Name: rs1320753
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.

rs1320753

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:189959144 (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: G=0.484797 (128321/264690, TOPMED)
G=0.47509 (28376/59728, ALFA)
A=0.40508 (11446/28256, 14KJPN) (+ 19 more)
A=0.40388 (6769/16760, 8.3KJPN)
A=0.4641 (2972/6404, 1000G_30x)
A=0.4601 (2304/5008, 1000G)
G=0.3605 (1615/4480, Estonian)
G=0.4598 (1772/3854, ALSPAC)
G=0.4563 (1692/3708, TWINSUK)
A=0.3812 (1117/2930, KOREAN)
A=0.4909 (1023/2084, HGDP_Stanford)
A=0.4841 (914/1888, HapMap)
A=0.4028 (738/1832, Korea1K)
G=0.446 (445/998, GoNL)
A=0.488 (293/600, NorthernSweden)
G=0.331 (117/354, SGDP_PRJ)
A=0.495 (107/216, Qatari)
A=0.350 (75/214, Vietnamese)
G=0.24 (11/46, Siberian)
G=0.47 (19/40, GENOME_DK)
G=0.5 (4/8, Ancient Sardinia)
A=0.5 (4/8, Ancient Sardinia)

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	59728	G=0.47509	A=0.52491, T=0.00000
European	Sub	50568	G=0.45527	A=0.54473, T=0.00000
African	Sub	2432	G=0.6476	A=0.3524, T=0.0000
African Others	Sub	96	G=0.73	A=0.27, T=0.00
African American	Sub	2336	G=0.6443	A=0.3557, T=0.0000
Asian	Sub	110	G=0.755	A=0.245, T=0.000
East Asian	Sub	88	G=0.78	A=0.22, T=0.00
Other Asian	Sub	22	G=0.64	A=0.36, T=0.00
Latin American 1	Sub	138	G=0.609	A=0.391, T=0.000
Latin American 2	Sub	774	G=0.557	A=0.443, T=0.000
South Asian	Sub	4894	G=0.5537	A=0.4463, T=0.0000
Other	Sub	812	G=0.580	A=0.420, 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=0.484797	A=0.515203
Allele Frequency Aggregator	Total	Global	59728	G=0.47509	A=0.52491, T=0.00000
Allele Frequency Aggregator	European	Sub	50568	G=0.45527	A=0.54473, T=0.00000
Allele Frequency Aggregator	South Asian	Sub	4894	G=0.5537	A=0.4463, T=0.0000
Allele Frequency Aggregator	African	Sub	2432	G=0.6476	A=0.3524, T=0.0000
Allele Frequency Aggregator	Other	Sub	812	G=0.580	A=0.420, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	774	G=0.557	A=0.443, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	138	G=0.609	A=0.391, T=0.000
Allele Frequency Aggregator	Asian	Sub	110	G=0.755	A=0.245, T=0.000
14KJPN	JAPANESE	Study-wide	28256	G=0.59492	A=0.40508
8.3KJPN	JAPANESE	Study-wide	16760	G=0.59612	A=0.40388
1000Genomes_30x	Global	Study-wide	6404	G=0.5359	A=0.4641
1000Genomes_30x	African	Sub	1786	G=0.4793	A=0.5207
1000Genomes_30x	Europe	Sub	1266	G=0.4526	A=0.5474
1000Genomes_30x	South Asian	Sub	1202	G=0.5699	A=0.4301
1000Genomes_30x	East Asian	Sub	1170	G=0.6256	A=0.3744
1000Genomes_30x	American	Sub	980	G=0.598	A=0.402
1000Genomes	Global	Study-wide	5008	G=0.5399	A=0.4601
1000Genomes	African	Sub	1322	G=0.4705	A=0.5295
1000Genomes	East Asian	Sub	1008	G=0.6240	A=0.3760
1000Genomes	Europe	Sub	1006	G=0.4573	A=0.5427
1000Genomes	South Asian	Sub	978	G=0.586	A=0.414
1000Genomes	American	Sub	694	G=0.605	A=0.395
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.3605	A=0.6395
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.4598	A=0.5402
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.4563	A=0.5437
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.6188	A=0.3812, C=0.0000
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	G=0.5091	A=0.4909
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	G=0.594	A=0.406
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	G=0.486	A=0.514
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	G=0.520	A=0.480
HGDP-CEPH-db Supplement 1	Europe	Sub	320	G=0.428	A=0.572
HGDP-CEPH-db Supplement 1	Africa	Sub	242	G=0.442	A=0.558
HGDP-CEPH-db Supplement 1	America	Sub	216	G=0.384	A=0.616
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	G=1.00	A=0.00
HapMap	Global	Study-wide	1888	G=0.5159	A=0.4841
HapMap	American	Sub	768	G=0.510	A=0.490
HapMap	African	Sub	690	G=0.493	A=0.507
HapMap	Asian	Sub	254	G=0.626	A=0.374
HapMap	Europe	Sub	176	G=0.472	A=0.528
Korean Genome Project	KOREAN	Study-wide	1832	G=0.5972	A=0.4028
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.446	A=0.554
Northern Sweden	ACPOP	Study-wide	600	G=0.512	A=0.488
SGDP_PRJ	Global	Study-wide	354	G=0.331	A=0.669
Qatari	Global	Study-wide	216	G=0.505	A=0.495
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.650	A=0.350
Siberian	Global	Study-wide	46	G=0.24	A=0.76
The Danish reference pan genome	Danish	Study-wide	40	G=0.47	A=0.53
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	8	G=0.5	A=0.5

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.189959144G>A
GRCh38.p14 chr 1	NC_000001.11:g.189959144G>C
GRCh38.p14 chr 1	NC_000001.11:g.189959144G>T
GRCh37.p13 chr 1	NC_000001.10:g.189928274G>A
GRCh37.p13 chr 1	NC_000001.10:g.189928274G>C
GRCh37.p13 chr 1	NC_000001.10:g.189928274G>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.189959144=	NC_000001.11:g.189959144G>A	NC_000001.11:g.189959144G>C	NC_000001.11:g.189959144G>T
GRCh37.p13 chr 1	NC_000001.10:g.189928274=	NC_000001.10:g.189928274G>A	NC_000001.10:g.189928274G>C	NC_000001.10:g.189928274G>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#.

94 SubSNP, 23 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2089182	Oct 23, 2000 (88)
2	CSHL-HAPMAP	ss19852883	Feb 27, 2004 (120)
3	PERLEGEN	ss24238057	Sep 20, 2004 (123)
4	ABI	ss43819452	Mar 15, 2006 (126)
5	ILLUMINA	ss66768987	Dec 01, 2006 (127)
6	ILLUMINA	ss67064495	Dec 01, 2006 (127)
7	ILLUMINA	ss67392757	Dec 01, 2006 (127)
8	ILLUMINA	ss70420687	May 17, 2007 (127)
9	ILLUMINA	ss70597790	May 26, 2008 (130)
10	ILLUMINA	ss71142455	May 17, 2007 (127)
11	ILLUMINA	ss75768676	Dec 06, 2007 (129)
12	KRIBB_YJKIM	ss83717757	Dec 15, 2007 (130)
13	BCMHGSC_JDW	ss87909726	Mar 23, 2008 (129)
14	BGI	ss102806725	Dec 01, 2009 (131)
15	1000GENOMES	ss108796302	Jan 23, 2009 (130)
16	ILLUMINA-UK	ss119147486	Feb 15, 2009 (130)
17	ILLUMINA	ss121627541	Dec 01, 2009 (131)
18	ENSEMBL	ss138123893	Dec 01, 2009 (131)
19	ENSEMBL	ss142870747	Dec 01, 2009 (131)
20	ILLUMINA	ss153335113	Dec 01, 2009 (131)
21	GMI	ss156061371	Dec 01, 2009 (131)
22	ILLUMINA	ss159248904	Dec 01, 2009 (131)
23	COMPLETE_GENOMICS	ss165589755	Jul 04, 2010 (132)
24	ILLUMINA	ss170316580	Jul 04, 2010 (132)
25	ILLUMINA	ss172354455	Jul 04, 2010 (132)
26	BUSHMAN	ss199391501	Jul 04, 2010 (132)
27	BCM-HGSC-SUB	ss205163160	Jul 04, 2010 (132)
28	1000GENOMES	ss210696682	Jul 14, 2010 (132)
29	1000GENOMES	ss218784819	Jul 14, 2010 (132)
30	1000GENOMES	ss230828681	Jul 14, 2010 (132)
31	1000GENOMES	ss238455456	Jul 15, 2010 (132)
32	BL	ss253694797	May 09, 2011 (134)
33	GMI	ss276145052	May 04, 2012 (137)
34	PJP	ss290687559	May 09, 2011 (134)
35	TISHKOFF	ss554974583	Apr 25, 2013 (138)
36	SSMP	ss648576477	Apr 25, 2013 (138)
37	ILLUMINA	ss825389961	Apr 01, 2015 (144)
38	ILLUMINA	ss832761176	Jul 12, 2019 (153)
39	EVA-GONL	ss975942309	Aug 21, 2014 (142)
40	JMKIDD_LAB	ss1068459487	Aug 21, 2014 (142)
41	1000GENOMES	ss1293908071	Aug 21, 2014 (142)
42	DDI	ss1426054748	Apr 01, 2015 (144)
43	EVA_GENOME_DK	ss1574555366	Apr 01, 2015 (144)
44	EVA_DECODE	ss1585335547	Apr 01, 2015 (144)
45	EVA_UK10K_ALSPAC	ss1601738592	Apr 01, 2015 (144)
46	EVA_UK10K_TWINSUK	ss1644732625	Apr 01, 2015 (144)
47	EVA_SVP	ss1712390582	Apr 01, 2015 (144)
48	HAMMER_LAB	ss1795459590	Sep 08, 2015 (146)
49	WEILL_CORNELL_DGM	ss1919177230	Feb 12, 2016 (147)
50	GENOMED	ss1966926860	Jul 19, 2016 (147)
51	JJLAB	ss2020105857	Sep 14, 2016 (149)
52	USC_VALOUEV	ss2148132975	Dec 20, 2016 (150)
53	HUMAN_LONGEVITY	ss2168556968	Dec 20, 2016 (150)
54	SYSTEMSBIOZJU	ss2624560890	Nov 08, 2017 (151)
55	GRF	ss2698118724	Nov 08, 2017 (151)
56	GNOMAD	ss2764098408	Nov 08, 2017 (151)
57	SWEGEN	ss2988146748	Nov 08, 2017 (151)
58	BIOINF_KMB_FNS_UNIBA	ss3023812336	Nov 08, 2017 (151)
59	CSHL	ss3343825404	Nov 08, 2017 (151)
60	ILLUMINA	ss3637802914	Oct 11, 2018 (152)
61	ILLUMINA	ss3638917265	Oct 11, 2018 (152)
62	ILLUMINA	ss3639457190	Oct 11, 2018 (152)
63	ILLUMINA	ss3642810592	Oct 11, 2018 (152)
64	URBANLAB	ss3646845424	Oct 11, 2018 (152)
65	EGCUT_WGS	ss3656100627	Jul 12, 2019 (153)
66	EVA_DECODE	ss3688259863	Jul 12, 2019 (153)
67	ACPOP	ss3727698161	Jul 12, 2019 (153)
68	EVA	ss3747107373	Jul 12, 2019 (153)
69	PACBIO	ss3783636410	Jul 12, 2019 (153)
70	PACBIO	ss3789256575	Jul 12, 2019 (153)
71	PACBIO	ss3794128729	Jul 12, 2019 (153)
72	KHV_HUMAN_GENOMES	ss3800112009	Jul 12, 2019 (153)
73	EVA	ss3826551291	Apr 25, 2020 (154)
74	EVA	ss3836672766	Apr 25, 2020 (154)
75	EVA	ss3842083391	Apr 25, 2020 (154)
76	HGDP	ss3847357429	Apr 25, 2020 (154)
77	SGDP_PRJ	ss3850513518	Apr 25, 2020 (154)
78	KRGDB	ss3895782217	Apr 25, 2020 (154)
79	KOGIC	ss3946128462	Apr 25, 2020 (154)
80	EVA	ss3984840834	Apr 25, 2021 (155)
81	TOPMED	ss4476969770	Apr 25, 2021 (155)
82	TOMMO_GENOMICS	ss5147585550	Apr 25, 2021 (155)
83	1000G_HIGH_COVERAGE	ss5245146292	Oct 12, 2022 (156)
84	EVA	ss5323606965	Oct 12, 2022 (156)
85	HUGCELL_USP	ss5445645999	Oct 12, 2022 (156)
86	EVA	ss5506120584	Oct 12, 2022 (156)
87	1000G_HIGH_COVERAGE	ss5518909451	Oct 12, 2022 (156)
88	SANFORD_IMAGENETICS	ss5627078679	Oct 12, 2022 (156)
89	TOMMO_GENOMICS	ss5675101189	Oct 12, 2022 (156)
90	YY_MCH	ss5801473890	Oct 12, 2022 (156)
91	EVA	ss5833001620	Oct 12, 2022 (156)
92	EVA	ss5849207002	Oct 12, 2022 (156)
93	EVA	ss5911227352	Oct 12, 2022 (156)
94	EVA	ss5938898246	Oct 12, 2022 (156)
95	1000Genomes	NC_000001.10 - 189928274	Oct 11, 2018 (152)
96	1000Genomes_30x	NC_000001.11 - 189959144	Oct 12, 2022 (156)
97	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 189928274	Oct 11, 2018 (152)
98	Genetic variation in the Estonian population	NC_000001.10 - 189928274	Oct 11, 2018 (152)
99	The Danish reference pan genome	NC_000001.10 - 189928274	Apr 25, 2020 (154)
100	gnomAD - Genomes Submission ignored due to conflicting rows: Row 34138705 (NC_000001.11:189959143:G:A 74452/139800) Row 34138706 (NC_000001.11:189959143:G:T 19/139852)	-	Apr 25, 2021 (155)
101	gnomAD - Genomes Submission ignored due to conflicting rows: Row 34138705 (NC_000001.11:189959143:G:A 74452/139800) Row 34138706 (NC_000001.11:189959143:G:T 19/139852)	-	Apr 25, 2021 (155)
102	Genome of the Netherlands Release 5	NC_000001.10 - 189928274	Apr 25, 2020 (154)
103	HGDP-CEPH-db Supplement 1	NC_000001.9 - 188194897	Apr 25, 2020 (154)
104	HapMap	NC_000001.11 - 189959144	Apr 25, 2020 (154)
105	KOREAN population from KRGDB	NC_000001.10 - 189928274	Apr 25, 2020 (154)
106	Korean Genome Project	NC_000001.11 - 189959144	Apr 25, 2020 (154)
107	Northern Sweden	NC_000001.10 - 189928274	Jul 12, 2019 (153)
108	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 189928274	Apr 25, 2021 (155)
109	Qatari	NC_000001.10 - 189928274	Apr 25, 2020 (154)
110	SGDP_PRJ	NC_000001.10 - 189928274	Apr 25, 2020 (154)
111	Siberian	NC_000001.10 - 189928274	Apr 25, 2020 (154)
112	8.3KJPN	NC_000001.10 - 189928274	Apr 25, 2021 (155)
113	14KJPN	NC_000001.11 - 189959144	Oct 12, 2022 (156)
114	TopMed	NC_000001.11 - 189959144	Apr 25, 2021 (155)
115	UK 10K study - Twins	NC_000001.10 - 189928274	Oct 11, 2018 (152)
116	A Vietnamese Genetic Variation Database	NC_000001.10 - 189928274	Jul 12, 2019 (153)
117	ALFA	NC_000001.11 - 189959144	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)
rs17373585	Oct 07, 2004 (123)
rs60400025	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss3638917265, ss3639457190	NC_000001.8:186659930:G:A	NC_000001.11:189959143:G:A	(self)
35321, ss87909726, ss108796302, ss119147486, ss165589755, ss199391501, ss205163160, ss210696682, ss253694797, ss276145052, ss290687559, ss825389961, ss1585335547, ss1712390582, ss3642810592, ss3847357429	NC_000001.9:188194896:G:A	NC_000001.11:189959143:G:A	(self)
4735305, 2597295, 1838875, 1809213, 1131143, 2959611, 983026, 66761, 1219160, 2530498, 649329, 5554857, 2597295, 559016, ss218784819, ss230828681, ss238455456, ss554974583, ss648576477, ss832761176, ss975942309, ss1068459487, ss1293908071, ss1426054748, ss1574555366, ss1601738592, ss1644732625, ss1795459590, ss1919177230, ss1966926860, ss2020105857, ss2148132975, ss2624560890, ss2698118724, ss2764098408, ss2988146748, ss3343825404, ss3637802914, ss3656100627, ss3727698161, ss3747107373, ss3783636410, ss3789256575, ss3794128729, ss3826551291, ss3836672766, ss3850513518, ss3895782217, ss3984840834, ss5147585550, ss5323606965, ss5506120584, ss5627078679, ss5833001620, ss5938898246	NC_000001.10:189928273:G:A	NC_000001.11:189959143:G:A	(self)
6435386, 227864, 2506463, 8938293, 40576105, 6404762443, ss2168556968, ss3023812336, ss3646845424, ss3688259863, ss3800112009, ss3842083391, ss3946128462, ss4476969770, ss5245146292, ss5445645999, ss5518909451, ss5675101189, ss5801473890, ss5849207002, ss5911227352	NC_000001.11:189959143:G:A	NC_000001.11:189959143:G:A	(self)
ss2089182, ss24238057, ss43819452, ss66768987, ss67064495, ss67392757, ss70420687, ss70597790, ss71142455, ss75768676, ss83717757, ss102806725, ss121627541, ss138123893, ss142870747, ss153335113, ss156061371, ss159248904, ss170316580, ss172354455	NT_004487.19:41416915:G:A	NC_000001.11:189959143:G:A	(self)
ss19852883	NT_004671.15:1283259:G:A	NC_000001.11:189959143:G:A	(self)
2959611, ss3895782217	NC_000001.10:189928273:G:C	NC_000001.11:189959143:G:C	(self)
ss2764098408	NC_000001.10:189928273:G:T	NC_000001.11:189959143:G:T	(self)
6404762443	NC_000001.11:189959143:G:T	NC_000001.11:189959143: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 rs1320753

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1320753