Name: rs55921549
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.

rs55921549

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:66786562 (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>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.272526 (72135/264690, TOPMED)
C=0.07843 (2216/28256, 14KJPN)
C=0.08085 (1355/16760, 8.3KJPN) (+ 15 more)
C=0.18545 (2449/13206, ALFA)
C=0.2206 (1413/6404, 1000G_30x)
C=0.2147 (1075/5008, 1000G)
C=0.3815 (1709/4480, Estonian)
C=0.3116 (1201/3854, ALSPAC)
C=0.3147 (1167/3708, TWINSUK)
C=0.0722 (211/2922, KOREAN)
C=0.0808 (148/1832, Korea1K)
C=0.287 (286/998, GoNL)
C=0.380 (228/600, NorthernSweden)
C=0.264 (57/216, Qatari)
C=0.090 (19/212, Vietnamese)
G=0.433 (71/164, SGDP_PRJ)
C=0.35 (14/40, GENOME_DK)
G=0.39 (7/18, Siberian)

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	13206	G=0.81455	A=0.00000, C=0.18545, T=0.00000
European	Sub	10586	G=0.77801	A=0.00000, C=0.22199, T=0.00000
African	Sub	1538	G=0.9766	A=0.0000, C=0.0234, T=0.0000
African Others	Sub	64	G=0.95	A=0.00, C=0.05, T=0.00
African American	Sub	1474	G=0.9776	A=0.0000, C=0.0224, T=0.0000
Asian	Sub	96	G=1.00	A=0.00, C=0.00, T=0.00
East Asian	Sub	76	G=1.00	A=0.00, C=0.00, T=0.00
Other Asian	Sub	20	G=1.00	A=0.00, C=0.00, T=0.00
Latin American 1	Sub	84	G=1.00	A=0.00, C=0.00, T=0.00
Latin American 2	Sub	344	G=1.000	A=0.000, C=0.000, T=0.000
South Asian	Sub	66	G=0.97	A=0.00, C=0.03, T=0.00
Other	Sub	492	G=0.876	A=0.000, C=0.124, T=0.000

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=0.727474	C=0.272526
14KJPN	JAPANESE	Study-wide	28256	G=0.92157	C=0.07843
8.3KJPN	JAPANESE	Study-wide	16760	G=0.91915	C=0.08085
Allele Frequency Aggregator	Total	Global	13206	G=0.81455	A=0.00000, C=0.18545, T=0.00000
Allele Frequency Aggregator	European	Sub	10586	G=0.77801	A=0.00000, C=0.22199, T=0.00000
Allele Frequency Aggregator	African	Sub	1538	G=0.9766	A=0.0000, C=0.0234, T=0.0000
Allele Frequency Aggregator	Other	Sub	492	G=0.876	A=0.000, C=0.124, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	344	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	96	G=1.00	A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator	Latin American 1	Sub	84	G=1.00	A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	66	G=0.97	A=0.00, C=0.03, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.7794	C=0.2206
1000Genomes_30x	African	Sub	1786	G=0.7324	C=0.2676
1000Genomes_30x	Europe	Sub	1266	G=0.7038	C=0.2962
1000Genomes_30x	South Asian	Sub	1202	G=0.8245	C=0.1755
1000Genomes_30x	East Asian	Sub	1170	G=0.8991	C=0.1009
1000Genomes_30x	American	Sub	980	G=0.764	C=0.236
1000Genomes	Global	Study-wide	5008	G=0.7853	C=0.2147
1000Genomes	African	Sub	1322	G=0.7330	C=0.2670
1000Genomes	East Asian	Sub	1008	G=0.8988	C=0.1012
1000Genomes	Europe	Sub	1006	G=0.7078	C=0.2922
1000Genomes	South Asian	Sub	978	G=0.827	C=0.173
1000Genomes	American	Sub	694	G=0.774	C=0.226
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.6185	C=0.3815
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6884	C=0.3116
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6853	C=0.3147
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9278	C=0.0722
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9192	C=0.0808
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.713	C=0.287
Northern Sweden	ACPOP	Study-wide	600	G=0.620	C=0.380
Qatari	Global	Study-wide	216	G=0.736	C=0.264
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.910	C=0.090
SGDP_PRJ	Global	Study-wide	164	G=0.433	C=0.567
The Danish reference pan genome	Danish	Study-wide	40	G=0.65	C=0.35
Siberian	Global	Study-wide	18	G=0.39	C=0.61

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.66786562G>A
GRCh38.p14 chr 1	NC_000001.11:g.66786562G>C
GRCh38.p14 chr 1	NC_000001.11:g.66786562G>T
GRCh37.p13 chr 1	NC_000001.10:g.67252245G>A
GRCh37.p13 chr 1	NC_000001.10:g.67252245G>C
GRCh37.p13 chr 1	NC_000001.10:g.67252245G>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	C	T
GRCh38.p14 chr 1	NC_000001.11:g.66786562=	NC_000001.11:g.66786562G>A	NC_000001.11:g.66786562G>C	NC_000001.11:g.66786562G>T
GRCh37.p13 chr 1	NC_000001.10:g.67252245=	NC_000001.10:g.67252245G>A	NC_000001.10:g.67252245G>C	NC_000001.10:g.67252245G>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#.

56 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss79019660	Dec 06, 2007 (129)
2	1000GENOMES	ss108274058	Jan 23, 2009 (130)
3	ILLUMINA-UK	ss118767284	Feb 14, 2009 (130)
4	GMI	ss155119666	Dec 01, 2009 (131)
5	1000GENOMES	ss210545286	Jul 14, 2010 (132)
6	1000GENOMES	ss218430762	Jul 14, 2010 (132)
7	1000GENOMES	ss230568105	Jul 14, 2010 (132)
8	1000GENOMES	ss238256317	Jul 15, 2010 (132)
9	GMI	ss275859470	May 04, 2012 (137)
10	GMI	ss284064776	Apr 25, 2013 (138)
11	PJP	ss290528652	May 09, 2011 (134)
12	TISHKOFF	ss554206554	Apr 25, 2013 (138)
13	SSMP	ss648079352	Apr 25, 2013 (138)
14	EVA-GONL	ss975246426	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1067953428	Aug 21, 2014 (142)
16	1000GENOMES	ss1291219653	Aug 21, 2014 (142)
17	DDI	ss1425837266	Apr 01, 2015 (144)
18	EVA_GENOME_DK	ss1574120392	Apr 01, 2015 (144)
19	EVA_DECODE	ss1584615875	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1600348549	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1643342582	Apr 01, 2015 (144)
22	WEILL_CORNELL_DGM	ss1918454479	Feb 12, 2016 (147)
23	GENOMED	ss1966766418	Jul 19, 2016 (147)
24	JJLAB	ss2019744570	Sep 14, 2016 (149)
25	USC_VALOUEV	ss2147760340	Dec 20, 2016 (150)
26	HUMAN_LONGEVITY	ss2163186116	Dec 20, 2016 (150)
27	GRF	ss2697677954	Nov 08, 2017 (151)
28	GNOMAD	ss2756070278	Nov 08, 2017 (151)
29	SWEGEN	ss2986947915	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3023634052	Nov 08, 2017 (151)
31	CSHL	ss3343492693	Nov 08, 2017 (151)
32	EGCUT_WGS	ss3655017930	Jul 12, 2019 (153)
33	EVA_DECODE	ss3686932944	Jul 12, 2019 (153)
34	ACPOP	ss3727119017	Jul 12, 2019 (153)
35	EVA	ss3746306043	Jul 12, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3799312754	Jul 12, 2019 (153)
37	EVA	ss3826214454	Apr 25, 2020 (154)
38	EVA	ss3836494682	Apr 25, 2020 (154)
39	EVA	ss3841901222	Apr 25, 2020 (154)
40	SGDP_PRJ	ss3849018554	Apr 25, 2020 (154)
41	KRGDB	ss3894045981	Apr 25, 2020 (154)
42	KOGIC	ss3944672467	Apr 25, 2020 (154)
43	TOPMED	ss4452619894	Apr 25, 2021 (155)
44	TOMMO_GENOMICS	ss5144316459	Apr 25, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5242552938	Oct 12, 2022 (156)
46	EVA	ss5319250186	Oct 12, 2022 (156)
47	HUGCELL_USP	ss5443587738	Oct 12, 2022 (156)
48	EVA	ss5505879864	Oct 12, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5514972347	Oct 12, 2022 (156)
50	SANFORD_IMAGENETICS	ss5625691869	Oct 12, 2022 (156)
51	TOMMO_GENOMICS	ss5669193329	Oct 12, 2022 (156)
52	YY_MCH	ss5800667949	Oct 12, 2022 (156)
53	EVA	ss5832069970	Oct 12, 2022 (156)
54	EVA	ss5848941591	Oct 12, 2022 (156)
55	EVA	ss5908588599	Oct 12, 2022 (156)
56	EVA	ss5937530538	Oct 12, 2022 (156)
57	1000Genomes	NC_000001.10 - 67252245	Oct 11, 2018 (152)
58	1000Genomes_30x	NC_000001.11 - 66786562	Oct 12, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 67252245	Oct 11, 2018 (152)
60	Genetic variation in the Estonian population	NC_000001.10 - 67252245	Oct 11, 2018 (152)
61	The Danish reference pan genome	NC_000001.10 - 67252245	Apr 25, 2020 (154)
62	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13748098 (NC_000001.11:66786561:G:A 3/139786) Row 13748099 (NC_000001.11:66786561:G:C 40344/139672) Row 13748100 (NC_000001.11:66786561:G:T 3/139786)	-	Apr 25, 2021 (155)
63	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13748098 (NC_000001.11:66786561:G:A 3/139786) Row 13748099 (NC_000001.11:66786561:G:C 40344/139672) Row 13748100 (NC_000001.11:66786561:G:T 3/139786)	-	Apr 25, 2021 (155)
64	gnomAD - Genomes Submission ignored due to conflicting rows: Row 13748098 (NC_000001.11:66786561:G:A 3/139786) Row 13748099 (NC_000001.11:66786561:G:C 40344/139672) Row 13748100 (NC_000001.11:66786561:G:T 3/139786)	-	Apr 25, 2021 (155)
65	Genome of the Netherlands Release 5	NC_000001.10 - 67252245	Apr 25, 2020 (154)
66	KOREAN population from KRGDB	NC_000001.10 - 67252245	Apr 25, 2020 (154)
67	Korean Genome Project	NC_000001.11 - 66786562	Apr 25, 2020 (154)
68	Northern Sweden	NC_000001.10 - 67252245	Jul 12, 2019 (153)
69	Qatari	NC_000001.10 - 67252245	Apr 25, 2020 (154)
70	SGDP_PRJ	NC_000001.10 - 67252245	Apr 25, 2020 (154)
71	Siberian	NC_000001.10 - 67252245	Apr 25, 2020 (154)
72	8.3KJPN	NC_000001.10 - 67252245	Apr 25, 2021 (155)
73	14KJPN	NC_000001.11 - 66786562	Oct 12, 2022 (156)
74	TopMed	NC_000001.11 - 66786562	Apr 25, 2021 (155)
75	UK 10K study - Twins	NC_000001.10 - 67252245	Oct 11, 2018 (152)
76	A Vietnamese Genetic Variation Database	NC_000001.10 - 67252245	Jul 12, 2019 (153)
77	ALFA	NC_000001.11 - 66786562	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
9216378533	NC_000001.11:66786561:G:A	NC_000001.11:66786561:G:A	(self)
ss79019660	NC_000001.8:66964265:G:C	NC_000001.11:66786561:G:C	(self)
ss108274058, ss118767284, ss210545286, ss275859470, ss284064776, ss290528652, ss1584615875	NC_000001.9:67024832:G:C	NC_000001.11:66786561:G:C	(self)
1949650, 1068207, 756178, 1536015, 455940, 1223375, 403882, 496409, 1035534, 276694, 2285766, 1068207, 223689, ss218430762, ss230568105, ss238256317, ss554206554, ss648079352, ss975246426, ss1067953428, ss1291219653, ss1425837266, ss1574120392, ss1600348549, ss1643342582, ss1918454479, ss1966766418, ss2019744570, ss2147760340, ss2697677954, ss2756070278, ss2986947915, ss3343492693, ss3655017930, ss3727119017, ss3746306043, ss3826214454, ss3836494682, ss3849018554, ss3894045981, ss5144316459, ss5319250186, ss5505879864, ss5625691869, ss5832069970, ss5937530538	NC_000001.10:67252244:G:C	NC_000001.11:66786561:G:C	(self)
2498282, 1050468, 3030433, 16226229, 9216378533, ss2163186116, ss3023634052, ss3686932944, ss3799312754, ss3841901222, ss3944672467, ss4452619894, ss5242552938, ss5443587738, ss5514972347, ss5669193329, ss5800667949, ss5848941591, ss5908588599	NC_000001.11:66786561:G:C	NC_000001.11:66786561:G:C	(self)
ss155119666	NT_032977.9:37224162:G:C	NC_000001.11:66786561:G:C	(self)
9216378533	NC_000001.11:66786561:G:T	NC_000001.11:66786561:G: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 rs55921549

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

rs55921549