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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.

rs12057140

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:4280953 (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>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.032453 (8590/264690, TOPMED)
G=0.031416 (4407/140278, GnomAD)
G=0.00004 (1/28258, 14KJPN) (+ 9 more)
G=0.02247 (324/14420, ALFA)
G=0.0331 (212/6404, 1000G_30x)
G=0.0323 (162/5008, 1000G)
G=0.0005 (2/3854, ALSPAC)
G=0.0005 (2/3708, TWINSUK)
G=0.003 (1/328, HapMap)
G=0.019 (4/216, Qatari)
C=0.50 (14/28, SGDP_PRJ)
G=0.50 (14/28, SGDP_PRJ)
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 14420 C=0.97753 G=0.02247
European Sub 9824 C=0.9994 G=0.0006
African Sub 2946 C=0.8995 G=0.1005
African Others Sub 114 C=0.904 G=0.096
African American Sub 2832 C=0.8994 G=0.1006
Asian Sub 112 C=1.000 G=0.000
East Asian Sub 86 C=1.00 G=0.00
Other Asian Sub 26 C=1.00 G=0.00
Latin American 1 Sub 146 C=0.959 G=0.041
Latin American 2 Sub 610 C=0.997 G=0.003
South Asian Sub 98 C=1.00 G=0.00
Other Sub 684 C=0.980 G=0.020


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 C=0.967547 G=0.032453
gnomAD - Genomes Global Study-wide 140278 C=0.968584 G=0.031416
gnomAD - Genomes European Sub 75972 C=0.99970 G=0.00030
gnomAD - Genomes African Sub 42030 C=0.90052 G=0.09948
gnomAD - Genomes American Sub 13666 C=0.98932 G=0.01068
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 C=0.9735 G=0.0265
14KJPN JAPANESE Study-wide 28258 C=0.99996 G=0.00004
Allele Frequency Aggregator Total Global 14420 C=0.97753 G=0.02247
Allele Frequency Aggregator European Sub 9824 C=0.9994 G=0.0006
Allele Frequency Aggregator African Sub 2946 C=0.8995 G=0.1005
Allele Frequency Aggregator Other Sub 684 C=0.980 G=0.020
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.997 G=0.003
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.959 G=0.041
Allele Frequency Aggregator Asian Sub 112 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9669 G=0.0331
1000Genomes_30x African Sub 1786 C=0.8841 G=0.1159
1000Genomes_30x Europe Sub 1266 C=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 G=0.0000
1000Genomes_30x American Sub 980 C=0.995 G=0.005
1000Genomes Global Study-wide 5008 C=0.9677 G=0.0323
1000Genomes African Sub 1322 C=0.8805 G=0.1195
1000Genomes East Asian Sub 1008 C=1.0000 G=0.0000
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=0.994 G=0.006
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9995 G=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9995 G=0.0005
HapMap Global Study-wide 328 C=0.997 G=0.003
HapMap American Sub 120 C=1.000 G=0.000
HapMap African Sub 118 C=0.992 G=0.008
HapMap Asian Sub 90 C=1.00 G=0.00
Qatari Global Study-wide 216 C=0.981 G=0.019
SGDP_PRJ Global Study-wide 28 C=0.50 G=0.50
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.4280953C>G
GRCh37.p13 chr 1 NC_000001.10:g.4341013C>G
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 C= G
GRCh38.p14 chr 1 NC_000001.11:g.4280953= NC_000001.11:g.4280953C>G
GRCh37.p13 chr 1 NC_000001.10:g.4341013= NC_000001.10:g.4341013C>G
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#.

23 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18135779 Feb 28, 2004 (120)
2 1000GENOMES ss218206133 Jul 14, 2010 (132)
3 TISHKOFF ss553738541 Apr 25, 2013 (138)
4 JMKIDD_LAB ss1067630831 Aug 21, 2014 (142)
5 1000GENOMES ss1289468101 Aug 21, 2014 (142)
6 EVA_UK10K_ALSPAC ss1599435974 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1642430007 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1917996888 Feb 12, 2016 (147)
9 HUMAN_LONGEVITY ss2159606962 Dec 20, 2016 (150)
10 GNOMAD ss2751015496 Nov 08, 2017 (151)
11 EVA_DECODE ss3686056618 Jul 12, 2019 (153)
12 KHV_HUMAN_GENOMES ss3798782674 Jul 12, 2019 (153)
13 SGDP_PRJ ss3848079365 Apr 25, 2020 (154)
14 TOPMED ss4437430047 Apr 25, 2021 (155)
15 1000G_HIGH_COVERAGE ss5240983169 Oct 12, 2022 (156)
16 EVA ss5316400023 Oct 12, 2022 (156)
17 HUGCELL_USP ss5442207005 Oct 12, 2022 (156)
18 1000G_HIGH_COVERAGE ss5512654963 Oct 12, 2022 (156)
19 SANFORD_IMAGENETICS ss5624817420 Oct 12, 2022 (156)
20 TOMMO_GENOMICS ss5666440714 Oct 12, 2022 (156)
21 EVA ss5831465886 Oct 12, 2022 (156)
22 EVA ss5906827510 Oct 12, 2022 (156)
23 EVA ss5936642201 Oct 12, 2022 (156)
24 1000Genomes NC_000001.10 - 4341013 Oct 11, 2018 (152)
25 1000Genomes_30x NC_000001.11 - 4280953 Oct 12, 2022 (156)
26 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 4341013 Oct 11, 2018 (152)
27 gnomAD - Genomes NC_000001.11 - 4280953 Apr 25, 2021 (155)
28 HapMap NC_000001.11 - 4280953 Apr 25, 2020 (154)
29 Qatari NC_000001.10 - 4341013 Apr 25, 2020 (154)
30 SGDP_PRJ NC_000001.10 - 4341013 Apr 25, 2020 (154)
31 14KJPN NC_000001.11 - 4280953 Oct 12, 2022 (156)
32 TopMed NC_000001.11 - 4280953 Apr 25, 2021 (155)
33 UK 10K study - Twins NC_000001.10 - 4341013 Oct 11, 2018 (152)
34 ALFA NC_000001.11 - 4280953 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
136758, 63012, 38818, 96345, 63012, ss218206133, ss553738541, ss1067630831, ss1289468101, ss1599435974, ss1642430007, ss1917996888, ss2751015496, ss3848079365, ss5316400023, ss5624817420, ss5831465886, ss5936642201 NC_000001.10:4341012:C:G NC_000001.11:4280952:C:G (self)
180898, 971176, 3611, 277818, 1036382, 8851819167, ss2159606962, ss3686056618, ss3798782674, ss4437430047, ss5240983169, ss5442207005, ss5512654963, ss5666440714, ss5906827510 NC_000001.11:4280952:C:G NC_000001.11:4280952:C:G (self)
ss18135779 NT_004547.16:344645:C:G NC_000001.11:4280952:C:G (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 rs12057140

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