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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.

rs10018902

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:120941346 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.036371 (9627/264690, TOPMED)
A=0.004495 (567/126148, ALFA)
A=0.0364 (233/6404, 1000G_30x) (+ 7 more)
A=0.0327 (164/5008, 1000G)
A=0.0005 (2/3854, ALSPAC)
A=0.0000 (0/3708, TWINSUK)
A=0.086 (67/782, HapMap)
A=0.023 (5/216, Qatari)
G=0.36 (10/28, SGDP_PRJ)
A=0.0 (0/10, Ancient Sardinia)
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 126148 G=0.995505 A=0.004495, T=0.000000
European Sub 110444 G=0.999556 A=0.000444, T=0.000000
African Sub 6462 G=0.9369 A=0.0631, T=0.0000
African Others Sub 210 G=0.910 A=0.090, T=0.000
African American Sub 6252 G=0.9378 A=0.0622, T=0.0000
Asian Sub 622 G=1.000 A=0.000, T=0.000
East Asian Sub 490 G=1.000 A=0.000, T=0.000
Other Asian Sub 132 G=1.000 A=0.000, T=0.000
Latin American 1 Sub 672 G=0.954 A=0.046, T=0.000
Latin American 2 Sub 2192 G=0.9973 A=0.0027, T=0.0000
South Asian Sub 184 G=1.000 A=0.000, T=0.000
Other Sub 5572 G=0.9869 A=0.0131, T=0.0000


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=0.963629 A=0.036371
Allele Frequency Aggregator Total Global 126148 G=0.995505 A=0.004495, T=0.000000
Allele Frequency Aggregator European Sub 110444 G=0.999556 A=0.000444, T=0.000000
Allele Frequency Aggregator African Sub 6462 G=0.9369 A=0.0631, T=0.0000
Allele Frequency Aggregator Other Sub 5572 G=0.9869 A=0.0131, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 2192 G=0.9973 A=0.0027, T=0.0000
Allele Frequency Aggregator Latin American 1 Sub 672 G=0.954 A=0.046, T=0.000
Allele Frequency Aggregator Asian Sub 622 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 184 G=1.000 A=0.000, T=0.000
1000Genomes_30x Global Study-wide 6404 G=0.9636 A=0.0364
1000Genomes_30x African Sub 1786 G=0.8774 A=0.1226
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.986 A=0.014
1000Genomes Global Study-wide 5008 G=0.9673 A=0.0327
1000Genomes African Sub 1322 G=0.8843 A=0.1157
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=0.984 A=0.016
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9995 A=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=1.0000 A=0.0000
HapMap Global Study-wide 782 G=0.914 A=0.086
HapMap African Sub 684 G=0.918 A=0.082
HapMap American Sub 98 G=0.89 A=0.11
Qatari Global Study-wide 216 G=0.977 A=0.023
SGDP_PRJ Global Study-wide 28 G=0.36 A=0.64
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 10 G=1.0 A=0.0
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 4 NC_000004.12:g.120941346G>A
GRCh38.p14 chr 4 NC_000004.12:g.120941346G>T
GRCh37.p13 chr 4 NC_000004.11:g.121862501G>A
GRCh37.p13 chr 4 NC_000004.11:g.121862501G>T
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 T
GRCh38.p14 chr 4 NC_000004.12:g.120941346= NC_000004.12:g.120941346G>A NC_000004.12:g.120941346G>T
GRCh37.p13 chr 4 NC_000004.11:g.121862501= NC_000004.11:g.121862501G>A NC_000004.11:g.121862501G>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, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13865412 Dec 05, 2003 (119)
2 ILLUMINA ss75240933 Dec 07, 2007 (129)
3 KRIBB_YJKIM ss119610601 Dec 01, 2009 (131)
4 ILLUMINA ss159852420 Dec 01, 2009 (131)
5 ILLUMINA ss169517987 Jul 04, 2010 (132)
6 1000GENOMES ss221179570 Jul 14, 2010 (132)
7 ILLUMINA ss479158337 May 04, 2012 (137)
8 ILLUMINA ss479160058 May 04, 2012 (137)
9 ILLUMINA ss479476303 Sep 08, 2015 (146)
10 ILLUMINA ss484380351 May 04, 2012 (137)
11 ILLUMINA ss536566045 Sep 08, 2015 (146)
12 TISHKOFF ss557814574 Apr 25, 2013 (138)
13 ILLUMINA ss778344110 Sep 08, 2015 (146)
14 ILLUMINA ss782636466 Sep 08, 2015 (146)
15 ILLUMINA ss783606001 Sep 08, 2015 (146)
16 ILLUMINA ss831886570 Sep 08, 2015 (146)
17 ILLUMINA ss833798746 Sep 08, 2015 (146)
18 JMKIDD_LAB ss1071906273 Aug 21, 2014 (142)
19 1000GENOMES ss1311569489 Aug 21, 2014 (142)
20 EVA_DECODE ss1590117703 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1611047677 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1654041710 Apr 01, 2015 (144)
23 ILLUMINA ss1752495242 Sep 08, 2015 (146)
24 HAMMER_LAB ss1802115523 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1923853253 Feb 12, 2016 (147)
26 HUMAN_LONGEVITY ss2266639791 Dec 20, 2016 (150)
27 ILLUMINA ss2634170990 Nov 08, 2017 (151)
28 GNOMAD ss2814556992 Nov 08, 2017 (151)
29 AFFY ss2985929689 Nov 08, 2017 (151)
30 ILLUMINA ss3022410640 Nov 08, 2017 (151)
31 ILLUMINA ss3629054480 Oct 12, 2018 (152)
32 ILLUMINA ss3632104425 Oct 12, 2018 (152)
33 ILLUMINA ss3633347428 Oct 12, 2018 (152)
34 ILLUMINA ss3634066881 Oct 12, 2018 (152)
35 ILLUMINA ss3634968747 Oct 12, 2018 (152)
36 ILLUMINA ss3635749518 Oct 12, 2018 (152)
37 ILLUMINA ss3636673934 Oct 12, 2018 (152)
38 ILLUMINA ss3637502059 Oct 12, 2018 (152)
39 ILLUMINA ss3638509084 Oct 12, 2018 (152)
40 ILLUMINA ss3640676040 Oct 12, 2018 (152)
41 ILLUMINA ss3643458749 Oct 12, 2018 (152)
42 ILLUMINA ss3652898576 Oct 12, 2018 (152)
43 ILLUMINA ss3726166673 Jul 13, 2019 (153)
44 ILLUMINA ss3745268989 Jul 13, 2019 (153)
45 ILLUMINA ss3772763487 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3805493004 Jul 13, 2019 (153)
47 SGDP_PRJ ss3859924906 Apr 26, 2020 (154)
48 EVA ss3985092912 Apr 26, 2021 (155)
49 TOPMED ss4629858257 Apr 26, 2021 (155)
50 1000G_HIGH_COVERAGE ss5260807930 Oct 17, 2022 (156)
51 EVA ss5351905496 Oct 17, 2022 (156)
52 HUGCELL_USP ss5459388338 Oct 17, 2022 (156)
53 EVA ss5507704536 Oct 17, 2022 (156)
54 1000G_HIGH_COVERAGE ss5542752535 Oct 17, 2022 (156)
55 SANFORD_IMAGENETICS ss5624566182 Oct 17, 2022 (156)
56 SANFORD_IMAGENETICS ss5635966134 Oct 17, 2022 (156)
57 EVA ss5865261482 Oct 17, 2022 (156)
58 EVA ss5964367281 Oct 17, 2022 (156)
59 1000Genomes NC_000004.11 - 121862501 Oct 12, 2018 (152)
60 1000Genomes_30x NC_000004.12 - 120941346 Oct 17, 2022 (156)
61 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 121862501 Oct 12, 2018 (152)
62 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 163183200 (NC_000004.12:120941345:G:A 4873/140146)
Row 163183201 (NC_000004.12:120941345:G:T 1/140162)

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

Submission ignored due to conflicting rows:
Row 163183200 (NC_000004.12:120941345:G:A 4873/140146)
Row 163183201 (NC_000004.12:120941345:G:T 1/140162)

- Apr 26, 2021 (155)
64 HapMap NC_000004.12 - 120941346 Apr 26, 2020 (154)
65 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000004.11 - 121862501 Apr 26, 2021 (155)
66 Qatari NC_000004.11 - 121862501 Apr 26, 2020 (154)
67 SGDP_PRJ NC_000004.11 - 121862501 Apr 26, 2020 (154)
68 TopMed NC_000004.12 - 120941346 Apr 26, 2021 (155)
69 UK 10K study - Twins NC_000004.11 - 121862501 Oct 12, 2018 (152)
70 ALFA NC_000004.12 - 120941346 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss479158337, ss1590117703, ss3643458749 NC_000004.10:122081950:G:A NC_000004.12:120941345:G:A (self)
23035063, 12814791, 318839, 5895183, 11941886, 12814791, ss221179570, ss479160058, ss479476303, ss484380351, ss536566045, ss557814574, ss778344110, ss782636466, ss783606001, ss831886570, ss833798746, ss1071906273, ss1311569489, ss1611047677, ss1654041710, ss1752495242, ss1802115523, ss1923853253, ss2634170990, ss2814556992, ss2985929689, ss3022410640, ss3629054480, ss3632104425, ss3633347428, ss3634066881, ss3634968747, ss3635749518, ss3636673934, ss3637502059, ss3638509084, ss3640676040, ss3652898576, ss3745268989, ss3772763487, ss3859924906, ss3985092912, ss5351905496, ss5507704536, ss5624566182, ss5635966134, ss5964367281 NC_000004.11:121862500:G:A NC_000004.12:120941345:G:A (self)
30278470, 2699011, 467235813, 12002845281, ss2266639791, ss3726166673, ss3805493004, ss4629858257, ss5260807930, ss5459388338, ss5542752535, ss5865261482 NC_000004.12:120941345:G:A NC_000004.12:120941345:G:A (self)
ss13865412 NT_016354.16:46357631:G:A NC_000004.12:120941345:G:A (self)
ss75240933, ss119610601, ss159852420, ss169517987 NT_016354.19:46410221:G:A NC_000004.12:120941345:G:A (self)
12002845281 NC_000004.12:120941345:G:T NC_000004.12:120941345:G: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 rs10018902

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