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.

rs12057144

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:51198526 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.170445 (45115/264690, TOPMED)
G=0.15104 (4268/28258, 14KJPN)
G=0.15400 (2581/16760, 8.3KJPN) (+ 15 more)
G=0.03808 (596/15650, ALFA)
G=0.1710 (1095/6404, 1000G_30x)
G=0.1665 (834/5008, 1000G)
G=0.0759 (340/4480, Estonian)
G=0.0789 (304/3854, ALSPAC)
G=0.0863 (320/3708, TWINSUK)
G=0.0840 (246/2930, KOREAN)
G=0.097 (97/998, GoNL)
G=0.077 (46/600, NorthernSweden)
G=0.004 (2/534, MGP)
G=0.134 (29/216, Qatari)
G=0.023 (5/214, Vietnamese)
A=0.395 (60/152, SGDP_PRJ)
G=0.07 (3/40, GENOME_DK)
A=0.42 (5/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01562 : 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 15650 A=0.96192 G=0.03808, T=0.00000
European Sub 12938 A=0.95873 G=0.04127, T=0.00000
African Sub 1334 A=0.9723 G=0.0277, T=0.0000
African Others Sub 42 A=0.95 G=0.05, T=0.00
African American Sub 1292 A=0.9729 G=0.0271, T=0.0000
Asian Sub 84 A=1.00 G=0.00, T=0.00
East Asian Sub 66 A=1.00 G=0.00, T=0.00
Other Asian Sub 18 A=1.00 G=0.00, T=0.00
Latin American 1 Sub 106 A=1.000 G=0.000, T=0.000
Latin American 2 Sub 534 A=1.000 G=0.000, T=0.000
South Asian Sub 90 A=0.99 G=0.01, T=0.00
Other Sub 564 A=0.957 G=0.043, T=0.000


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 A=0.829555 G=0.170445
14KJPN JAPANESE Study-wide 28258 A=0.84896 G=0.15104
8.3KJPN JAPANESE Study-wide 16760 A=0.84600 G=0.15400
Allele Frequency Aggregator Total Global 15650 A=0.96192 G=0.03808, T=0.00000
Allele Frequency Aggregator European Sub 12938 A=0.95873 G=0.04127, T=0.00000
Allele Frequency Aggregator African Sub 1334 A=0.9723 G=0.0277, T=0.0000
Allele Frequency Aggregator Other Sub 564 A=0.957 G=0.043, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 534 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 106 A=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 90 A=0.99 G=0.01, T=0.00
Allele Frequency Aggregator Asian Sub 84 A=1.00 G=0.00, T=0.00
1000Genomes_30x Global Study-wide 6404 A=0.8289 G=0.1710, T=0.0002
1000Genomes_30x African Sub 1786 A=0.6030 G=0.3964, T=0.0006
1000Genomes_30x Europe Sub 1266 A=0.9123 G=0.0877, T=0.0000
1000Genomes_30x South Asian Sub 1202 A=0.9077 G=0.0923, T=0.0000
1000Genomes_30x East Asian Sub 1170 A=0.9188 G=0.0812, T=0.0000
1000Genomes_30x American Sub 980 A=0.929 G=0.071, T=0.000
1000Genomes Global Study-wide 5008 A=0.8335 G=0.1665
1000Genomes African Sub 1322 A=0.6029 G=0.3971
1000Genomes East Asian Sub 1008 A=0.9117 G=0.0883
1000Genomes Europe Sub 1006 A=0.9155 G=0.0845
1000Genomes South Asian Sub 978 A=0.916 G=0.084
1000Genomes American Sub 694 A=0.924 G=0.076
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9241 G=0.0759
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9211 G=0.0789
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9137 G=0.0863
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.9160 G=0.0840
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.903 G=0.097
Northern Sweden ACPOP Study-wide 600 A=0.923 G=0.077
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.996 G=0.004
Qatari Global Study-wide 216 A=0.866 G=0.134
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.977 G=0.023
SGDP_PRJ Global Study-wide 152 A=0.395 G=0.592, T=0.013
The Danish reference pan genome Danish Study-wide 40 A=0.93 G=0.07
Siberian Global Study-wide 12 A=0.42 G=0.58
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 1 NC_000001.11:g.51198526A>G
GRCh38.p14 chr 1 NC_000001.11:g.51198526A>T
GRCh37.p13 chr 1 NC_000001.10:g.51664198A>G
GRCh37.p13 chr 1 NC_000001.10:g.51664198A>T
Gene: LINC01562, long intergenic non-protein coding RNA 1562 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01562 transcript NR_147076.1: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 A= G T
GRCh38.p14 chr 1 NC_000001.11:g.51198526= NC_000001.11:g.51198526A>G NC_000001.11:g.51198526A>T
GRCh37.p13 chr 1 NC_000001.10:g.51664198= NC_000001.10:g.51664198A>G NC_000001.10:g.51664198A>T
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#.

58 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18135791 Feb 28, 2004 (120)
2 SSAHASNP ss20429371 Apr 05, 2004 (121)
3 HUMANGENOME_JCVI ss99206789 Feb 06, 2009 (130)
4 1000GENOMES ss110420272 Jan 24, 2009 (130)
5 ILLUMINA-UK ss118681208 Dec 01, 2009 (131)
6 ENSEMBL ss138947518 Dec 01, 2009 (131)
7 BUSHMAN ss198425942 Jul 04, 2010 (132)
8 1000GENOMES ss210451065 Jul 14, 2010 (132)
9 1000GENOMES ss218371472 Jul 14, 2010 (132)
10 1000GENOMES ss230525138 Jul 14, 2010 (132)
11 1000GENOMES ss238221604 Jul 15, 2010 (132)
12 GMI ss275817840 May 04, 2012 (137)
13 PJP ss290507103 May 09, 2011 (134)
14 TISHKOFF ss554085691 Apr 25, 2013 (138)
15 SSMP ss647903888 Apr 25, 2013 (138)
16 EVA-GONL ss975133562 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1067866094 Aug 21, 2014 (142)
18 1000GENOMES ss1290788578 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1574043318 Apr 01, 2015 (144)
20 EVA_DECODE ss1584498947 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1600119400 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1643113433 Apr 01, 2015 (144)
23 EVA_MGP ss1710904691 Apr 01, 2015 (144)
24 HAMMER_LAB ss1794320243 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1918342483 Feb 12, 2016 (147)
26 GENOMED ss1966740707 Jul 19, 2016 (147)
27 JJLAB ss2019686007 Sep 14, 2016 (149)
28 USC_VALOUEV ss2147699235 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2162287602 Dec 20, 2016 (150)
30 GRF ss2697611374 Nov 08, 2017 (151)
31 GNOMAD ss2754855929 Nov 08, 2017 (151)
32 SWEGEN ss2986773873 Nov 08, 2017 (151)
33 CSHL ss3343443002 Nov 08, 2017 (151)
34 BIOINF_KMB_FNS_UNIBA ss3645041351 Oct 11, 2018 (152)
35 URBANLAB ss3646657919 Oct 11, 2018 (152)
36 EGCUT_WGS ss3654837647 Jul 12, 2019 (153)
37 EVA_DECODE ss3686719810 Jul 12, 2019 (153)
38 ACPOP ss3727024494 Jul 12, 2019 (153)
39 EVA ss3746171888 Jul 12, 2019 (153)
40 KHV_HUMAN_GENOMES ss3799181338 Jul 12, 2019 (153)
41 EVA ss3826158292 Apr 25, 2020 (154)
42 EVA ss3836467189 Apr 25, 2020 (154)
43 EVA ss3841873124 Apr 25, 2020 (154)
44 SGDP_PRJ ss3848792637 Apr 25, 2020 (154)
45 KRGDB ss3893792961 Apr 25, 2020 (154)
46 TOPMED ss4448838451 Apr 25, 2021 (155)
47 TOMMO_GENOMICS ss5143829247 Apr 25, 2021 (155)
48 1000G_HIGH_COVERAGE ss5242177404 Oct 17, 2022 (156)
49 EVA ss5318557761 Oct 17, 2022 (156)
50 HUGCELL_USP ss5443247859 Oct 17, 2022 (156)
51 1000G_HIGH_COVERAGE ss5514410586 Oct 17, 2022 (156)
52 SANFORD_IMAGENETICS ss5625477782 Oct 17, 2022 (156)
53 TOMMO_GENOMICS ss5668564116 Oct 17, 2022 (156)
54 YY_MCH ss5800573619 Oct 17, 2022 (156)
55 EVA ss5831923416 Oct 17, 2022 (156)
56 EVA ss5848894746 Oct 17, 2022 (156)
57 EVA ss5908153549 Oct 17, 2022 (156)
58 EVA ss5937306821 Oct 17, 2022 (156)
59 1000Genomes NC_000001.10 - 51664198 Oct 11, 2018 (152)
60 1000Genomes_30x NC_000001.11 - 51198526 Oct 17, 2022 (156)
61 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 51664198 Oct 11, 2018 (152)
62 Genetic variation in the Estonian population NC_000001.10 - 51664198 Oct 11, 2018 (152)
63 The Danish reference pan genome NC_000001.10 - 51664198 Apr 25, 2020 (154)
64 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 10645057 (NC_000001.11:51198525:A:G 23114/140162)
Row 10645058 (NC_000001.11:51198525:A:T 10/140206)

- Apr 25, 2021 (155)
65 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 10645057 (NC_000001.11:51198525:A:G 23114/140162)
Row 10645058 (NC_000001.11:51198525:A:T 10/140206)

- Apr 25, 2021 (155)
66 Genome of the Netherlands Release 5 NC_000001.10 - 51664198 Apr 25, 2020 (154)
67 KOREAN population from KRGDB NC_000001.10 - 51664198 Apr 25, 2020 (154)
68 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 51664198 Apr 25, 2020 (154)
69 Northern Sweden NC_000001.10 - 51664198 Jul 12, 2019 (153)
70 Qatari NC_000001.10 - 51664198 Apr 25, 2020 (154)
71 SGDP_PRJ NC_000001.10 - 51664198 Apr 25, 2020 (154)
72 Siberian NC_000001.10 - 51664198 Apr 25, 2020 (154)
73 8.3KJPN NC_000001.10 - 51664198 Apr 25, 2021 (155)
74 14KJPN NC_000001.11 - 51198526 Oct 17, 2022 (156)
75 TopMed NC_000001.11 - 51198526 Apr 25, 2021 (155)
76 UK 10K study - Twins NC_000001.10 - 51664198 Oct 11, 2018 (152)
77 A Vietnamese Genetic Variation Database NC_000001.10 - 51664198 Jul 12, 2019 (153)
78 ALFA NC_000001.11 - 51198526 Apr 25, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss110420272, ss118681208, ss198425942, ss210451065, ss275817840, ss290507103, ss1584498947 NC_000001.9:51436785:A:G NC_000001.11:51198525:A:G (self)
1502912, 816631, 575895, 1491876, 346004, 970355, 21443, 309359, 384413, 809617, 215589, 1798554, 816631, 168033, ss218371472, ss230525138, ss238221604, ss554085691, ss647903888, ss975133562, ss1067866094, ss1290788578, ss1574043318, ss1600119400, ss1643113433, ss1710904691, ss1794320243, ss1918342483, ss1966740707, ss2019686007, ss2147699235, ss2697611374, ss2754855929, ss2986773873, ss3343443002, ss3654837647, ss3727024494, ss3746171888, ss3826158292, ss3836467189, ss3848792637, ss3893792961, ss5143829247, ss5318557761, ss5625477782, ss5831923416, ss5937306821 NC_000001.10:51664197:A:G NC_000001.11:51198525:A:G (self)
1936521, 2401220, 12444786, 9913270307, ss2162287602, ss3645041351, ss3646657919, ss3686719810, ss3799181338, ss3841873124, ss4448838451, ss5242177404, ss5443247859, ss5514410586, ss5668564116, ss5800573619, ss5848894746, ss5908153549 NC_000001.11:51198525:A:G NC_000001.11:51198525:A:G (self)
ss18135791, ss20429371 NT_032977.6:13227268:A:G NC_000001.11:51198525:A:G (self)
ss99206789, ss138947518 NT_032977.9:21636115:A:G NC_000001.11:51198525:A:G (self)
809617, ss3848792637, ss5625477782 NC_000001.10:51664197:A:T NC_000001.11:51198525:A:T (self)
1936521, 9913270307, ss5514410586 NC_000001.11:51198525:A:T NC_000001.11:51198525:A:T (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 rs12057144

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