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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1004254

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr18:74397206 (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=0.301186 (79721/264690, TOPMED)
G=0.301392 (42216/140070, GnomAD)
G=0.25161 (7110/28258, 14KJPN) (+ 16 more)
G=0.24934 (4710/18890, ALFA)
G=0.24988 (4188/16760, 8.3KJPN)
G=0.3162 (2025/6404, 1000G_30x)
G=0.3099 (1552/5008, 1000G)
G=0.2007 (899/4480, Estonian)
G=0.1783 (687/3854, ALSPAC)
G=0.1947 (722/3708, TWINSUK)
G=0.2464 (722/2930, KOREAN)
G=0.2647 (485/1832, Korea1K)
G=0.209 (209/998, GoNL)
G=0.195 (117/600, NorthernSweden)
A=0.360 (90/250, SGDP_PRJ)
G=0.273 (59/216, Qatari)
G=0.202 (42/208, Vietnamese)
G=0.25 (10/40, GENOME_DK)
A=0.33 (12/36, Siberian)
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 18890 A=0.75066 G=0.24934
European Sub 14286 A=0.80638 G=0.19362
African Sub 2946 A=0.4688 G=0.5312
African Others Sub 114 A=0.386 G=0.614
African American Sub 2832 A=0.4721 G=0.5279
Asian Sub 112 A=0.812 G=0.188
East Asian Sub 86 A=0.83 G=0.17
Other Asian Sub 26 A=0.77 G=0.23
Latin American 1 Sub 146 A=0.740 G=0.260
Latin American 2 Sub 610 A=0.838 G=0.162
South Asian Sub 98 A=0.79 G=0.21
Other Sub 692 A=0.711 G=0.289


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=0.698814 G=0.301186
gnomAD - Genomes Global Study-wide 140070 A=0.698608 G=0.301392
gnomAD - Genomes European Sub 75882 A=0.79799 G=0.20201
gnomAD - Genomes African Sub 41950 A=0.47628 G=0.52372
gnomAD - Genomes American Sub 13638 A=0.77995 G=0.22005
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=0.7776 G=0.2224
gnomAD - Genomes East Asian Sub 3132 A=0.8094 G=0.1906
gnomAD - Genomes Other Sub 2150 A=0.7298 G=0.2702
14KJPN JAPANESE Study-wide 28258 A=0.74839 G=0.25161
Allele Frequency Aggregator Total Global 18890 A=0.75066 G=0.24934
Allele Frequency Aggregator European Sub 14286 A=0.80638 G=0.19362
Allele Frequency Aggregator African Sub 2946 A=0.4688 G=0.5312
Allele Frequency Aggregator Other Sub 692 A=0.711 G=0.289
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.838 G=0.162
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.740 G=0.260
Allele Frequency Aggregator Asian Sub 112 A=0.812 G=0.188
Allele Frequency Aggregator South Asian Sub 98 A=0.79 G=0.21
8.3KJPN JAPANESE Study-wide 16760 A=0.75012 G=0.24988
1000Genomes_30x Global Study-wide 6404 A=0.6838 G=0.3162
1000Genomes_30x African Sub 1786 A=0.4104 G=0.5896
1000Genomes_30x Europe Sub 1266 A=0.8041 G=0.1959
1000Genomes_30x South Asian Sub 1202 A=0.7704 G=0.2296
1000Genomes_30x East Asian Sub 1170 A=0.7821 G=0.2179
1000Genomes_30x American Sub 980 A=0.803 G=0.197
1000Genomes Global Study-wide 5008 A=0.6901 G=0.3099
1000Genomes African Sub 1322 A=0.4153 G=0.5847
1000Genomes East Asian Sub 1008 A=0.7837 G=0.2163
1000Genomes Europe Sub 1006 A=0.7942 G=0.2058
1000Genomes South Asian Sub 978 A=0.775 G=0.225
1000Genomes American Sub 694 A=0.807 G=0.193
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.7993 G=0.2007
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8217 G=0.1783
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8053 G=0.1947
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.7536 G=0.2464, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.7353 G=0.2647
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.791 G=0.209
Northern Sweden ACPOP Study-wide 600 A=0.805 G=0.195
SGDP_PRJ Global Study-wide 250 A=0.360 G=0.640
Qatari Global Study-wide 216 A=0.727 G=0.273
A Vietnamese Genetic Variation Database Global Study-wide 208 A=0.798 G=0.202
The Danish reference pan genome Danish Study-wide 40 A=0.75 G=0.25
Siberian Global Study-wide 36 A=0.33 G=0.67
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 18 NC_000018.10:g.74397206A>G
GRCh38.p14 chr 18 NC_000018.10:g.74397206A>T
GRCh37.p13 chr 18 NC_000018.9:g.72064441A>G
GRCh37.p13 chr 18 NC_000018.9:g.72064441A>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 A= G T
GRCh38.p14 chr 18 NC_000018.10:g.74397206= NC_000018.10:g.74397206A>G NC_000018.10:g.74397206A>T
GRCh37.p13 chr 18 NC_000018.9:g.72064441= NC_000018.9:g.72064441A>G NC_000018.9:g.72064441A>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#.

60 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1974117 Oct 18, 2000 (87)
2 KWOK ss1974119 Oct 18, 2000 (87)
3 SC_JCM ss2652386 Nov 08, 2000 (89)
4 TSC-CSHL ss2893759 Jan 22, 2001 (92)
5 ABI ss40957419 Mar 13, 2006 (126)
6 HGSV ss84767321 Dec 15, 2007 (130)
7 GMI ss155431815 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss168523268 Jul 04, 2010 (132)
9 COMPLETE_GENOMICS ss170322633 Jul 04, 2010 (132)
10 COMPLETE_GENOMICS ss172002180 Jul 04, 2010 (132)
11 BUSHMAN ss203502113 Jul 04, 2010 (132)
12 GMI ss283070739 May 04, 2012 (137)
13 1000GENOMES ss340228292 May 09, 2011 (134)
14 TISHKOFF ss565766371 Apr 25, 2013 (138)
15 SSMP ss661610431 Apr 25, 2013 (138)
16 EVA-GONL ss993941180 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1081662727 Aug 21, 2014 (142)
18 1000GENOMES ss1361804992 Aug 21, 2014 (142)
19 EVA_GENOME_DK ss1578495053 Apr 01, 2015 (144)
20 EVA_UK10K_ALSPAC ss1637299197 Apr 01, 2015 (144)
21 EVA_UK10K_TWINSUK ss1680293230 Apr 01, 2015 (144)
22 HAMMER_LAB ss1809142966 Sep 08, 2015 (146)
23 WEILL_CORNELL_DGM ss1937410053 Feb 12, 2016 (147)
24 GENOMED ss1968577724 Jul 19, 2016 (147)
25 JJLAB ss2029480697 Sep 14, 2016 (149)
26 USC_VALOUEV ss2157988313 Dec 20, 2016 (150)
27 HUMAN_LONGEVITY ss2223184955 Dec 20, 2016 (150)
28 SYSTEMSBIOZJU ss2629239860 Nov 08, 2017 (151)
29 GRF ss2702587060 Nov 08, 2017 (151)
30 GNOMAD ss2958865843 Nov 08, 2017 (151)
31 SWEGEN ss3016846980 Nov 08, 2017 (151)
32 BIOINF_KMB_FNS_UNIBA ss3028572068 Nov 08, 2017 (151)
33 CSHL ss3352121657 Nov 08, 2017 (151)
34 EGCUT_WGS ss3683702963 Jul 13, 2019 (153)
35 EVA_DECODE ss3702050391 Jul 13, 2019 (153)
36 ACPOP ss3742725056 Jul 13, 2019 (153)
37 EVA ss3755637204 Jul 13, 2019 (153)
38 PACBIO ss3788429072 Jul 13, 2019 (153)
39 PACBIO ss3793353119 Jul 13, 2019 (153)
40 PACBIO ss3798239599 Jul 13, 2019 (153)
41 KHV_HUMAN_GENOMES ss3820895548 Jul 13, 2019 (153)
42 EVA ss3835274994 Apr 27, 2020 (154)
43 EVA ss3841259393 Apr 27, 2020 (154)
44 EVA ss3846762594 Apr 27, 2020 (154)
45 SGDP_PRJ ss3887433013 Apr 27, 2020 (154)
46 KRGDB ss3937336672 Apr 27, 2020 (154)
47 KOGIC ss3980518551 Apr 27, 2020 (154)
48 TOPMED ss5063507651 Apr 26, 2021 (155)
49 TOMMO_GENOMICS ss5226040799 Apr 26, 2021 (155)
50 1000G_HIGH_COVERAGE ss5305976425 Oct 16, 2022 (156)
51 EVA ss5432671724 Oct 16, 2022 (156)
52 HUGCELL_USP ss5498683324 Oct 16, 2022 (156)
53 1000G_HIGH_COVERAGE ss5611171911 Oct 16, 2022 (156)
54 SANFORD_IMAGENETICS ss5661692743 Oct 16, 2022 (156)
55 TOMMO_GENOMICS ss5784077426 Oct 16, 2022 (156)
56 YY_MCH ss5817275160 Oct 16, 2022 (156)
57 EVA ss5827820250 Oct 16, 2022 (156)
58 EVA ss5852145990 Oct 16, 2022 (156)
59 EVA ss5874873250 Oct 16, 2022 (156)
60 EVA ss5953125818 Oct 16, 2022 (156)
61 1000Genomes NC_000018.9 - 72064441 Oct 12, 2018 (152)
62 1000Genomes_30x NC_000018.10 - 74397206 Oct 16, 2022 (156)
63 The Avon Longitudinal Study of Parents and Children NC_000018.9 - 72064441 Oct 12, 2018 (152)
64 Genetic variation in the Estonian population NC_000018.9 - 72064441 Oct 12, 2018 (152)
65 The Danish reference pan genome NC_000018.9 - 72064441 Apr 27, 2020 (154)
66 gnomAD - Genomes NC_000018.10 - 74397206 Apr 26, 2021 (155)
67 Genome of the Netherlands Release 5 NC_000018.9 - 72064441 Apr 27, 2020 (154)
68 KOREAN population from KRGDB NC_000018.9 - 72064441 Apr 27, 2020 (154)
69 Korean Genome Project NC_000018.10 - 74397206 Apr 27, 2020 (154)
70 Northern Sweden NC_000018.9 - 72064441 Jul 13, 2019 (153)
71 Qatari NC_000018.9 - 72064441 Apr 27, 2020 (154)
72 SGDP_PRJ NC_000018.9 - 72064441 Apr 27, 2020 (154)
73 Siberian NC_000018.9 - 72064441 Apr 27, 2020 (154)
74 8.3KJPN NC_000018.9 - 72064441 Apr 26, 2021 (155)
75 14KJPN NC_000018.10 - 74397206 Oct 16, 2022 (156)
76 TopMed NC_000018.10 - 74397206 Apr 26, 2021 (155)
77 UK 10K study - Twins NC_000018.9 - 72064441 Oct 12, 2018 (152)
78 A Vietnamese Genetic Variation Database NC_000018.9 - 72064441 Jul 13, 2019 (153)
79 ALFA NC_000018.10 - 74397206 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)
rs59693050 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84767321, ss168523268, ss170322633, ss172002180, ss203502113, ss283070739 NC_000018.8:70215420:A:G NC_000018.10:74397205:A:G (self)
75162834, 41665196, 29441211, 4683397, 18563892, 44514066, 16009921, 19451975, 39449993, 10504667, 84010106, 41665196, 9213254, ss340228292, ss565766371, ss661610431, ss993941180, ss1081662727, ss1361804992, ss1578495053, ss1637299197, ss1680293230, ss1809142966, ss1937410053, ss1968577724, ss2029480697, ss2157988313, ss2629239860, ss2702587060, ss2958865843, ss3016846980, ss3352121657, ss3683702963, ss3742725056, ss3755637204, ss3788429072, ss3793353119, ss3798239599, ss3835274994, ss3841259393, ss3887433013, ss3937336672, ss5226040799, ss5432671724, ss5661692743, ss5827820250, ss5953125818 NC_000018.9:72064440:A:G NC_000018.10:74397205:A:G (self)
98697846, 530121816, 36896552, 117914530, 279053314, 8252891285, ss2223184955, ss3028572068, ss3702050391, ss3820895548, ss3846762594, ss3980518551, ss5063507651, ss5305976425, ss5498683324, ss5611171911, ss5784077426, ss5817275160, ss5852145990, ss5874873250 NC_000018.10:74397205:A:G NC_000018.10:74397205:A:G (self)
ss1974117, ss1974119, ss2652386, ss2893759, ss40957419, ss155431815 NT_025028.14:19855304:A:G NC_000018.10:74397205:A:G (self)
44514066, ss3937336672 NC_000018.9:72064440:A:T NC_000018.10:74397205: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 rs1004254

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