Name: rs269307
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.

rs269307

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:52676467 (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>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.283131 (74942/264690, TOPMED)
T=0.298574 (41826/140086, GnomAD)
T=0.01607 (454/28258, 14KJPN) (+ 16 more)
T=0.01504 (252/16760, 8.3KJPN)
T=0.22688 (3013/13280, ALFA)
T=0.2242 (1436/6404, 1000G_30x)
T=0.2224 (1114/5008, 1000G)
T=0.4033 (1807/4480, Estonian)
T=0.3531 (1361/3854, ALSPAC)
T=0.3759 (1394/3708, TWINSUK)
T=0.0291 (85/2922, KOREAN)
T=0.0164 (30/1832, Korea1K)
T=0.329 (328/998, GoNL)
T=0.412 (247/600, NorthernSweden)
T=0.319 (69/216, Qatari)
T=0.019 (4/212, Vietnamese)
C=0.440 (66/150, SGDP_PRJ)
T=0.47 (19/40, GENOME_DK)
C=0.47 (15/32, 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	13280	C=0.77312	A=0.00000, T=0.22688
European	Sub	10214	C=0.72577	A=0.00000, T=0.27423
African	Sub	1978	C=0.9287	A=0.0000, T=0.0713
African Others	Sub	80	C=0.91	A=0.00, T=0.09
African American	Sub	1898	C=0.9294	A=0.0000, T=0.0706
Asian	Sub	110	C=1.000	A=0.000, T=0.000
East Asian	Sub	84	C=1.00	A=0.00, T=0.00
Other Asian	Sub	26	C=1.00	A=0.00, T=0.00
Latin American 1	Sub	76	C=1.00	A=0.00, T=0.00
Latin American 2	Sub	394	C=1.000	A=0.000, T=0.000
South Asian	Sub	42	C=0.98	A=0.00, T=0.02
Other	Sub	466	C=0.850	A=0.000, T=0.150

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=0.716869	T=0.283131
gnomAD - Genomes	Global	Study-wide	140086	C=0.701426	T=0.298574
gnomAD - Genomes	European	Sub	75852	C=0.64675	T=0.35325
gnomAD - Genomes	African	Sub	41996	C=0.76172	T=0.23828
gnomAD - Genomes	American	Sub	13632	C=0.75880	T=0.24120
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.6793	T=0.3207
gnomAD - Genomes	East Asian	Sub	3130	C=0.9824	T=0.0176
gnomAD - Genomes	Other	Sub	2152	C=0.7142	T=0.2858
14KJPN	JAPANESE	Study-wide	28258	C=0.98393	T=0.01607
8.3KJPN	JAPANESE	Study-wide	16760	C=0.98496	T=0.01504
Allele Frequency Aggregator	Total	Global	13280	C=0.77312	A=0.00000, T=0.22688
Allele Frequency Aggregator	European	Sub	10214	C=0.72577	A=0.00000, T=0.27423
Allele Frequency Aggregator	African	Sub	1978	C=0.9287	A=0.0000, T=0.0713
Allele Frequency Aggregator	Other	Sub	466	C=0.850	A=0.000, T=0.150
Allele Frequency Aggregator	Latin American 2	Sub	394	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	110	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	76	C=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	42	C=0.98	A=0.00, T=0.02
1000Genomes_30x	Global	Study-wide	6404	C=0.7758	T=0.2242
1000Genomes_30x	African	Sub	1786	C=0.7895	T=0.2105
1000Genomes_30x	Europe	Sub	1266	C=0.6390	T=0.3610
1000Genomes_30x	South Asian	Sub	1202	C=0.6947	T=0.3053
1000Genomes_30x	East Asian	Sub	1170	C=0.9872	T=0.0128
1000Genomes_30x	American	Sub	980	C=0.774	T=0.226
1000Genomes	Global	Study-wide	5008	C=0.7776	T=0.2224
1000Genomes	African	Sub	1322	C=0.7912	T=0.2088
1000Genomes	East Asian	Sub	1008	C=0.9861	T=0.0139
1000Genomes	Europe	Sub	1006	C=0.6362	T=0.3638
1000Genomes	South Asian	Sub	978	C=0.687	T=0.313
1000Genomes	American	Sub	694	C=0.781	T=0.219
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.5967	T=0.4033
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6469	T=0.3531
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6241	T=0.3759
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9709	T=0.0291
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9836	T=0.0164
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.671	T=0.329
Northern Sweden	ACPOP	Study-wide	600	C=0.588	T=0.412
Qatari	Global	Study-wide	216	C=0.681	T=0.319
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.981	T=0.019
SGDP_PRJ	Global	Study-wide	150	C=0.440	T=0.560
The Danish reference pan genome	Danish	Study-wide	40	C=0.53	T=0.47
Siberian	Global	Study-wide	32	C=0.47	T=0.53

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.52676467C>A
GRCh38.p14 chr 1	NC_000001.11:g.52676467C>T
GRCh37.p13 chr 1	NC_000001.10:g.53142139C>A
GRCh37.p13 chr 1	NC_000001.10:g.53142139C>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=	A	T
GRCh38.p14 chr 1	NC_000001.11:g.52676467=	NC_000001.11:g.52676467C>A	NC_000001.11:g.52676467C>T
GRCh37.p13 chr 1	NC_000001.10:g.53142139=	NC_000001.10:g.53142139C>A	NC_000001.10:g.53142139C>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#.

57 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss350482	Jul 12, 2000 (79)
2	SC_JCM	ss500089	Jul 16, 2000 (87)
3	KWOK	ss1159769	Oct 04, 2000 (86)
4	KWOK	ss1160811	Oct 04, 2000 (86)
5	BCMHGSC_JDW	ss87423941	Mar 23, 2008 (129)
6	COMPLETE_GENOMICS	ss166500225	Jul 04, 2010 (132)
7	BUSHMAN	ss198434572	Jul 04, 2010 (132)
8	BCM-HGSC-SUB	ss205379291	Jul 04, 2010 (132)
9	1000GENOMES	ss210521891	Jul 14, 2010 (132)
10	1000GENOMES	ss218375307	Jul 14, 2010 (132)
11	1000GENOMES	ss230527716	Jul 14, 2010 (132)
12	1000GENOMES	ss238223047	Jul 15, 2010 (132)
13	PJP	ss290507965	May 09, 2011 (134)
14	TISHKOFF	ss554093361	Apr 25, 2013 (138)
15	SSMP	ss647915576	Apr 25, 2013 (138)
16	EVA-GONL	ss975142877	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1067872747	Aug 21, 2014 (142)
18	1000GENOMES	ss1290826315	Aug 21, 2014 (142)
19	DDI	ss1425802279	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1574047572	Apr 01, 2015 (144)
21	EVA_DECODE	ss1584508734	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1600138680	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1643132713	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1794330067	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1918351180	Feb 12, 2016 (147)
26	GENOMED	ss1966741407	Jul 19, 2016 (147)
27	JJLAB	ss2019690229	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2147703880	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2162369321	Dec 20, 2016 (150)
30	GRF	ss2697615398	Nov 08, 2017 (151)
31	GNOMAD	ss2754968412	Nov 08, 2017 (151)
32	SWEGEN	ss2986789896	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3023605609	Nov 08, 2017 (151)
34	CSHL	ss3343446088	Nov 08, 2017 (151)
35	URBANLAB	ss3646659140	Oct 11, 2018 (152)
36	EGCUT_WGS	ss3654853389	Jul 12, 2019 (153)
37	EVA_DECODE	ss3686737815	Jul 12, 2019 (153)
38	ACPOP	ss3727031853	Jul 12, 2019 (153)
39	EVA	ss3746182158	Jul 12, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3799191770	Jul 12, 2019 (153)
41	EVA	ss3826162185	Apr 25, 2020 (154)
42	SGDP_PRJ	ss3848811146	Apr 25, 2020 (154)
43	KRGDB	ss3893816295	Apr 25, 2020 (154)
44	KOGIC	ss3944475166	Apr 25, 2020 (154)
45	TOPMED	ss4449187820	Apr 25, 2021 (155)
46	TOMMO_GENOMICS	ss5143874608	Apr 25, 2021 (155)
47	1000G_HIGH_COVERAGE	ss5242211156	Oct 17, 2022 (156)
48	EVA	ss5318617951	Oct 17, 2022 (156)
49	HUGCELL_USP	ss5443278338	Oct 17, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5514460556	Oct 17, 2022 (156)
51	SANFORD_IMAGENETICS	ss5625495713	Oct 17, 2022 (156)
52	TOMMO_GENOMICS	ss5668624137	Oct 17, 2022 (156)
53	YY_MCH	ss5800580366	Oct 17, 2022 (156)
54	EVA	ss5831935919	Oct 17, 2022 (156)
55	EVA	ss5848897441	Oct 17, 2022 (156)
56	EVA	ss5908192004	Oct 17, 2022 (156)
57	EVA	ss5937326005	Oct 17, 2022 (156)
58	1000Genomes	NC_000001.10 - 53142139	Oct 11, 2018 (152)
59	1000Genomes_30x	NC_000001.11 - 52676467	Oct 17, 2022 (156)
60	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 53142139	Oct 11, 2018 (152)
61	Genetic variation in the Estonian population	NC_000001.10 - 53142139	Oct 11, 2018 (152)
62	The Danish reference pan genome	NC_000001.10 - 53142139	Apr 25, 2020 (154)
63	gnomAD - Genomes	NC_000001.11 - 52676467	Apr 25, 2021 (155)
64	Genome of the Netherlands Release 5	NC_000001.10 - 53142139	Apr 25, 2020 (154)
65	KOREAN population from KRGDB	NC_000001.10 - 53142139	Apr 25, 2020 (154)
66	Korean Genome Project	NC_000001.11 - 52676467	Apr 25, 2020 (154)
67	Northern Sweden	NC_000001.10 - 53142139	Jul 12, 2019 (153)
68	Qatari	NC_000001.10 - 53142139	Apr 25, 2020 (154)
69	SGDP_PRJ	NC_000001.10 - 53142139	Apr 25, 2020 (154)
70	Siberian	NC_000001.10 - 53142139	Apr 25, 2020 (154)
71	8.3KJPN	NC_000001.10 - 53142139	Apr 25, 2021 (155)
72	14KJPN	NC_000001.11 - 52676467	Oct 17, 2022 (156)
73	TopMed	NC_000001.11 - 52676467	Apr 25, 2021 (155)
74	UK 10K study - Twins	NC_000001.10 - 53142139	Oct 11, 2018 (152)
75	A Vietnamese Genetic Variation Database	NC_000001.10 - 53142139	Jul 12, 2019 (153)
76	ALFA	NC_000001.11 - 52676467	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)
rs387588	Oct 23, 2000 (87)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
11277966021	NC_000001.11:52676466:C:A	NC_000001.11:52676466:C:A	(self)
ss87423941, ss166500225, ss198434572, ss205379291, ss210521891, ss290507965, ss1584508734	NC_000001.9:52914726:C:T	NC_000001.11:52676466:C:T	(self)
1542270, 838146, 591637, 1494670, 354963, 993689, 316718, 393110, 828126, 220234, 1843915, 838146, 171264, ss218375307, ss230527716, ss238223047, ss554093361, ss647915576, ss975142877, ss1067872747, ss1290826315, ss1425802279, ss1574047572, ss1600138680, ss1643132713, ss1794330067, ss1918351180, ss1966741407, ss2019690229, ss2147703880, ss2697615398, ss2754968412, ss2986789896, ss3343446088, ss3654853389, ss3727031853, ss3746182158, ss3826162185, ss3848811146, ss3893816295, ss5143874608, ss5318617951, ss5625495713, ss5831935919, ss5937326005	NC_000001.10:53142138:C:T	NC_000001.11:52676466:C:T	(self)
1986491, 10934402, 853167, 2461241, 12794155, 11277966021, ss2162369321, ss3023605609, ss3646659140, ss3686737815, ss3799191770, ss3944475166, ss4449187820, ss5242211156, ss5443278338, ss5514460556, ss5668624137, ss5800580366, ss5848897441, ss5908192004	NC_000001.11:52676466:C:T	NC_000001.11:52676466:C:T	(self)
ss350482, ss500089, ss1159769, ss1160811	NT_032977.9:23114056:C:T	NC_000001.11:52676466: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 rs269307

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

rs269307