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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.

rs156901

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:16513967 (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 / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.07102 (2007/28258, 14KJPN)
T=0.49994 (8379/16760, 8.3KJPN)
C=0.2778 (1779/6404, 1000G_30x) (+ 5 more)
T=0.3230 (1949/6034, ALFA)
T=0.4427 (2217/5008, 1000G)
C=0.4908 (1438/2930, KOREAN)
C=0.485 (229/472, SGDP_PRJ)
C=0.25 (12/48, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RNU1-1 : 500B Downstream 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 6034 C=0.6768 G=0.0002, T=0.3230
European Sub 5708 C=0.6591 G=0.0002, T=0.3407
African Sub 60 C=1.00 G=0.00, T=0.00
African Others Sub 0 C=0 G=0, T=0
African American Sub 60 C=1.00 G=0.00, T=0.00
Asian Sub 0 C=0 G=0, T=0
East Asian Sub 0 C=0 G=0, T=0
Other Asian Sub 0 C=0 G=0, T=0
Latin American 1 Sub 24 C=1.00 G=0.00, T=0.00
Latin American 2 Sub 150 C=1.000 G=0.000, T=0.000
South Asian Sub 20 C=1.00 G=0.00, T=0.00
Other Sub 72 C=0.94 G=0.00, T=0.06


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
14KJPN JAPANESE Study-wide 28258 C=0.07102 T=0.92898
8.3KJPN JAPANESE Study-wide 16760 C=0.50006 T=0.49994
1000Genomes_30x Global Study-wide 6404 C=0.2778 G=0.0075, T=0.7147
1000Genomes_30x African Sub 1786 C=0.1411 G=0.0224, T=0.8365
1000Genomes_30x Europe Sub 1266 C=0.3989 G=0.0000, T=0.6011
1000Genomes_30x South Asian Sub 1202 C=0.3952 G=0.0008, T=0.6040
1000Genomes_30x East Asian Sub 1170 C=0.0726 G=0.0000, T=0.9274
1000Genomes_30x American Sub 980 C=0.471 G=0.007, T=0.521
Allele Frequency Aggregator Total Global 6034 C=0.6768 G=0.0002, T=0.3230
Allele Frequency Aggregator European Sub 5708 C=0.6591 G=0.0002, T=0.3407
Allele Frequency Aggregator Latin American 2 Sub 150 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 72 C=0.94 G=0.00, T=0.06
Allele Frequency Aggregator African Sub 60 C=1.00 G=0.00, T=0.00
Allele Frequency Aggregator Latin American 1 Sub 24 C=1.00 G=0.00, T=0.00
Allele Frequency Aggregator South Asian Sub 20 C=1.00 G=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 0 C=0 G=0, T=0
1000Genomes Global Study-wide 5008 C=0.5573 T=0.4427
1000Genomes African Sub 1322 C=0.4864 T=0.5136
1000Genomes East Asian Sub 1008 C=0.4980 T=0.5020
1000Genomes Europe Sub 1006 C=0.6044 T=0.3956
1000Genomes South Asian Sub 978 C=0.593 T=0.407
1000Genomes American Sub 694 C=0.660 T=0.340
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.4908 T=0.5092
SGDP_PRJ Global Study-wide 472 C=0.485 T=0.515
Siberian Global Study-wide 48 C=0.25 T=0.75
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.16513967C>G
GRCh38.p14 chr 1 NC_000001.11:g.16513967C>T
GRCh37.p13 chr 1 NC_000001.10:g.16840462C>G
GRCh37.p13 chr 1 NC_000001.10:g.16840462C>T
GRCh38.p14 chr 1 fix patch HG1343_HG173_HG459_PATCH NW_025791756.1:g.318281T>C
GRCh38.p14 chr 1 fix patch HG1343_HG173_HG459_PATCH NW_025791756.1:g.318281T>G
Gene: RNU1-1, RNA, U1 small nuclear 1 (minus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
RNU1-1 transcript NR_004430.2:n. N/A Downstream Transcript 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 C= G T
GRCh38.p14 chr 1 NC_000001.11:g.16513967= NC_000001.11:g.16513967C>G NC_000001.11:g.16513967C>T
GRCh37.p13 chr 1 NC_000001.10:g.16840462= NC_000001.10:g.16840462C>G NC_000001.10:g.16840462C>T
GRCh38.p14 chr 1 fix patch HG1343_HG173_HG459_PATCH NW_025791756.1:g.318281T>C NW_025791756.1:g.318281T>G NW_025791756.1:g.318281=
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#.

60 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss357338 Jul 12, 2000 (79)
2 KWOK ss358009 Jul 12, 2000 (87)
3 KWOK ss360334 Jul 12, 2000 (79)
4 KWOK ss362238 Jul 12, 2000 (87)
5 SC_JCM ss591569 Jul 16, 2000 (80)
6 SC_JCM ss808837 Aug 11, 2000 (85)
7 KWOK ss1098213 Oct 04, 2000 (86)
8 KWOK ss1098818 Oct 04, 2000 (86)
9 KWOK ss1099492 Oct 04, 2000 (86)
10 KWOK ss1099973 Oct 04, 2000 (86)
11 KWOK ss1813268 Oct 18, 2000 (87)
12 KWOK ss1813544 Oct 18, 2000 (87)
13 KWOK ss1939685 Oct 18, 2000 (87)
14 KWOK ss1940215 Oct 18, 2000 (87)
15 TSC-CSHL ss2858049 Jan 22, 2001 (92)
16 SC_JCM ss6303161 Feb 20, 2003 (111)
17 BCM_SSAHASNP ss9839793 Jul 11, 2003 (116)
18 WI_SSAHASNP ss11370556 Jul 11, 2003 (116)
19 SC_SNP ss13047983 Dec 05, 2003 (119)
20 SC_SNP ss15432377 Feb 27, 2004 (120)
21 SSAHASNP ss20457660 Apr 05, 2004 (121)
22 HGSV ss84229791 Dec 15, 2007 (130)
23 HUMANGENOME_JCVI ss99189418 Feb 05, 2009 (130)
24 BGI ss102722450 Dec 01, 2009 (131)
25 ENSEMBL ss139177531 Dec 01, 2009 (131)
26 GMI ss154685993 Dec 01, 2009 (131)
27 BUSHMAN ss198079538 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss205484014 Jul 04, 2010 (132)
29 BL ss252942423 May 09, 2011 (134)
30 GMI ss275730006 May 04, 2012 (137)
31 GMI ss284007213 Apr 25, 2013 (138)
32 PJP ss290700321 May 09, 2011 (134)
33 1000GENOMES ss1289834522 Aug 21, 2014 (142)
34 DDI ss1425726111 Apr 01, 2015 (144)
35 GENOMED ss1966692563 Jul 19, 2016 (147)
36 USC_VALOUEV ss2147562923 Dec 20, 2016 (150)
37 GRF ss2697464016 Nov 08, 2017 (151)
38 GNOMAD ss2752068507 Nov 08, 2017 (151)
39 SWEGEN ss2986371743 Nov 08, 2017 (151)
40 CSHL ss3343337972 Nov 08, 2017 (151)
41 URBANLAB ss3646609189 Oct 11, 2018 (152)
42 EVA_DECODE ss3686242254 Jul 12, 2019 (153)
43 PACBIO ss3783335281 Jul 12, 2019 (153)
44 PACBIO ss3789007902 Jul 12, 2019 (153)
45 PACBIO ss3793880634 Jul 12, 2019 (153)
46 KHV_HUMAN_GENOMES ss3798898198 Jul 12, 2019 (153)
47 EVA ss3836409347 Apr 25, 2020 (154)
48 EVA ss3841813640 Apr 25, 2020 (154)
49 SGDP_PRJ ss3848290102 Apr 25, 2020 (154)
50 KRGDB ss3893187457 Apr 25, 2020 (154)
51 TOMMO_GENOMICS ss5142672451 Apr 27, 2021 (155)
52 1000G_HIGH_COVERAGE ss5241325390 Oct 12, 2022 (156)
53 1000G_HIGH_COVERAGE ss5241325391 Oct 12, 2022 (156)
54 EVA ss5317007068 Oct 12, 2022 (156)
55 1000G_HIGH_COVERAGE ss5513148911 Oct 12, 2022 (156)
56 SANFORD_IMAGENETICS ss5625009106 Oct 12, 2022 (156)
57 TOMMO_GENOMICS ss5667041058 Oct 12, 2022 (156)
58 YY_MCH ss5800362980 Oct 12, 2022 (156)
59 EVA ss5848800893 Oct 12, 2022 (156)
60 EVA ss5979937273 Oct 12, 2022 (156)
61 1000Genomes NC_000001.10 - 16840462 Oct 11, 2018 (152)
62 1000Genomes_30x NC_000001.11 - 16513967 Oct 12, 2022 (156)
63 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 3605558 (NC_000001.11:16513966:C:G 1022/132536)
Row 3605559 (NC_000001.11:16513966:C:T 87142/132436)

- Apr 27, 2021 (155)
64 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 3605558 (NC_000001.11:16513966:C:G 1022/132536)
Row 3605559 (NC_000001.11:16513966:C:T 87142/132436)

- Apr 27, 2021 (155)
65 KOREAN population from KRGDB NC_000001.10 - 16840462 Apr 25, 2020 (154)
66 SGDP_PRJ NC_000001.10 - 16840462 Apr 25, 2020 (154)
67 Siberian NC_000001.10 - 16840462 Apr 25, 2020 (154)
68 8.3KJPN NC_000001.10 - 16840462 Apr 27, 2021 (155)
69 14KJPN NC_000001.11 - 16513967 Oct 12, 2022 (156)
70 ALFA NC_000001.11 - 16513967 Apr 27, 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)
rs157153 Oct 23, 2000 (87)
rs636146 Sep 19, 2000 (85)
rs59601177 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2752068507, ss5625009106 NC_000001.10:16840461:C:G NC_000001.11:16513966:C:G (self)
674846, 4213666732, ss5241325391, ss5513148911 NC_000001.11:16513966:C:G NC_000001.11:16513966:C:G (self)
ss84229791 NC_000001.8:16585767:C:T NC_000001.11:16513966:C:T (self)
ss198079538, ss205484014, ss252942423, ss275730006, ss284007213, ss290700321 NC_000001.9:16713048:C:T NC_000001.11:16513966:C:T (self)
515968, 364851, 307082, 79277, 641758, ss1289834522, ss1425726111, ss1966692563, ss2147562923, ss2697464016, ss2752068507, ss2986371743, ss3343337972, ss3783335281, ss3789007902, ss3793880634, ss3836409347, ss3848290102, ss3893187457, ss5142672451, ss5317007068, ss5625009106, ss5979937273 NC_000001.10:16840461:C:T NC_000001.11:16513966:C:T (self)
674846, 878162, 4213666732, ss3646609189, ss3686242254, ss3798898198, ss3841813640, ss5241325390, ss5513148911, ss5667041058, ss5800362980, ss5848800893 NC_000001.11:16513966:C:T NC_000001.11:16513966:C:T (self)
ss357338, ss358009, ss360334, ss362238, ss591569, ss808837, ss1098213, ss1098818, ss1099492, ss1099973, ss1813268, ss1813544, ss1939685, ss1940215, ss2858049, ss6303161, ss99189418, ss102722450, ss139177531, ss154685993 NT_004610.19:3520549:C:T NC_000001.11:16513966:C:T (self)
ss9839793, ss11370556, ss13047983 NT_077920.1:404201:C:T NC_000001.11:16513966:C:T (self)
ss15432377, ss20457660 NT_077920.2:404201:C:T NC_000001.11:16513966:C: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 rs156901

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