Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

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.

rs504964

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr20:24214761 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.415535 (109988/264690, TOPMED)
G=0.22061 (6234/28258, 14KJPN)
G=0.21599 (3620/16760, 8.3KJPN) (+ 15 more)
C=0.4367 (4036/9242, ALFA)
G=0.3969 (2542/6404, 1000G_30x)
G=0.3924 (1965/5008, 1000G)
G=0.4174 (1870/4480, Estonian)
G=0.4549 (1753/3854, ALSPAC)
G=0.4550 (1687/3708, TWINSUK)
G=0.2546 (746/2930, KOREAN)
G=0.3571 (635/1778, HapMap)
G=0.465 (464/998, GoNL)
G=0.305 (183/600, NorthernSweden)
G=0.285 (125/438, SGDP_PRJ)
G=0.269 (58/216, Qatari)
G=0.319 (69/216, Vietnamese)
G=0.34 (17/50, Siberian)
C=0.47 (19/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01721 : Intron Variant
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 9242 G=0.5633 A=0.0000, C=0.4367
European Sub 8278 G=0.5387 A=0.0000, C=0.4613
African Sub 426 G=0.805 A=0.000, C=0.195
African Others Sub 14 G=0.64 A=0.00, C=0.36
African American Sub 412 G=0.811 A=0.000, C=0.189
Asian Sub 20 G=0.80 A=0.00, C=0.20
East Asian Sub 14 G=0.86 A=0.00, C=0.14
Other Asian Sub 6 G=0.7 A=0.0, C=0.3
Latin American 1 Sub 16 G=1.00 A=0.00, C=0.00
Latin American 2 Sub 178 G=1.000 A=0.000, C=0.000
South Asian Sub 16 G=0.88 A=0.00, C=0.12
Other Sub 308 G=0.584 A=0.000, C=0.416


Help

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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 G=0.415535 C=0.584465
14KJPN JAPANESE Study-wide 28258 G=0.22061 C=0.77939
8.3KJPN JAPANESE Study-wide 16760 G=0.21599 C=0.78401
Allele Frequency Aggregator Total Global 9242 G=0.5633 A=0.0000, C=0.4367
Allele Frequency Aggregator European Sub 8278 G=0.5387 A=0.0000, C=0.4613
Allele Frequency Aggregator African Sub 426 G=0.805 A=0.000, C=0.195
Allele Frequency Aggregator Other Sub 308 G=0.584 A=0.000, C=0.416
Allele Frequency Aggregator Latin American 2 Sub 178 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 20 G=0.80 A=0.00, C=0.20
Allele Frequency Aggregator Latin American 1 Sub 16 G=1.00 A=0.00, C=0.00
Allele Frequency Aggregator South Asian Sub 16 G=0.88 A=0.00, C=0.12
1000Genomes_30x Global Study-wide 6404 G=0.3969 A=0.0053, C=0.5978
1000Genomes_30x African Sub 1786 G=0.3371 A=0.0185, C=0.6445
1000Genomes_30x Europe Sub 1266 G=0.4463 A=0.0008, C=0.5529
1000Genomes_30x South Asian Sub 1202 G=0.4584 A=0.0000, C=0.5416
1000Genomes_30x East Asian Sub 1170 G=0.3171 A=0.0000, C=0.6829
1000Genomes_30x American Sub 980 G=0.462 A=0.000, C=0.538
1000Genomes Global Study-wide 5008 G=0.3924 A=0.0048, C=0.6028
1000Genomes African Sub 1322 G=0.3290 A=0.0174, C=0.6536
1000Genomes East Asian Sub 1008 G=0.3135 A=0.0000, C=0.6865
1000Genomes Europe Sub 1006 G=0.4483 A=0.0010, C=0.5507
1000Genomes South Asian Sub 978 G=0.453 A=0.000, C=0.547
1000Genomes American Sub 694 G=0.461 A=0.000, C=0.539
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.4174 C=0.5826
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.4549 C=0.5451
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.4550 C=0.5450
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2546 C=0.7454
HapMap Global Study-wide 1778 G=0.3571 C=0.6429
HapMap American Sub 768 G=0.405 C=0.595
HapMap African Sub 582 G=0.313 C=0.687
HapMap Asian Sub 252 G=0.206 C=0.794
HapMap Europe Sub 176 G=0.511 C=0.489
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.465 C=0.535
Northern Sweden ACPOP Study-wide 600 G=0.305 C=0.695
SGDP_PRJ Global Study-wide 438 G=0.285 A=0.005, C=0.710
Qatari Global Study-wide 216 G=0.269 C=0.731
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.319 C=0.681
Siberian Global Study-wide 50 G=0.34 C=0.66
The Danish reference pan genome Danish Study-wide 40 G=0.53 C=0.47
Help

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 20 NC_000020.11:g.24214761G>A
GRCh38.p14 chr 20 NC_000020.11:g.24214761G>C
GRCh37.p13 chr 20 NC_000020.10:g.24195397G>A
GRCh37.p13 chr 20 NC_000020.10:g.24195397G>C
Gene: LINC01721, long intergenic non-protein coding RNA 1721 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01721 transcript NR_040102.1:n. N/A Intron Variant
Help

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
Help

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
GRCh38.p14 chr 20 NC_000020.11:g.24214761= NC_000020.11:g.24214761G>A NC_000020.11:g.24214761G>C
GRCh37.p13 chr 20 NC_000020.10:g.24195397= NC_000020.10:g.24195397G>A NC_000020.10:g.24195397G>C
Help

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#.

80 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss674995 Aug 11, 2000 (83)
2 SC_JCM ss3881721 Sep 28, 2001 (100)
3 SC_SNP ss8344252 Apr 21, 2003 (114)
4 BCM_SSAHASNP ss10963325 Jul 11, 2003 (116)
5 SC_SNP ss18347993 Feb 28, 2004 (123)
6 AFFY ss66470993 Nov 30, 2006 (127)
7 AFFY ss76278073 Dec 07, 2007 (129)
8 HGSV ss78218634 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss81424207 Dec 16, 2007 (130)
10 HGSV ss82666974 Dec 15, 2007 (130)
11 BCMHGSC_JDW ss91672979 Mar 24, 2008 (129)
12 BGI ss106184412 Feb 05, 2009 (130)
13 1000GENOMES ss111888941 Jan 25, 2009 (130)
14 1000GENOMES ss113225786 Jan 25, 2009 (130)
15 ILLUMINA-UK ss117520745 Feb 14, 2009 (130)
16 ENSEMBL ss138226684 Dec 01, 2009 (131)
17 GMI ss156291040 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss168016826 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss169385021 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss172019901 Jul 04, 2010 (132)
21 AFFY ss173099164 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss208579797 Jul 04, 2010 (132)
23 1000GENOMES ss228314343 Jul 14, 2010 (132)
24 1000GENOMES ss237804595 Jul 15, 2010 (132)
25 1000GENOMES ss243982962 Jul 15, 2010 (132)
26 BL ss255555326 May 09, 2011 (134)
27 GMI ss283340797 May 04, 2012 (137)
28 GMI ss287440818 Apr 25, 2013 (138)
29 PJP ss292634588 May 09, 2011 (134)
30 TISHKOFF ss566203737 Apr 25, 2013 (138)
31 SSMP ss662077617 Apr 25, 2013 (138)
32 EVA-GONL ss994648934 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1082154646 Aug 21, 2014 (142)
34 1000GENOMES ss1364471846 Aug 21, 2014 (142)
35 1000GENOMES ss1364471847 Aug 21, 2014 (142)
36 DDI ss1429027425 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1579480712 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1638632290 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1681626323 Apr 01, 2015 (144)
40 EVA_DECODE ss1698708068 Apr 01, 2015 (144)
41 EVA_SVP ss1713689063 Apr 01, 2015 (144)
42 HAMMER_LAB ss1809469965 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1938156265 Feb 12, 2016 (147)
44 GENOMED ss1969117438 Jul 19, 2016 (147)
45 JJLAB ss2029863198 Sep 14, 2016 (149)
46 USC_VALOUEV ss2158415787 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2242153849 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2629426864 Nov 08, 2017 (151)
49 GRF ss2704093302 Nov 08, 2017 (151)
50 GNOMAD ss2966564473 Nov 08, 2017 (151)
51 SWEGEN ss3018028329 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3028764280 Nov 08, 2017 (151)
53 CSHL ss3352467320 Nov 08, 2017 (151)
54 EGCUT_WGS ss3684753453 Jul 13, 2019 (153)
55 EVA_DECODE ss3706759791 Jul 13, 2019 (153)
56 ACPOP ss3743336884 Jul 13, 2019 (153)
57 EVA ss3758552396 Jul 13, 2019 (153)
58 PACBIO ss3788626517 Jul 13, 2019 (153)
59 PACBIO ss3793522795 Jul 13, 2019 (153)
60 PACBIO ss3798409975 Jul 13, 2019 (153)
61 KHV_HUMAN_GENOMES ss3821719153 Jul 13, 2019 (153)
62 KHV_HUMAN_GENOMES ss3821719154 Jul 13, 2019 (153)
63 EVA ss3835639767 Apr 27, 2020 (154)
64 EVA ss3841446368 Apr 27, 2020 (154)
65 EVA ss3846954590 Apr 27, 2020 (154)
66 SGDP_PRJ ss3888943730 Apr 27, 2020 (154)
67 KRGDB ss3939151797 Apr 27, 2020 (154)
68 TOPMED ss5085809123 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5229288806 Apr 26, 2021 (155)
70 1000G_HIGH_COVERAGE ss5308434977 Oct 13, 2022 (156)
71 1000G_HIGH_COVERAGE ss5308434978 Oct 13, 2022 (156)
72 HUGCELL_USP ss5500803787 Oct 13, 2022 (156)
73 HUGCELL_USP ss5500803788 Oct 13, 2022 (156)
74 1000G_HIGH_COVERAGE ss5614698442 Oct 13, 2022 (156)
75 SANFORD_IMAGENETICS ss5663067131 Oct 13, 2022 (156)
76 TOMMO_GENOMICS ss5788401720 Oct 13, 2022 (156)
77 YY_MCH ss5817904675 Oct 13, 2022 (156)
78 EVA ss5845584146 Oct 13, 2022 (156)
79 EVA ss5853112665 Oct 13, 2022 (156)
80 EVA ss5957983383 Oct 13, 2022 (156)
81 1000Genomes NC_000020.10 - 24195397 Oct 12, 2018 (152)
82 1000Genomes_30x NC_000020.11 - 24214761 Oct 13, 2022 (156)
83 The Avon Longitudinal Study of Parents and Children NC_000020.10 - 24195397 Oct 12, 2018 (152)
84 Genetic variation in the Estonian population NC_000020.10 - 24195397 Oct 12, 2018 (152)
85 The Danish reference pan genome NC_000020.10 - 24195397 Apr 27, 2020 (154)
86 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 549366147 (NC_000020.11:24214760:G:A 513/140112)
Row 549366148 (NC_000020.11:24214760:G:C 82713/140052)

- Apr 26, 2021 (155)
87 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 549366147 (NC_000020.11:24214760:G:A 513/140112)
Row 549366148 (NC_000020.11:24214760:G:C 82713/140052)

- Apr 26, 2021 (155)
88 Genome of the Netherlands Release 5 NC_000020.10 - 24195397 Apr 27, 2020 (154)
89 HapMap NC_000020.11 - 24214761 Apr 27, 2020 (154)
90 KOREAN population from KRGDB NC_000020.10 - 24195397 Apr 27, 2020 (154)
91 Northern Sweden NC_000020.10 - 24195397 Jul 13, 2019 (153)
92 Qatari NC_000020.10 - 24195397 Apr 27, 2020 (154)
93 SGDP_PRJ NC_000020.10 - 24195397 Apr 27, 2020 (154)
94 Siberian NC_000020.10 - 24195397 Apr 27, 2020 (154)
95 8.3KJPN NC_000020.10 - 24195397 Apr 26, 2021 (155)
96 14KJPN NC_000020.11 - 24214761 Oct 13, 2022 (156)
97 TopMed NC_000020.11 - 24214761 Apr 26, 2021 (155)
98 UK 10K study - Twins NC_000020.10 - 24195397 Oct 12, 2018 (152)
99 A Vietnamese Genetic Variation Database NC_000020.10 - 24195397 Jul 13, 2019 (153)
100 ALFA NC_000020.11 - 24214761 Apr 26, 2021 (155)
Help

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)
rs12176842 Sep 24, 2004 (123)
rs59160302 May 25, 2008 (130)
rs61709983 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
77924974, 40960710, ss1364471846, ss2966564473, ss3888943730, ss5663067131 NC_000020.10:24195396:G:A NC_000020.11:24214760:G:A (self)
102224377, 368792599, ss2242153849, ss3821719154, ss5308434978, ss5500803788, ss5614698442 NC_000020.11:24214760:G:A NC_000020.11:24214760:G:A (self)
ss66470993, ss76278073, ss78218634, ss82666974, ss91672979, ss111888941, ss113225786, ss117520745, ss168016826, ss169385021, ss172019901, ss173099164, ss208579797, ss255555326, ss283340797, ss287440818, ss292634588, ss1698708068, ss1713689063 NC_000020.9:24143396:G:C NC_000020.11:24214760:G:C (self)
77924974, 43144983, 30491701, 5645651, 19224897, 46329191, 16621749, 20198187, 40960710, 10932141, 87258113, 43144983, 9527023, ss228314343, ss237804595, ss243982962, ss566203737, ss662077617, ss994648934, ss1082154646, ss1364471847, ss1429027425, ss1579480712, ss1638632290, ss1681626323, ss1809469965, ss1938156265, ss1969117438, ss2029863198, ss2158415787, ss2629426864, ss2704093302, ss2966564473, ss3018028329, ss3352467320, ss3684753453, ss3743336884, ss3758552396, ss3788626517, ss3793522795, ss3798409975, ss3835639767, ss3841446368, ss3888943730, ss3939151797, ss5229288806, ss5663067131, ss5845584146, ss5957983383 NC_000020.10:24195396:G:C NC_000020.11:24214760:G:C (self)
102224377, 2102441, 122238824, 360918068, 368792599, ss2242153849, ss3028764280, ss3706759791, ss3821719153, ss3846954590, ss5085809123, ss5308434977, ss5500803787, ss5614698442, ss5788401720, ss5817904675, ss5853112665 NC_000020.11:24214760:G:C NC_000020.11:24214760:G:C (self)
ss674995, ss3881721, ss8344252, ss10963325, ss18347993, ss81424207, ss106184412, ss138226684, ss156291040 NT_011387.8:24135396:G:C NC_000020.11:24214760:G:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs504964

Help

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.

Software version is: 2.0.1.post761+d5e8e07