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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.

rs1000792

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99574544 (GRCh38.p13) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.152869 (40463/264690, TOPMED)
G=0.141487 (21115/149236, ALFA)
G=0.149992 (21010/140074, GnomAD) (+ 14 more)
G=0.22959 (3848/16760, 8.3KJPN)
G=0.1629 (816/5008, 1000G)
G=0.1792 (803/4480, Estonian)
G=0.1357 (523/3854, ALSPAC)
G=0.1270 (471/3708, TWINSUK)
G=0.2505 (734/2930, KOREAN)
G=0.1772 (335/1890, HapMap)
G=0.129 (129/998, GoNL)
G=0.153 (92/600, NorthernSweden)
G=0.157 (34/216, Qatari)
G=0.153 (33/216, Vietnamese)
A=0.410 (64/156, SGDP_PRJ)
G=0.20 (8/40, GENOME_DK)
A=0.46 (11/24, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.99574544A>G
GRCh37.p13 chr 1 NC_000001.10:g.100040100A>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

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 149236 A=0.858513 G=0.141487
European Sub 128424 A=0.866170 G=0.133830
African Sub 6676 A=0.8550 G=0.1450
African Others Sub 242 A=0.868 G=0.132
African American Sub 6434 A=0.8545 G=0.1455
Asian Sub 630 A=0.816 G=0.184
East Asian Sub 498 A=0.789 G=0.211
Other Asian Sub 132 A=0.917 G=0.083
Latin American 1 Sub 752 A=0.840 G=0.160
Latin American 2 Sub 6330 A=0.7186 G=0.2814
South Asian Sub 184 A=0.864 G=0.136
Other Sub 6240 A=0.8529 G=0.1471


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=0.847131 G=0.152869
gnomAD - Genomes Global Study-wide 140074 A=0.850008 G=0.149992
gnomAD - Genomes European Sub 75880 A=0.85737 G=0.14263
gnomAD - Genomes African Sub 41970 A=0.85995 G=0.14005
gnomAD - Genomes American Sub 13622 A=0.77323 G=0.22677
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9230 G=0.0770
gnomAD - Genomes East Asian Sub 3128 A=0.7893 G=0.2107
gnomAD - Genomes Other Sub 2150 A=0.8581 G=0.1419
8.3KJPN JAPANESE Study-wide 16760 A=0.77041 G=0.22959
1000Genomes Global Study-wide 5008 A=0.8371 G=0.1629
1000Genomes African Sub 1322 A=0.8782 G=0.1218
1000Genomes East Asian Sub 1008 A=0.8185 G=0.1815
1000Genomes Europe Sub 1006 A=0.8410 G=0.1590
1000Genomes South Asian Sub 978 A=0.854 G=0.146
1000Genomes American Sub 694 A=0.756 G=0.244
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.8208 G=0.1792
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.8643 G=0.1357
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.8730 G=0.1270
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.7495 G=0.2505
HapMap Global Study-wide 1890 A=0.8228 G=0.1772
HapMap American Sub 768 A=0.807 G=0.193
HapMap African Sub 692 A=0.848 G=0.152
HapMap Asian Sub 254 A=0.780 G=0.220
HapMap Europe Sub 176 A=0.852 G=0.148
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.871 G=0.129
Northern Sweden ACPOP Study-wide 600 A=0.847 G=0.153
Qatari Global Study-wide 216 A=0.843 G=0.157
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.847 G=0.153
SGDP_PRJ Global Study-wide 156 A=0.410 G=0.590
The Danish reference pan genome Danish Study-wide 40 A=0.80 G=0.20
Siberian Global Study-wide 24 A=0.46 G=0.54
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
GRCh38.p13 chr 1 NC_000001.11:g.99574544= NC_000001.11:g.99574544A>G
GRCh37.p13 chr 1 NC_000001.10:g.100040100= NC_000001.10:g.100040100A>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#.

72 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1460767 Oct 05, 2000 (86)
2 SC_SNP ss15426138 Feb 27, 2004 (120)
3 PERLEGEN ss24243939 Sep 20, 2004 (123)
4 PERLEGEN ss68775399 May 16, 2007 (127)
5 ILLUMINA ss75098888 Dec 06, 2007 (129)
6 KRIBB_YJKIM ss119377510 Dec 01, 2009 (131)
7 ILLUMINA ss159850963 Dec 01, 2009 (131)
8 ILLUMINA ss169498320 Jul 04, 2010 (132)
9 1000GENOMES ss210458573 Jul 14, 2010 (132)
10 1000GENOMES ss218548595 Jul 14, 2010 (132)
11 1000GENOMES ss230656698 Jul 14, 2010 (132)
12 1000GENOMES ss238323671 Jul 15, 2010 (132)
13 GMI ss275945287 May 04, 2012 (137)
14 ILLUMINA ss479154549 May 04, 2012 (137)
15 ILLUMINA ss479156237 May 04, 2012 (137)
16 ILLUMINA ss479470478 Sep 08, 2015 (146)
17 ILLUMINA ss484378490 May 04, 2012 (137)
18 ILLUMINA ss536564732 Sep 08, 2015 (146)
19 TISHKOFF ss554480447 Apr 25, 2013 (138)
20 SSMP ss648253867 Apr 25, 2013 (138)
21 ILLUMINA ss780667401 Aug 21, 2014 (142)
22 ILLUMINA ss782635529 Sep 08, 2015 (146)
23 ILLUMINA ss783605076 Aug 21, 2014 (142)
24 ILLUMINA ss831885610 Sep 08, 2015 (146)
25 ILLUMINA ss836163224 Aug 21, 2014 (142)
26 EVA-GONL ss975482923 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1068127612 Aug 21, 2014 (142)
28 1000GENOMES ss1292107386 Aug 21, 2014 (142)
29 EVA_GENOME_DK ss1574271469 Apr 01, 2015 (144)
30 EVA_DECODE ss1584861215 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1600816770 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1643810803 Apr 01, 2015 (144)
33 EVA_SVP ss1712357137 Apr 01, 2015 (144)
34 ILLUMINA ss1751859107 Sep 08, 2015 (146)
35 HAMMER_LAB ss1794807536 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1918682526 Feb 12, 2016 (147)
37 GENOMED ss1966820759 Jul 19, 2016 (147)
38 JJLAB ss2019862735 Sep 14, 2016 (149)
39 USC_VALOUEV ss2147881444 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2165030572 Dec 20, 2016 (150)
41 TOPMED ss2327381380 Dec 20, 2016 (150)
42 ILLUMINA ss2632553613 Nov 08, 2017 (151)
43 GRF ss2697808779 Nov 08, 2017 (151)
44 GNOMAD ss2758637117 Nov 08, 2017 (151)
45 SWEGEN ss2987305594 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3023694966 Nov 08, 2017 (151)
47 TOPMED ss3084648521 Nov 08, 2017 (151)
48 CSHL ss3343595882 Nov 08, 2017 (151)
49 ILLUMINA ss3626165269 Oct 11, 2018 (152)
50 ILLUMINA ss3630587787 Oct 11, 2018 (152)
51 ILLUMINA ss3632903277 Oct 11, 2018 (152)
52 ILLUMINA ss3633598275 Oct 11, 2018 (152)
53 ILLUMINA ss3634339249 Oct 11, 2018 (152)
54 ILLUMINA ss3635291886 Oct 11, 2018 (152)
55 ILLUMINA ss3636016805 Oct 11, 2018 (152)
56 ILLUMINA ss3637042342 Oct 11, 2018 (152)
57 ILLUMINA ss3637775448 Oct 11, 2018 (152)
58 ILLUMINA ss3640046609 Oct 11, 2018 (152)
59 ILLUMINA ss3642785633 Oct 11, 2018 (152)
60 EGCUT_WGS ss3655390662 Jul 12, 2019 (153)
61 EVA_DECODE ss3687367020 Jul 12, 2019 (153)
62 ACPOP ss3727314007 Jul 12, 2019 (153)
63 ILLUMINA ss3744640218 Jul 12, 2019 (153)
64 EVA ss3746574033 Jul 12, 2019 (153)
65 ILLUMINA ss3772141455 Jul 12, 2019 (153)
66 KHV_HUMAN_GENOMES ss3799574810 Jul 12, 2019 (153)
67 EVA ss3826326523 Apr 25, 2020 (154)
68 SGDP_PRJ ss3849477442 Apr 25, 2020 (154)
69 KRGDB ss3894555474 Apr 25, 2020 (154)
70 EVA ss4016927687 Apr 25, 2021 (155)
71 TOPMED ss4460695828 Apr 25, 2021 (155)
72 TOMMO_GENOMICS ss5145313031 Apr 25, 2021 (155)
73 1000Genomes NC_000001.10 - 100040100 Oct 11, 2018 (152)
74 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100040100 Oct 11, 2018 (152)
75 Genetic variation in the Estonian population NC_000001.10 - 100040100 Oct 11, 2018 (152)
76 The Danish reference pan genome NC_000001.10 - 100040100 Apr 25, 2020 (154)
77 gnomAD - Genomes NC_000001.11 - 99574544 Apr 25, 2021 (155)
78 Genome of the Netherlands Release 5 NC_000001.10 - 100040100 Apr 25, 2020 (154)
79 HapMap NC_000001.11 - 99574544 Apr 25, 2020 (154)
80 KOREAN population from KRGDB NC_000001.10 - 100040100 Apr 25, 2020 (154)
81 Northern Sweden NC_000001.10 - 100040100 Jul 12, 2019 (153)
82 Qatari NC_000001.10 - 100040100 Apr 25, 2020 (154)
83 SGDP_PRJ NC_000001.10 - 100040100 Apr 25, 2020 (154)
84 Siberian NC_000001.10 - 100040100 Apr 25, 2020 (154)
85 8.3KJPN NC_000001.10 - 100040100 Apr 25, 2021 (155)
86 TopMed NC_000001.11 - 99574544 Apr 25, 2021 (155)
87 UK 10K study - Twins NC_000001.10 - 100040100 Oct 11, 2018 (152)
88 A Vietnamese Genetic Variation Database NC_000001.10 - 100040100 Jul 12, 2019 (153)
89 ALFA NC_000001.11 - 99574544 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).

Associated ID History Updated (Build)
rs17413077 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss210458573, ss275945287, ss479154549, ss1584861215, ss1712357137, ss3642785633 NC_000001.9:99812687:A:G NC_000001.11:99574543:A:G (self)
2870951, 1583691, 1128910, 1628918, 687020, 1732868, 598872, 724456, 1494422, 397798, 3282338, 1583691, 341136, ss218548595, ss230656698, ss238323671, ss479156237, ss479470478, ss484378490, ss536564732, ss554480447, ss648253867, ss780667401, ss782635529, ss783605076, ss831885610, ss836163224, ss975482923, ss1068127612, ss1292107386, ss1574271469, ss1600816770, ss1643810803, ss1751859107, ss1794807536, ss1918682526, ss1966820759, ss2019862735, ss2147881444, ss2327381380, ss2632553613, ss2697808779, ss2758637117, ss2987305594, ss3343595882, ss3626165269, ss3630587787, ss3632903277, ss3633598275, ss3634339249, ss3635291886, ss3636016805, ss3637042342, ss3637775448, ss3640046609, ss3655390662, ss3727314007, ss3744640218, ss3746574033, ss3772141455, ss3826326523, ss3849477442, ss3894555474, ss4016927687, ss5145313031 NC_000001.10:100040099:A:G NC_000001.11:99574543:A:G (self)
20295353, 136529, 15306103, 24302163, 6426636288, ss2165030572, ss3023694966, ss3084648521, ss3687367020, ss3799574810, ss4460695828 NC_000001.11:99574543:A:G NC_000001.11:99574543:A:G (self)
ss15426138 NT_028050.13:8229043:A:G NC_000001.11:99574543:A:G (self)
ss1460767, ss24243939, ss68775399, ss75098888, ss119377510, ss159850963, ss169498320 NT_032977.9:70012017:A:G NC_000001.11:99574543:A: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 rs1000792

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.post596+ae089ad