Name: rs1320749
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.

rs1320749

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:189973112 (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>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.344274 (91126/264690, TOPMED)
C=0.366376 (51275/139952, GnomAD)
C=0.40218 (11364/28256, 14KJPN) (+ 17 more)
C=0.40066 (6715/16760, 8.3KJPN)
C=0.34613 (4301/12426, ALFA)
C=0.2981 (1909/6404, 1000G_30x)
C=0.3001 (1503/5008, 1000G)
G=0.3848 (1724/4480, Estonian)
C=0.4881 (1881/3854, ALSPAC)
C=0.4906 (1819/3708, TWINSUK)
C=0.3754 (1100/2930, KOREAN)
C=0.2837 (534/1882, HapMap)
C=0.3947 (723/1832, Korea1K)
G=0.497 (496/998, GoNL)
C=0.447 (268/600, NorthernSweden)
G=0.350 (100/286, SGDP_PRJ)
C=0.352 (76/216, Qatari)
C=0.297 (63/212, Vietnamese)
G=0.26 (12/46, Siberian)
C=0.42 (17/40, 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	12426	G=0.65387	C=0.34613, T=0.00000
European	Sub	9162	G=0.5470	C=0.4530, T=0.0000
African	Sub	2512	G=0.9769	C=0.0231, T=0.0000
African Others	Sub	112	G=1.000	C=0.000, T=0.000
African American	Sub	2400	G=0.9758	C=0.0242, T=0.0000
Asian	Sub	40	G=0.97	C=0.03, T=0.00
East Asian	Sub	32	G=1.00	C=0.00, T=0.00
Other Asian	Sub	8	G=0.9	C=0.1, T=0.0
Latin American 1	Sub	62	G=1.00	C=0.00, T=0.00
Latin American 2	Sub	178	G=1.000	C=0.000, T=0.000
South Asian	Sub	46	G=0.96	C=0.04, T=0.00
Other	Sub	426	G=0.789	C=0.211, 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=0.655726	C=0.344274
gnomAD - Genomes	Global	Study-wide	139952	G=0.633624	C=0.366376
gnomAD - Genomes	European	Sub	75786	G=0.49235	C=0.50765
gnomAD - Genomes	African	Sub	41940	G=0.90205	C=0.09795
gnomAD - Genomes	American	Sub	13626	G=0.60238	C=0.39762
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	G=0.5852	C=0.4148
gnomAD - Genomes	East Asian	Sub	3126	G=0.6273	C=0.3727
gnomAD - Genomes	Other	Sub	2152	G=0.6594	C=0.3406
14KJPN	JAPANESE	Study-wide	28256	G=0.59782	C=0.40218
8.3KJPN	JAPANESE	Study-wide	16760	G=0.59934	C=0.40066
Allele Frequency Aggregator	Total	Global	12426	G=0.65387	C=0.34613, T=0.00000
Allele Frequency Aggregator	European	Sub	9162	G=0.5470	C=0.4530, T=0.0000
Allele Frequency Aggregator	African	Sub	2512	G=0.9769	C=0.0231, T=0.0000
Allele Frequency Aggregator	Other	Sub	426	G=0.789	C=0.211, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	178	G=1.000	C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	62	G=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	46	G=0.96	C=0.04, T=0.00
Allele Frequency Aggregator	Asian	Sub	40	G=0.97	C=0.03, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.7019	C=0.2981
1000Genomes_30x	African	Sub	1786	G=0.9681	C=0.0319
1000Genomes_30x	Europe	Sub	1266	G=0.5213	C=0.4787
1000Genomes_30x	South Asian	Sub	1202	G=0.5874	C=0.4126
1000Genomes_30x	East Asian	Sub	1170	G=0.6419	C=0.3581
1000Genomes_30x	American	Sub	980	G=0.662	C=0.338
1000Genomes	Global	Study-wide	5008	G=0.6999	C=0.3001
1000Genomes	African	Sub	1322	G=0.9614	C=0.0386
1000Genomes	East Asian	Sub	1008	G=0.6419	C=0.3581
1000Genomes	Europe	Sub	1006	G=0.5278	C=0.4722
1000Genomes	South Asian	Sub	978	G=0.601	C=0.399
1000Genomes	American	Sub	694	G=0.674	C=0.326
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.3848	C=0.6152
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.5119	C=0.4881
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.5094	C=0.4906
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.6246	C=0.3754
HapMap	Global	Study-wide	1882	G=0.7163	C=0.2837
HapMap	American	Sub	762	G=0.592	C=0.408
HapMap	African	Sub	692	G=0.929	C=0.071
HapMap	Asian	Sub	254	G=0.630	C=0.370
HapMap	Europe	Sub	174	G=0.540	C=0.460
Korean Genome Project	KOREAN	Study-wide	1832	G=0.6053	C=0.3947
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.497	C=0.503
Northern Sweden	ACPOP	Study-wide	600	G=0.553	C=0.447
SGDP_PRJ	Global	Study-wide	286	G=0.350	C=0.650
Qatari	Global	Study-wide	216	G=0.648	C=0.352
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.703	C=0.297
Siberian	Global	Study-wide	46	G=0.26	C=0.74
The Danish reference pan genome	Danish	Study-wide	40	G=0.57	C=0.42

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.189973112G>C
GRCh38.p14 chr 1	NC_000001.11:g.189973112G>T
GRCh37.p13 chr 1	NC_000001.10:g.189942242G>C
GRCh37.p13 chr 1	NC_000001.10:g.189942242G>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=	C	T
GRCh38.p14 chr 1	NC_000001.11:g.189973112=	NC_000001.11:g.189973112G>C	NC_000001.11:g.189973112G>T
GRCh37.p13 chr 1	NC_000001.10:g.189942242=	NC_000001.10:g.189942242G>C	NC_000001.10:g.189942242G>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#.

74 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2089178	Oct 23, 2000 (88)
2	PERLEGEN	ss24238094	Sep 20, 2004 (123)
3	ABI	ss43849164	Mar 15, 2006 (126)
4	AFFY	ss66468988	Nov 30, 2006 (127)
5	PERLEGEN	ss68787501	May 17, 2007 (127)
6	AFFY	ss76274326	Dec 06, 2007 (129)
7	HGSV	ss78270533	Dec 06, 2007 (129)
8	KRIBB_YJKIM	ss81459586	Dec 15, 2007 (130)
9	BCMHGSC_JDW	ss87909779	Mar 23, 2008 (129)
10	HUMANGENOME_JCVI	ss99271635	Feb 06, 2009 (130)
11	BGI	ss102806753	Dec 01, 2009 (131)
12	1000GENOMES	ss108796422	Jan 23, 2009 (130)
13	ENSEMBL	ss131725846	Dec 01, 2009 (131)
14	ENSEMBL	ss138123922	Dec 01, 2009 (131)
15	GMI	ss156061540	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss165589928	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss167382958	Jul 04, 2010 (132)
18	AFFY	ss173069485	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss205197893	Jul 04, 2010 (132)
20	1000GENOMES	ss230828729	Jul 14, 2010 (132)
21	1000GENOMES	ss238455488	Jul 15, 2010 (132)
22	BL	ss253694870	May 09, 2011 (134)
23	GMI	ss276145100	May 04, 2012 (137)
24	PJP	ss290687587	May 09, 2011 (134)
25	TISHKOFF	ss554974670	Apr 25, 2013 (138)
26	SSMP	ss648576544	Apr 25, 2013 (138)
27	EVA-GONL	ss975942434	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1068459565	Aug 21, 2014 (142)
29	1000GENOMES	ss1293908498	Aug 21, 2014 (142)
30	DDI	ss1426054793	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1574555446	Apr 01, 2015 (144)
32	EVA_DECODE	ss1585335681	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1601738813	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1644732846	Apr 01, 2015 (144)
35	EVA_SVP	ss1712390588	Apr 01, 2015 (144)
36	WEILL_CORNELL_DGM	ss1919177327	Feb 12, 2016 (147)
37	GENOMED	ss1966926893	Jul 19, 2016 (147)
38	JJLAB	ss2020105918	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2148133024	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2168557900	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2624560927	Nov 08, 2017 (151)
42	GRF	ss2698118783	Nov 08, 2017 (151)
43	GNOMAD	ss2764099583	Nov 08, 2017 (151)
44	SWEGEN	ss2988146906	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3023812367	Nov 08, 2017 (151)
46	CSHL	ss3343825457	Nov 08, 2017 (151)
47	URBANLAB	ss3646845458	Oct 11, 2018 (152)
48	EGCUT_WGS	ss3656100793	Jul 12, 2019 (153)
49	EVA_DECODE	ss3688260058	Jul 12, 2019 (153)
50	ACPOP	ss3727698245	Jul 12, 2019 (153)
51	EVA	ss3747107491	Jul 12, 2019 (153)
52	PACBIO	ss3783636451	Jul 12, 2019 (153)
53	PACBIO	ss3789256613	Jul 12, 2019 (153)
54	PACBIO	ss3794128767	Jul 12, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3800112131	Jul 12, 2019 (153)
56	EVA	ss3826551349	Apr 25, 2020 (154)
57	EVA	ss3836672808	Apr 25, 2020 (154)
58	EVA	ss3842083433	Apr 25, 2020 (154)
59	SGDP_PRJ	ss3850513725	Apr 25, 2020 (154)
60	KRGDB	ss3895782430	Apr 25, 2020 (154)
61	KOGIC	ss3946128648	Apr 25, 2020 (154)
62	TOPMED	ss4476973584	Apr 25, 2021 (155)
63	TOMMO_GENOMICS	ss5147585983	Apr 25, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5245146628	Oct 12, 2022 (156)
65	EVA	ss5323607661	Oct 12, 2022 (156)
66	HUGCELL_USP	ss5445646322	Oct 12, 2022 (156)
67	1000G_HIGH_COVERAGE	ss5518910075	Oct 12, 2022 (156)
68	SANFORD_IMAGENETICS	ss5627078892	Oct 12, 2022 (156)
69	TOMMO_GENOMICS	ss5675101758	Oct 12, 2022 (156)
70	YY_MCH	ss5801473977	Oct 12, 2022 (156)
71	EVA	ss5833001768	Oct 12, 2022 (156)
72	EVA	ss5849207049	Oct 12, 2022 (156)
73	EVA	ss5911227776	Oct 12, 2022 (156)
74	EVA	ss5938898465	Oct 12, 2022 (156)
75	1000Genomes	NC_000001.10 - 189942242	Oct 11, 2018 (152)
76	1000Genomes_30x	NC_000001.11 - 189973112	Oct 12, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 189942242	Oct 11, 2018 (152)
78	Genetic variation in the Estonian population	NC_000001.10 - 189942242	Oct 11, 2018 (152)
79	The Danish reference pan genome	NC_000001.10 - 189942242	Apr 25, 2020 (154)
80	gnomAD - Genomes	NC_000001.11 - 189973112	Apr 25, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000001.10 - 189942242	Apr 25, 2020 (154)
82	HapMap	NC_000001.11 - 189973112	Apr 25, 2020 (154)
83	KOREAN population from KRGDB	NC_000001.10 - 189942242	Apr 25, 2020 (154)
84	Korean Genome Project	NC_000001.11 - 189973112	Apr 25, 2020 (154)
85	Northern Sweden	NC_000001.10 - 189942242	Jul 12, 2019 (153)
86	Qatari	NC_000001.10 - 189942242	Apr 25, 2020 (154)
87	SGDP_PRJ	NC_000001.10 - 189942242	Apr 25, 2020 (154)
88	Siberian	NC_000001.10 - 189942242	Apr 25, 2020 (154)
89	8.3KJPN	NC_000001.10 - 189942242	Apr 25, 2021 (155)
90	14KJPN	NC_000001.11 - 189973112	Oct 12, 2022 (156)
91	TopMed	NC_000001.11 - 189973112	Apr 25, 2021 (155)
92	UK 10K study - Twins	NC_000001.10 - 189942242	Oct 11, 2018 (152)
93	A Vietnamese Genetic Variation Database	NC_000001.10 - 189942242	Jul 12, 2019 (153)
94	ALFA	NC_000001.11 - 189973112	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)
rs17365187	Oct 07, 2004 (123)
rs59967672	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78270533	NC_000001.8:186673898:G:C	NC_000001.11:189973111:G:C	(self)
ss66468988, ss76274326, ss87909779, ss108796422, ss165589928, ss167382958, ss173069485, ss205197893, ss253694870, ss276145100, ss290687587, ss1585335681, ss1712390588	NC_000001.9:188208864:G:C	NC_000001.11:189973111:G:C	(self)
4735752, 2597537, 1839041, 1809254, 1131268, 2959824, 983110, 1219257, 2530705, 649378, 5555290, 2597537, 559076, ss230828729, ss238455488, ss554974670, ss648576544, ss975942434, ss1068459565, ss1293908498, ss1426054793, ss1574555446, ss1601738813, ss1644732846, ss1919177327, ss1966926893, ss2020105918, ss2148133024, ss2624560927, ss2698118783, ss2764099583, ss2988146906, ss3343825457, ss3656100793, ss3727698245, ss3747107491, ss3783636451, ss3789256613, ss3794128767, ss3826551349, ss3836672808, ss3850513725, ss3895782430, ss5147585983, ss5323607661, ss5627078892, ss5833001768, ss5938898465	NC_000001.10:189942241:G:C	NC_000001.11:189973111:G:C	(self)
6436010, 34141781, 227885, 2506649, 8938862, 40579919, 10900232869, ss2168557900, ss3023812367, ss3646845458, ss3688260058, ss3800112131, ss3842083433, ss3946128648, ss4476973584, ss5245146628, ss5445646322, ss5518910075, ss5675101758, ss5801473977, ss5849207049, ss5911227776	NC_000001.11:189973111:G:C	NC_000001.11:189973111:G:C	(self)
ss2089178, ss24238094, ss43849164, ss68787501, ss81459586, ss99271635, ss102806753, ss131725846, ss138123922, ss156061540	NT_004487.19:41430883:G:C	NC_000001.11:189973111:G:C	(self)
10900232869	NC_000001.11:189973111:G:T	NC_000001.11:189973111: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 rs1320749

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

rs1320749