Name: rs4699726
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.

rs4699726

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:99178356 (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: T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.431165 (114125/264690, TOPMED)
C=0.439384 (61469/139898, GnomAD)
C=0.18713 (5288/28258, 14KJPN) (+ 17 more)
C=0.47782 (9026/18890, ALFA)
C=0.18502 (3101/16760, 8.3KJPN)
C=0.3838 (2458/6404, 1000G_30x)
C=0.3788 (1897/5008, 1000G)
T=0.4797 (2149/4480, Estonian)
T=0.4728 (1822/3854, ALSPAC)
T=0.4674 (1733/3708, TWINSUK)
C=0.2348 (686/2922, KOREAN)
C=0.2129 (390/1832, Korea1K)
T=0.447 (446/998, GoNL)
T=0.487 (292/600, NorthernSweden)
T=0.264 (104/394, SGDP_PRJ)
C=0.324 (105/324, HapMap)
C=0.440 (95/216, Qatari)
C=0.176 (38/216, Vietnamese)
T=0.30 (14/46, Siberian)
T=0.45 (18/40, GENOME_DK)

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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	T=0.52218	C=0.47782
European	Sub	14286	T=0.47389	C=0.52611
African	Sub	2946	T=0.7668	C=0.2332
African Others	Sub	114	T=0.789	C=0.211
African American	Sub	2832	T=0.7659	C=0.2341
Asian	Sub	112	T=0.812	C=0.188
East Asian	Sub	86	T=0.81	C=0.19
Other Asian	Sub	26	T=0.81	C=0.19
Latin American 1	Sub	146	T=0.589	C=0.411
Latin American 2	Sub	610	T=0.356	C=0.644
South Asian	Sub	98	T=0.58	C=0.42
Other	Sub	692	T=0.555	C=0.445

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	T=0.568835	C=0.431165
gnomAD - Genomes	Global	Study-wide	139898	T=0.560616	C=0.439384
gnomAD - Genomes	European	Sub	75748	T=0.46261	C=0.53739
gnomAD - Genomes	African	Sub	41956	T=0.76626	C=0.23374
gnomAD - Genomes	American	Sub	13604	T=0.42995	C=0.57005
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.5178	C=0.4822
gnomAD - Genomes	East Asian	Sub	3122	T=0.7806	C=0.2194
gnomAD - Genomes	Other	Sub	2150	T=0.5740	C=0.4260
14KJPN	JAPANESE	Study-wide	28258	T=0.81287	C=0.18713
Allele Frequency Aggregator	Total	Global	18890	T=0.52218	C=0.47782
Allele Frequency Aggregator	European	Sub	14286	T=0.47389	C=0.52611
Allele Frequency Aggregator	African	Sub	2946	T=0.7668	C=0.2332
Allele Frequency Aggregator	Other	Sub	692	T=0.555	C=0.445
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.356	C=0.644
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.589	C=0.411
Allele Frequency Aggregator	Asian	Sub	112	T=0.812	C=0.188
Allele Frequency Aggregator	South Asian	Sub	98	T=0.58	C=0.42
8.3KJPN	JAPANESE	Study-wide	16760	T=0.81498	C=0.18502
1000Genomes_30x	Global	Study-wide	6404	T=0.6162	C=0.3838
1000Genomes_30x	African	Sub	1786	T=0.8113	C=0.1887
1000Genomes_30x	Europe	Sub	1266	T=0.4542	C=0.5458
1000Genomes_30x	South Asian	Sub	1202	T=0.5507	C=0.4493
1000Genomes_30x	East Asian	Sub	1170	T=0.7761	C=0.2239
1000Genomes_30x	American	Sub	980	T=0.359	C=0.641
1000Genomes	Global	Study-wide	5008	T=0.6212	C=0.3788
1000Genomes	African	Sub	1322	T=0.8079	C=0.1921
1000Genomes	East Asian	Sub	1008	T=0.7817	C=0.2183
1000Genomes	Europe	Sub	1006	T=0.4553	C=0.5447
1000Genomes	South Asian	Sub	978	T=0.551	C=0.449
1000Genomes	American	Sub	694	T=0.372	C=0.628
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.4797	C=0.5203
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.4728	C=0.5272
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.4674	C=0.5326
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.7652	C=0.2348
Korean Genome Project	KOREAN	Study-wide	1832	T=0.7871	C=0.2129
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.447	C=0.553
Northern Sweden	ACPOP	Study-wide	600	T=0.487	C=0.513
SGDP_PRJ	Global	Study-wide	394	T=0.264	C=0.736
HapMap	Global	Study-wide	324	T=0.676	C=0.324
HapMap	American	Sub	120	T=0.450	C=0.550
HapMap	African	Sub	118	T=0.797	C=0.203
HapMap	Asian	Sub	86	T=0.83	C=0.17
Qatari	Global	Study-wide	216	T=0.560	C=0.440
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.824	C=0.176
Siberian	Global	Study-wide	46	T=0.30	C=0.70
The Danish reference pan genome	Danish	Study-wide	40	T=0.45	C=0.55

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.99178356T>C
GRCh37.p13 chr 4	NC_000004.11:g.100099513T>C

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	T=	C
GRCh38.p14 chr 4	NC_000004.12:g.99178356=	NC_000004.12:g.99178356T>C
GRCh37.p13 chr 4	NC_000004.11:g.100099513=	NC_000004.11:g.100099513T>C

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#.

68 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6473285	Feb 20, 2003 (111)
2	WI_SSAHASNP	ss11148163	Jul 11, 2003 (117)
3	SC_JCM	ss11236148	Jul 11, 2003 (117)
4	CSHL-HAPMAP	ss17018680	Feb 27, 2004 (120)
5	SSAHASNP	ss22207982	Apr 05, 2004 (121)
6	ABI	ss42193185	Mar 14, 2006 (126)
7	HGSV	ss78833586	Dec 06, 2007 (129)
8	BCMHGSC_JDW	ss92703118	Mar 24, 2008 (129)
9	HUMANGENOME_JCVI	ss98986749	Feb 06, 2009 (130)
10	1000GENOMES	ss108170575	Jan 23, 2009 (130)
11	ILLUMINA-UK	ss117113523	Dec 01, 2009 (131)
12	ENSEMBL	ss133258966	Dec 01, 2009 (131)
13	ENSEMBL	ss139781943	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss166943495	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss206580673	Jul 04, 2010 (132)
16	1000GENOMES	ss211458057	Jul 14, 2010 (132)
17	1000GENOMES	ss221098563	Jul 14, 2010 (132)
18	1000GENOMES	ss232514946	Jul 14, 2010 (132)
19	1000GENOMES	ss239780044	Jul 15, 2010 (132)
20	GMI	ss277844218	May 04, 2012 (137)
21	PJP	ss293147410	May 09, 2011 (134)
22	TISHKOFF	ss557720875	Apr 25, 2013 (138)
23	SSMP	ss651525461	Apr 25, 2013 (138)
24	EVA-GONL	ss980449620	Aug 21, 2014 (142)
25	JMKIDD_LAB	ss1071786820	Aug 21, 2014 (142)
26	1000GENOMES	ss1310978263	Aug 21, 2014 (142)
27	DDI	ss1429982558	Apr 01, 2015 (144)
28	EVA_GENOME_DK	ss1580687241	Apr 01, 2015 (144)
29	EVA_DECODE	ss1589953627	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1610735322	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1653729355	Apr 01, 2015 (144)
32	HAMMER_LAB	ss1801908542	Sep 08, 2015 (146)
33	WEILL_CORNELL_DGM	ss1923689770	Feb 12, 2016 (147)
34	GENOMED	ss1969816739	Jul 19, 2016 (147)
35	JJLAB	ss2022430817	Sep 14, 2016 (149)
36	USC_VALOUEV	ss2150559988	Dec 20, 2016 (150)
37	HUMAN_LONGEVITY	ss2265421649	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2625714393	Nov 08, 2017 (151)
39	GRF	ss2706036918	Nov 08, 2017 (151)
40	GNOMAD	ss2812849604	Nov 08, 2017 (151)
41	SWEGEN	ss2995209830	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3024990670	Nov 08, 2017 (151)
43	CSHL	ss3345861612	Nov 08, 2017 (151)
44	URBANLAB	ss3647802518	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3663105544	Jul 13, 2019 (153)
46	EVA_DECODE	ss3712656040	Jul 13, 2019 (153)
47	ACPOP	ss3731421450	Jul 13, 2019 (153)
48	EVA	ss3762166670	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3805315066	Jul 13, 2019 (153)
50	EVA	ss3828703327	Apr 26, 2020 (154)
51	EVA	ss3837792698	Apr 26, 2020 (154)
52	EVA	ss3843231085	Apr 26, 2020 (154)
53	SGDP_PRJ	ss3859609824	Apr 26, 2020 (154)
54	KRGDB	ss3905887204	Apr 26, 2020 (154)
55	KOGIC	ss3954741644	Apr 26, 2020 (154)
56	TOPMED	ss4624624545	Apr 26, 2021 (155)
57	TOMMO_GENOMICS	ss5167076782	Apr 26, 2021 (155)
58	1000G_HIGH_COVERAGE	ss5260287285	Oct 13, 2022 (156)
59	HUGCELL_USP	ss5458929835	Oct 13, 2022 (156)
60	EVA	ss5507641281	Oct 13, 2022 (156)
61	1000G_HIGH_COVERAGE	ss5541954336	Oct 13, 2022 (156)
62	SANFORD_IMAGENETICS	ss5635664880	Oct 13, 2022 (156)
63	TOMMO_GENOMICS	ss5701807511	Oct 13, 2022 (156)
64	YY_MCH	ss5805353747	Oct 13, 2022 (156)
65	EVA	ss5844423635	Oct 13, 2022 (156)
66	EVA	ss5854355826	Oct 13, 2022 (156)
67	EVA	ss5864675525	Oct 13, 2022 (156)
68	EVA	ss5964055474	Oct 13, 2022 (156)
69	1000Genomes	NC_000004.11 - 100099513	Oct 12, 2018 (152)
70	1000Genomes_30x	NC_000004.12 - 99178356	Oct 13, 2022 (156)
71	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 100099513	Oct 12, 2018 (152)
72	Genetic variation in the Estonian population	NC_000004.11 - 100099513	Oct 12, 2018 (152)
73	The Danish reference pan genome	NC_000004.11 - 100099513	Apr 26, 2020 (154)
74	gnomAD - Genomes	NC_000004.12 - 99178356	Apr 26, 2021 (155)
75	Genome of the Netherlands Release 5	NC_000004.11 - 100099513	Apr 26, 2020 (154)
76	HapMap	NC_000004.12 - 99178356	Apr 26, 2020 (154)
77	KOREAN population from KRGDB	NC_000004.11 - 100099513	Apr 26, 2020 (154)
78	Korean Genome Project	NC_000004.12 - 99178356	Apr 26, 2020 (154)
79	Northern Sweden	NC_000004.11 - 100099513	Jul 13, 2019 (153)
80	Qatari	NC_000004.11 - 100099513	Apr 26, 2020 (154)
81	SGDP_PRJ	NC_000004.11 - 100099513	Apr 26, 2020 (154)
82	Siberian	NC_000004.11 - 100099513	Apr 26, 2020 (154)
83	8.3KJPN	NC_000004.11 - 100099513	Apr 26, 2021 (155)
84	14KJPN	NC_000004.12 - 99178356	Oct 13, 2022 (156)
85	TopMed	NC_000004.12 - 99178356	Apr 26, 2021 (155)
86	UK 10K study - Twins	NC_000004.11 - 100099513	Oct 12, 2018 (152)
87	A Vietnamese Genetic Variation Database	NC_000004.11 - 100099513	Jul 13, 2019 (153)
88	ALFA	NC_000004.12 - 99178356	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)
rs6532804	Aug 27, 2003 (117)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78833586	NC_000004.9:100456690:T:C	NC_000004.12:99178355:T:C	(self)
ss92703118, ss108170575, ss117113523, ss166943495, ss206580673, ss211458057, ss277844218, ss293147410, ss1589953627	NC_000004.10:100318535:T:C	NC_000004.12:99178355:T:C	(self)
22420405, 12471452, 8843792, 6852180, 5513104, 13064598, 4706315, 5731700, 11626804, 3076342, 25046089, 12471452, 2744184, ss221098563, ss232514946, ss239780044, ss557720875, ss651525461, ss980449620, ss1071786820, ss1310978263, ss1429982558, ss1580687241, ss1610735322, ss1653729355, ss1801908542, ss1923689770, ss1969816739, ss2022430817, ss2150559988, ss2625714393, ss2706036918, ss2812849604, ss2995209830, ss3345861612, ss3663105544, ss3731421450, ss3762166670, ss3828703327, ss3837792698, ss3859609824, ss3905887204, ss5167076782, ss5507641281, ss5635664880, ss5844423635, ss5964055474	NC_000004.11:100099512:T:C	NC_000004.12:99178355:T:C	(self)
29480271, 158821219, 2670209, 11119645, 35644615, 462002101, 14422161233, ss2265421649, ss3024990670, ss3647802518, ss3712656040, ss3805315066, ss3843231085, ss3954741644, ss4624624545, ss5260287285, ss5458929835, ss5541954336, ss5701807511, ss5805353747, ss5854355826, ss5864675525	NC_000004.12:99178355:T:C	NC_000004.12:99178355:T:C	(self)
ss11148163, ss11236148	NT_016354.15:24594216:T:C	NC_000004.12:99178355:T:C	(self)
ss17018680, ss22207982	NT_016354.16:24594216:T:C	NC_000004.12:99178355:T:C	(self)
ss6473285, ss42193185, ss98986749, ss133258966, ss139781943	NT_016354.19:24647233:T:C	NC_000004.12:99178355:T:C	(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 rs4699726

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

rs4699726