, 2009 (130)
rs60628541	May 26, 2008 (130)
rs386557200	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss81397550, ss82580740	NC_000004.9:143121174:G:A	NC_000004.12:141842416:G:A	(self)
ss66248422, ss76393935, ss92807378, ss108410347, ss117218311, ss167240187, ss173462369, ss253580956, ss277967053, ss293204992, ss480422662, ss1590281781, ss1712712165	NC_000004.10:142983019:G:A	NC_000004.12:141842416:G:A	(self)
23643087, 13148353, 328911, 9342180, 6978622, 5825072, 13742562, 4969529, 85554, 6053118, 12253675, 3240646, 26358667, 13148353, 2901533, ss221259209, ss232633511, ss239873234, ss480436138, ss481221559, ss485008806, ss537038427, ss651726489, ss778480923, ss782950709, ss783912973, ss832206638, ss833936802, ss980769512, ss1072026634, ss1312154628, ss1430077359, ss1580813683, ss1611350730, ss1654344763, ss1752500809, ss1924011188, ss1969892197, ss2022592794, ss2150724292, ss2625792979, ss2634187566, ss2706216303, ss2816230841, ss2995694898, ss3346002640, ss3629082094, ss3632119748, ss3633351416, ss3634071026, ss3634973606, ss3635753569, ss3636680555, ss3637506130, ss3640680900, ss3663603932, ss3731684664, ss3745273836, ss3762515675, ss3772768300, ss3828853861, ss3860236695, ss3906565168, ss3984536192, ss5168389360, ss5314996481, ss5352839465, ss5507763759, ss5636270037, ss5799629125, ss5844830802, ss5964673701	NC_000004.11:142763569:G:A	NC_000004.12:141842416:G:A	(self)
31097745, 167465198, 2724819, 11659043, 37323895, 14148516500, ss2267847496, ss3025073726, ss3713226966, ss3805676600, ss3955281042, ss4634960212, ss5261319959, ss5459847416, ss5543571810, ss5703486791, ss5805612593, ss5854482597, ss5865844252	NC_000004.12:141842416:G:A	NC_000004.12:141842416:G:A	(self)
ss3017915, ss5199691, ss14789912, ss42331027, ss81687377, ss104125769, ss139928041, ss157996887, ss160501749	NT_016354.19:67311290:G:A	NC_000004.12:141842416:G:A	(self)
14148516500, ss4634960213	NC_000004.12:141842416:G:T	NC_000004.12:141842416:G:T	(self)

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

1 citation for rs2099884

PMID	Title	Author	Year	Journal
34834553	Innate-Immunity Genes in Obesity.	Mikhailova SV et al.	2021	Journal of personalized medicine

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

rs2099884