Name: rs1738879
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.

rs1738879

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr14:26010267 (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=0.445121 (117819/264690, TOPMED)
T=0.451479 (63049/139650, GnomAD)
C=0.48337 (13659/28258, 14KJPN) (+ 15 more)
T=0.47914 (9051/18890, ALFA)
C=0.48365 (8106/16760, 8.3KJPN)
T=0.4188 (2682/6404, 1000G_30x)
T=0.4237 (2122/5008, 1000G)
C=0.4975 (2229/4480, Estonian)
C=0.4728 (1822/3854, ALSPAC)
C=0.4946 (1834/3708, TWINSUK)
T=0.4549 (1333/2930, KOREAN)
T=0.4569 (837/1832, Korea1K)
C=0.473 (472/998, GoNL)
C=0.460 (276/600, NorthernSweden)
C=0.342 (121/354, SGDP_PRJ)
C=0.481 (104/216, Qatari)
C=0.39 (17/44, Siberian)
T=0.33 (13/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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=0.52086	T=0.47914
European	Sub	14286	C=0.49041	T=0.50959
African	Sub	2946	C=0.6249	T=0.3751
African Others	Sub	114	C=0.658	T=0.342
African American	Sub	2832	C=0.6236	T=0.3764
Asian	Sub	112	C=0.652	T=0.348
East Asian	Sub	86	C=0.64	T=0.36
Other Asian	Sub	26	C=0.69	T=0.31
Latin American 1	Sub	146	C=0.473	T=0.527
Latin American 2	Sub	610	C=0.657	T=0.343
South Asian	Sub	98	C=0.57	T=0.43
Other	Sub	692	C=0.568	T=0.432

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=0.554879	T=0.445121
gnomAD - Genomes	Global	Study-wide	139650	C=0.548521	T=0.451479
gnomAD - Genomes	European	Sub	75616	C=0.49717	T=0.50283
gnomAD - Genomes	African	Sub	41842	C=0.62550	T=0.37450
gnomAD - Genomes	American	Sub	13628	C=0.59605	T=0.40395
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.5262	T=0.4738
gnomAD - Genomes	East Asian	Sub	3098	C=0.5852	T=0.4148
gnomAD - Genomes	Other	Sub	2142	C=0.5369	T=0.4631
14KJPN	JAPANESE	Study-wide	28258	C=0.48337	T=0.51663
Allele Frequency Aggregator	Total	Global	18890	C=0.52086	T=0.47914
Allele Frequency Aggregator	European	Sub	14286	C=0.49041	T=0.50959
Allele Frequency Aggregator	African	Sub	2946	C=0.6249	T=0.3751
Allele Frequency Aggregator	Other	Sub	692	C=0.568	T=0.432
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.657	T=0.343
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.473	T=0.527
Allele Frequency Aggregator	Asian	Sub	112	C=0.652	T=0.348
Allele Frequency Aggregator	South Asian	Sub	98	C=0.57	T=0.43
8.3KJPN	JAPANESE	Study-wide	16760	C=0.48365	T=0.51635
1000Genomes_30x	Global	Study-wide	6404	C=0.5812	T=0.4188
1000Genomes_30x	African	Sub	1786	C=0.6506	T=0.3494
1000Genomes_30x	Europe	Sub	1266	C=0.4708	T=0.5292
1000Genomes_30x	South Asian	Sub	1202	C=0.5574	T=0.4426
1000Genomes_30x	East Asian	Sub	1170	C=0.6043	T=0.3957
1000Genomes_30x	American	Sub	980	C=0.599	T=0.401
1000Genomes	Global	Study-wide	5008	C=0.5763	T=0.4237
1000Genomes	African	Sub	1322	C=0.6573	T=0.3427
1000Genomes	East Asian	Sub	1008	C=0.5883	T=0.4117
1000Genomes	Europe	Sub	1006	C=0.4682	T=0.5318
1000Genomes	South Asian	Sub	978	C=0.552	T=0.448
1000Genomes	American	Sub	694	C=0.595	T=0.405
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.4975	T=0.5025
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.4728	T=0.5272
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.4946	T=0.5054
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5451	G=0.0000, T=0.4549
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5431	T=0.4569
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.473	T=0.527
Northern Sweden	ACPOP	Study-wide	600	C=0.460	T=0.540
SGDP_PRJ	Global	Study-wide	354	C=0.342	T=0.658
Qatari	Global	Study-wide	216	C=0.481	T=0.519
Siberian	Global	Study-wide	44	C=0.39	T=0.61
The Danish reference pan genome	Danish	Study-wide	40	C=0.68	T=0.33

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 14	NC_000014.9:g.26010267C>G
GRCh38.p14 chr 14	NC_000014.9:g.26010267C>T
GRCh37.p13 chr 14	NC_000014.8:g.26479473C>G
GRCh37.p13 chr 14	NC_000014.8:g.26479473C>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	C=	G	T
GRCh38.p14 chr 14	NC_000014.9:g.26010267=	NC_000014.9:g.26010267C>G	NC_000014.9:g.26010267C>T
GRCh37.p13 chr 14	NC_000014.8:g.26479473=	NC_000014.8:g.26479473C>G	NC_000014.8:g.26479473C>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#.

66 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss2581573	Nov 09, 2000 (89)
2	SSAHASNP	ss21206369	Apr 05, 2004 (126)
3	ABI	ss40518612	Mar 10, 2006 (126)
4	HGSV	ss77106627	Dec 06, 2007 (129)
5	HGSV	ss78015513	Dec 06, 2007 (129)
6	HGSV	ss81466161	Dec 15, 2007 (130)
7	HUMANGENOME_JCVI	ss96845862	Feb 04, 2009 (130)
8	1000GENOMES	ss108189574	Jan 23, 2009 (130)
9	ILLUMINA-UK	ss118386122	Feb 14, 2009 (130)
10	ENSEMBL	ss137085697	Dec 01, 2009 (131)
11	GMI	ss155548991	Dec 01, 2009 (131)
12	1000GENOMES	ss211489499	Jul 14, 2010 (132)
13	1000GENOMES	ss226471928	Jul 14, 2010 (132)
14	1000GENOMES	ss236469531	Jul 15, 2010 (132)
15	1000GENOMES	ss242919017	Jul 15, 2010 (132)
16	BL	ss254857011	May 09, 2011 (134)
17	GMI	ss281930752	May 04, 2012 (137)
18	GMI	ss286807928	Apr 25, 2013 (138)
19	SSMP	ss659643373	Apr 25, 2013 (138)
20	EVA-GONL	ss990948566	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1079505540	Aug 21, 2014 (142)
22	1000GENOMES	ss1350266951	Aug 21, 2014 (142)
23	DDI	ss1427363984	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1577132507	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1631349000	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1674343033	Apr 01, 2015 (144)
27	EVA_DECODE	ss1694939553	Apr 01, 2015 (144)
28	WEILL_CORNELL_DGM	ss1934324639	Feb 12, 2016 (147)
29	GENOMED	ss1967919031	Jul 19, 2016 (147)
30	JJLAB	ss2027937114	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2156309151	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2200457390	Dec 20, 2016 (150)
33	GRF	ss2700723829	Nov 08, 2017 (151)
34	GNOMAD	ss2925584746	Nov 08, 2017 (151)
35	SWEGEN	ss3011899921	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3027791662	Nov 08, 2017 (151)
37	CSHL	ss3350719228	Nov 08, 2017 (151)
38	URBANLAB	ss3650165054	Oct 12, 2018 (152)
39	EGCUT_WGS	ss3679139733	Jul 13, 2019 (153)
40	EVA_DECODE	ss3696314689	Jul 13, 2019 (153)
41	ACPOP	ss3740217478	Jul 13, 2019 (153)
42	EVA	ss3752099817	Jul 13, 2019 (153)
43	PACBIO	ss3787614498	Jul 13, 2019 (153)
44	PACBIO	ss3792661269	Jul 13, 2019 (153)
45	PACBIO	ss3797545344	Jul 13, 2019 (153)
46	KHV_HUMAN_GENOMES	ss3817431329	Jul 13, 2019 (153)
47	EVA	ss3833822570	Apr 27, 2020 (154)
48	EVA	ss3840503452	Apr 27, 2020 (154)
49	EVA	ss3845991263	Apr 27, 2020 (154)
50	SGDP_PRJ	ss3881114183	Apr 27, 2020 (154)
51	KRGDB	ss3930087710	Apr 27, 2020 (154)
52	KOGIC	ss3974571010	Apr 27, 2020 (154)
53	TOPMED	ss4964213796	Apr 26, 2021 (155)
54	TOMMO_GENOMICS	ss5212398997	Apr 26, 2021 (155)
55	1000G_HIGH_COVERAGE	ss5295571447	Oct 16, 2022 (156)
56	EVA	ss5414101792	Oct 16, 2022 (156)
57	HUGCELL_USP	ss5489693096	Oct 16, 2022 (156)
58	EVA	ss5511169130	Oct 16, 2022 (156)
59	1000G_HIGH_COVERAGE	ss5595507612	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5655844009	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5764962670	Oct 16, 2022 (156)
62	YY_MCH	ss5814590624	Oct 16, 2022 (156)
63	EVA	ss5840850157	Oct 16, 2022 (156)
64	EVA	ss5850956130	Oct 16, 2022 (156)
65	EVA	ss5900603622	Oct 16, 2022 (156)
66	EVA	ss5947263231	Oct 16, 2022 (156)
67	1000Genomes	NC_000014.8 - 26479473	Oct 12, 2018 (152)
68	1000Genomes_30x	NC_000014.9 - 26010267	Oct 16, 2022 (156)
69	The Avon Longitudinal Study of Parents and Children	NC_000014.8 - 26479473	Oct 12, 2018 (152)
70	Genetic variation in the Estonian population	NC_000014.8 - 26479473	Oct 12, 2018 (152)
71	The Danish reference pan genome	NC_000014.8 - 26479473	Apr 27, 2020 (154)
72	gnomAD - Genomes	NC_000014.9 - 26010267	Apr 26, 2021 (155)
73	Genome of the Netherlands Release 5	NC_000014.8 - 26479473	Apr 27, 2020 (154)
74	KOREAN population from KRGDB	NC_000014.8 - 26479473	Apr 27, 2020 (154)
75	Korean Genome Project	NC_000014.9 - 26010267	Apr 27, 2020 (154)
76	Northern Sweden	NC_000014.8 - 26479473	Jul 13, 2019 (153)
77	Qatari	NC_000014.8 - 26479473	Apr 27, 2020 (154)
78	SGDP_PRJ	NC_000014.8 - 26479473	Apr 27, 2020 (154)
79	Siberian	NC_000014.8 - 26479473	Apr 27, 2020 (154)
80	8.3KJPN	NC_000014.8 - 26479473	Apr 26, 2021 (155)
81	14KJPN	NC_000014.9 - 26010267	Oct 16, 2022 (156)
82	TopMed	NC_000014.9 - 26010267	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000014.8 - 26479473	Oct 12, 2018 (152)
84	ALFA	NC_000014.9 - 26010267	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)
rs12892406	Mar 10, 2006 (126)
rs58322499	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
37265104, ss3930087710	NC_000014.8:26479472:C:G	NC_000014.9:26010266:C:G	(self)
ss77106627, ss78015513, ss81466161, ss108189574, ss118386122, ss211489499, ss254857011, ss281930752, ss286807928, ss1694939553	NC_000014.7:25549312:C:T	NC_000014.9:26010266:C:T	(self)
63218456, 35117872, 24877981, 3524955, 15684994, 37265104, 13502343, 16366569, 33131163, 8825505, 70368304, 35117872, ss226471928, ss236469531, ss242919017, ss659643373, ss990948566, ss1079505540, ss1350266951, ss1427363984, ss1577132507, ss1631349000, ss1674343033, ss1934324639, ss1967919031, ss2027937114, ss2156309151, ss2700723829, ss2925584746, ss3011899921, ss3350719228, ss3679139733, ss3740217478, ss3752099817, ss3787614498, ss3792661269, ss3797545344, ss3833822570, ss3840503452, ss3881114183, ss3930087710, ss5212398997, ss5414101792, ss5511169130, ss5655844009, ss5840850157, ss5947263231	NC_000014.8:26479472:C:T	NC_000014.9:26010266:C:T	(self)
83033547, 445789027, 30949011, 98799774, 179759455, 3981403136, ss2200457390, ss3027791662, ss3650165054, ss3696314689, ss3817431329, ss3845991263, ss3974571010, ss4964213796, ss5295571447, ss5489693096, ss5595507612, ss5764962670, ss5814590624, ss5850956130, ss5900603622	NC_000014.9:26010266:C:T	NC_000014.9:26010266:C:T	(self)
ss21206369	NT_026437.10:6399600:C:T	NC_000014.9:26010266:C:T	(self)
ss2581573, ss40518612, ss96845862, ss137085697, ss155548991	NT_026437.12:7479472:C:T	NC_000014.9:26010266: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 rs1738879

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

rs1738879