Name: rs1976881
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.

rs1976881

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:79712315 (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>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.120005 (31764/264690, TOPMED)
T=0.115104 (16077/139674, GnomAD)
T=0.02966 (838/28258, 14KJPN) (+ 16 more)
T=0.08566 (1618/18888, ALFA)
T=0.02995 (502/16760, 8.3KJPN)
T=0.1309 (838/6404, 1000G_30x)
T=0.1284 (643/5008, 1000G)
T=0.0502 (225/4478, Estonian)
T=0.0576 (222/3854, ALSPAC)
T=0.0574 (213/3708, TWINSUK)
T=0.0212 (62/2930, KOREAN)
T=0.071 (71/998, GoNL)
T=0.070 (42/600, NorthernSweden)
T=0.060 (33/550, SGDP_PRJ)
T=0.174 (57/328, HapMap)
T=0.116 (25/216, Qatari)
T=0.053 (11/208, Vietnamese)
T=0.04 (2/56, Siberian)
T=0.07 (3/40, 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	18888	T=0.08566	C=0.91434
European	Sub	14284	T=0.05433	C=0.94567
African	Sub	2946	T=0.2400	C=0.7600
African Others	Sub	114	T=0.360	C=0.640
African American	Sub	2832	T=0.2352	C=0.7648
Asian	Sub	112	T=0.045	C=0.955
East Asian	Sub	86	T=0.02	C=0.98
Other Asian	Sub	26	T=0.12	C=0.88
Latin American 1	Sub	146	T=0.137	C=0.863
Latin American 2	Sub	610	T=0.051	C=0.949
South Asian	Sub	98	T=0.11	C=0.89
Other	Sub	692	T=0.098	C=0.902

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=0.120005	C=0.879995
gnomAD - Genomes	Global	Study-wide	139674	T=0.115104	C=0.884896
gnomAD - Genomes	European	Sub	75768	T=0.05555	C=0.94445
gnomAD - Genomes	African	Sub	41710	T=0.24658	C=0.75342
gnomAD - Genomes	American	Sub	13602	T=0.07477	C=0.92523
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.0611	C=0.9389
gnomAD - Genomes	East Asian	Sub	3124	T=0.0368	C=0.9632
gnomAD - Genomes	Other	Sub	2146	T=0.1156	C=0.8844
14KJPN	JAPANESE	Study-wide	28258	T=0.02966	C=0.97034
Allele Frequency Aggregator	Total	Global	18888	T=0.08566	C=0.91434
Allele Frequency Aggregator	European	Sub	14284	T=0.05433	C=0.94567
Allele Frequency Aggregator	African	Sub	2946	T=0.2400	C=0.7600
Allele Frequency Aggregator	Other	Sub	692	T=0.098	C=0.902
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.051	C=0.949
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.137	C=0.863
Allele Frequency Aggregator	Asian	Sub	112	T=0.045	C=0.955
Allele Frequency Aggregator	South Asian	Sub	98	T=0.11	C=0.89
8.3KJPN	JAPANESE	Study-wide	16760	T=0.02995	C=0.97005
1000Genomes_30x	Global	Study-wide	6404	T=0.1309	C=0.8691
1000Genomes_30x	African	Sub	1786	T=0.2660	C=0.7340
1000Genomes_30x	Europe	Sub	1266	T=0.0624	C=0.9376
1000Genomes_30x	South Asian	Sub	1202	T=0.1464	C=0.8536
1000Genomes_30x	East Asian	Sub	1170	T=0.0444	C=0.9556
1000Genomes_30x	American	Sub	980	T=0.057	C=0.943
1000Genomes	Global	Study-wide	5008	T=0.1284	C=0.8716
1000Genomes	African	Sub	1322	T=0.2648	C=0.7352
1000Genomes	East Asian	Sub	1008	T=0.0456	C=0.9544
1000Genomes	Europe	Sub	1006	T=0.0557	C=0.9443
1000Genomes	South Asian	Sub	978	T=0.152	C=0.848
1000Genomes	American	Sub	694	T=0.061	C=0.939
Genetic variation in the Estonian population	Estonian	Study-wide	4478	T=0.0502	C=0.9498
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0576	C=0.9424
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0574	C=0.9426
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0212	A=0.0000, C=0.9788, G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.071	C=0.929
Northern Sweden	ACPOP	Study-wide	600	T=0.070	C=0.930
SGDP_PRJ	Global	Study-wide	550	T=0.060	C=0.940
HapMap	Global	Study-wide	328	T=0.174	C=0.826
HapMap	American	Sub	120	T=0.100	C=0.900
HapMap	African	Sub	118	T=0.339	C=0.661
HapMap	Asian	Sub	90	T=0.06	C=0.94
Qatari	Global	Study-wide	216	T=0.116	C=0.884
A Vietnamese Genetic Variation Database	Global	Study-wide	208	T=0.053	C=0.947
Siberian	Global	Study-wide	56	T=0.04	C=0.96
The Danish reference pan genome	Danish	Study-wide	40	T=0.07	C=0.93

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 1	NC_000001.11:g.79712315T>A
GRCh38.p14 chr 1	NC_000001.11:g.79712315T>C
GRCh38.p14 chr 1	NC_000001.11:g.79712315T>G
GRCh37.p13 chr 1	NC_000001.10:g.80178000T>A
GRCh37.p13 chr 1	NC_000001.10:g.80178000T>C
GRCh37.p13 chr 1	NC_000001.10:g.80178000T>G

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=	A	C	G
GRCh38.p14 chr 1	NC_000001.11:g.79712315=	NC_000001.11:g.79712315T>A	NC_000001.11:g.79712315T>C	NC_000001.11:g.79712315T>G
GRCh37.p13 chr 1	NC_000001.10:g.80178000=	NC_000001.10:g.80178000T>A	NC_000001.10:g.80178000T>C	NC_000001.10:g.80178000T>G

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#.

79 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2881734	Jan 12, 2001 (92)
2	SC_JCM	ss6116243	Feb 20, 2003 (111)
3	CSHL-HAPMAP	ss17328072	Feb 27, 2004 (120)
4	CSHL-HAPMAP	ss19099496	Feb 27, 2004 (120)
5	SSAHASNP	ss20481200	Apr 05, 2004 (121)
6	ABI	ss41080601	Mar 14, 2006 (126)
7	ILLUMINA	ss65809531	Oct 15, 2006 (127)
8	HGSV	ss83359467	Dec 15, 2007 (130)
9	BCMHGSC_JDW	ss87566736	Mar 23, 2008 (129)
10	HUMANGENOME_JCVI	ss97951111	Feb 05, 2009 (130)
11	BGI	ss106579834	Feb 05, 2009 (130)
12	1000GENOMES	ss108343403	Jan 23, 2009 (130)
13	ILLUMINA-UK	ss118834313	Feb 14, 2009 (130)
14	ENSEMBL	ss138016135	Dec 01, 2009 (131)
15	ENSEMBL	ss138886829	Dec 01, 2009 (131)
16	GMI	ss155234423	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss164626166	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss166739438	Jul 04, 2010 (132)
19	BUSHMAN	ss198671649	Jul 04, 2010 (132)
20	BCM-HGSC-SUB	ss205142881	Jul 04, 2010 (132)
21	1000GENOMES	ss210567261	Jul 14, 2010 (132)
22	1000GENOMES	ss218477768	Jul 14, 2010 (132)
23	1000GENOMES	ss230602167	Jul 14, 2010 (132)
24	1000GENOMES	ss238281860	Jul 15, 2010 (132)
25	BL	ss253215321	May 09, 2011 (134)
26	GMI	ss275892308	May 04, 2012 (137)
27	GMI	ss284080584	Apr 25, 2013 (138)
28	PJP	ss290545755	May 09, 2011 (134)
29	TISHKOFF	ss554298829	Apr 25, 2013 (138)
30	SSMP	ss648157490	Apr 25, 2013 (138)
31	EVA-GONL	ss975337640	Aug 21, 2014 (142)
32	JMKIDD_LAB	ss1068022524	Aug 21, 2014 (142)
33	1000GENOMES	ss1291570462	Aug 21, 2014 (142)
34	DDI	ss1425867285	Apr 01, 2015 (144)
35	EVA_GENOME_DK	ss1574175639	Apr 01, 2015 (144)
36	EVA_DECODE	ss1584711358	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1600530980	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1643525013	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1794613567	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1918542179	Feb 12, 2016 (147)
41	GENOMED	ss1966787784	Jul 19, 2016 (147)
42	JJLAB	ss2019791209	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2147807363	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2163926461	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2624406378	Nov 08, 2017 (151)
46	GRF	ss2697727762	Nov 08, 2017 (151)
47	GNOMAD	ss2757086840	Nov 08, 2017 (151)
48	SWEGEN	ss2987084620	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3023657665	Nov 08, 2017 (151)
50	CSHL	ss3343531555	Nov 08, 2017 (151)
51	URBANLAB	ss3646700086	Oct 11, 2018 (152)
52	EGCUT_WGS	ss3655163605	Jul 12, 2019 (153)
53	EVA_DECODE	ss3687102387	Jul 12, 2019 (153)
54	ACPOP	ss3727194515	Jul 12, 2019 (153)
55	EVA	ss3746409188	Jul 12, 2019 (153)
56	PACBIO	ss3783456647	Jul 12, 2019 (153)
57	PACBIO	ss3789107776	Jul 12, 2019 (153)
58	PACBIO	ss3793980530	Jul 12, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3799415075	Jul 12, 2019 (153)
60	EVA	ss3826257864	Apr 25, 2020 (154)
61	EVA	ss3836517372	Apr 25, 2020 (154)
62	EVA	ss3841924395	Apr 25, 2020 (154)
63	SGDP_PRJ	ss3849197622	Apr 25, 2020 (154)
64	KRGDB	ss3894245244	Apr 25, 2020 (154)
65	TOPMED	ss4455826581	Apr 25, 2021 (155)
66	TOMMO_GENOMICS	ss5144702667	Apr 25, 2021 (155)
67	1000G_HIGH_COVERAGE	ss5242854028	Oct 12, 2022 (156)
68	EVA	ss5319814983	Oct 12, 2022 (156)
69	HUGCELL_USP	ss5443859431	Oct 12, 2022 (156)
70	EVA	ss5505913461	Oct 12, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5515446104	Oct 12, 2022 (156)
72	SANFORD_IMAGENETICS	ss5625865036	Oct 12, 2022 (156)
73	TOMMO_GENOMICS	ss5669689668	Oct 12, 2022 (156)
74	YY_MCH	ss5800741560	Oct 12, 2022 (156)
75	EVA	ss5832184871	Oct 12, 2022 (156)
76	EVA	ss5848977063	Oct 12, 2022 (156)
77	EVA	ss5908938855	Oct 12, 2022 (156)
78	EVA	ss5937712047	Oct 12, 2022 (156)
79	EVA	ss5979967091	Oct 12, 2022 (156)
80	1000Genomes	NC_000001.10 - 80178000	Oct 11, 2018 (152)
81	1000Genomes_30x	NC_000001.11 - 79712315	Oct 12, 2022 (156)
82	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 80178000	Oct 11, 2018 (152)
83	Genetic variation in the Estonian population	NC_000001.10 - 80178000	Oct 11, 2018 (152)
84	The Danish reference pan genome	NC_000001.10 - 80178000	Apr 25, 2020 (154)
85	gnomAD - Genomes	NC_000001.11 - 79712315	Apr 25, 2021 (155)
86	Genome of the Netherlands Release 5	NC_000001.10 - 80178000	Apr 25, 2020 (154)
87	HapMap	NC_000001.11 - 79712315	Apr 25, 2020 (154)
88	KOREAN population from KRGDB	NC_000001.10 - 80178000	Apr 25, 2020 (154)
89	Northern Sweden	NC_000001.10 - 80178000	Jul 12, 2019 (153)
90	Qatari	NC_000001.10 - 80178000	Apr 25, 2020 (154)
91	SGDP_PRJ	NC_000001.10 - 80178000	Apr 25, 2020 (154)
92	Siberian	NC_000001.10 - 80178000	Apr 25, 2020 (154)
93	8.3KJPN	NC_000001.10 - 80178000	Apr 25, 2021 (155)
94	14KJPN	NC_000001.11 - 79712315	Oct 12, 2022 (156)
95	TopMed	NC_000001.11 - 79712315	Apr 25, 2021 (155)
96	UK 10K study - Twins	NC_000001.10 - 80178000	Oct 11, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000001.10 - 80178000	Jul 12, 2019 (153)
98	ALFA	NC_000001.11 - 79712315	Apr 25, 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)
rs59315557	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
1422638, ss3894245244	NC_000001.10:80177999:T:A	NC_000001.11:79712314:T:A	(self)
ss83359467	NC_000001.8:79890020:T:C	NC_000001.11:79712314:T:C	(self)
ss87566736, ss108343403, ss118834313, ss164626166, ss166739438, ss198671649, ss205142881, ss210567261, ss253215321, ss275892308, ss284080584, ss290545755, ss1584711358	NC_000001.9:79950587:T:C	NC_000001.11:79712314:T:C	(self)
2313640, 1268825, 901853, 1572043, 545165, 1422638, 479380, 584109, 1214602, 323717, 2671974, 1268825, 269315, ss218477768, ss230602167, ss238281860, ss554298829, ss648157490, ss975337640, ss1068022524, ss1291570462, ss1425867285, ss1574175639, ss1600530980, ss1643525013, ss1794613567, ss1918542179, ss1966787784, ss2019791209, ss2147807363, ss2624406378, ss2697727762, ss2757086840, ss2987084620, ss3343531555, ss3655163605, ss3727194515, ss3746409188, ss3783456647, ss3789107776, ss3793980530, ss3826257864, ss3836517372, ss3849197622, ss3894245244, ss5144702667, ss5319814983, ss5505913461, ss5625865036, ss5832184871, ss5937712047, ss5979967091	NC_000001.10:80177999:T:C	NC_000001.11:79712314:T:C	(self)
2972039, 16346412, 106823, 3526772, 19432916, 4373355694, ss2163926461, ss3023657665, ss3646700086, ss3687102387, ss3799415075, ss3841924395, ss4455826581, ss5242854028, ss5443859431, ss5515446104, ss5669689668, ss5800741560, ss5848977063, ss5908938855	NC_000001.11:79712314:T:C	NC_000001.11:79712314:T:C	(self)
ss17328072, ss19099496, ss20481200	NT_026943.13:4998173:T:C	NC_000001.11:79712314:T:C	(self)
ss2881734, ss6116243, ss41080601, ss65809531, ss97951111, ss106579834, ss138016135, ss138886829, ss155234423	NT_032977.9:50149917:T:C	NC_000001.11:79712314:T:C	(self)
1422638, ss3894245244	NC_000001.10:80177999:T:G	NC_000001.11:79712314:T:G	(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 rs1976881

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

rs1976881