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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.

rs1000021

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr3:176750090 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.262579 (69502/264690, TOPMED)
C=0.272950 (38201/139956, GnomAD)
C=0.30603 (5781/18890, ALFA) (+ 15 more)
C=0.30149 (5053/16760, 8.3KJPN)
C=0.2350 (1177/5008, 1000G)
C=0.3621 (1622/4480, Estonian)
C=0.3446 (1328/3854, ALSPAC)
C=0.3536 (1311/3708, TWINSUK)
C=0.2966 (869/2930, KOREAN)
C=0.2740 (502/1832, Korea1K)
C=0.373 (372/998, GoNL)
C=0.397 (238/600, NorthernSweden)
G=0.373 (106/284, SGDP_PRJ)
C=0.315 (68/216, Qatari)
C=0.238 (51/214, Vietnamese)
C=0.096 (20/208, HapMap)
C=0.40 (16/40, GENOME_DK)
G=0.32 (7/22, 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 3 NC_000003.12:g.176750090G>A
GRCh38.p13 chr 3 NC_000003.12:g.176750090G>C
GRCh37.p13 chr 3 NC_000003.11:g.176467878G>A
GRCh37.p13 chr 3 NC_000003.11:g.176467878G>C
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
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 18890 G=0.69397 C=0.30603
European Sub 14286 G=0.65085 C=0.34915
African Sub 2946 G=0.9084 C=0.0916
African Others Sub 114 G=0.965 C=0.035
African American Sub 2832 G=0.9061 C=0.0939
Asian Sub 112 G=0.679 C=0.321
East Asian Sub 86 G=0.66 C=0.34
Other Asian Sub 26 G=0.73 C=0.27
Latin American 1 Sub 146 G=0.788 C=0.212
Latin American 2 Sub 610 G=0.628 C=0.372
South Asian Sub 98 G=0.72 C=0.28
Other Sub 692 G=0.708 C=0.292


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=0.737421 C=0.262579
gnomAD - Genomes Global Study-wide 139956 G=0.727050 C=0.272950
gnomAD - Genomes European Sub 75806 G=0.63999 C=0.36001
gnomAD - Genomes African Sub 41978 G=0.90412 C=0.09588
gnomAD - Genomes American Sub 13592 G=0.67738 C=0.32262
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.7149 C=0.2851
gnomAD - Genomes East Asian Sub 3112 G=0.6960 C=0.3040
gnomAD - Genomes Other Sub 2150 G=0.7172 C=0.2828
8.3KJPN JAPANESE Study-wide 16760 G=0.69851 C=0.30149
1000Genomes Global Study-wide 5008 G=0.7650 C=0.2350
1000Genomes African Sub 1322 G=0.9448 C=0.0552
1000Genomes East Asian Sub 1008 G=0.7163 C=0.2837
1000Genomes Europe Sub 1006 G=0.6431 C=0.3569
1000Genomes South Asian Sub 978 G=0.765 C=0.235
1000Genomes American Sub 694 G=0.670 C=0.330
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6379 C=0.3621
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6554 C=0.3446
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.6464 C=0.3536
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7034 A=0.0000, C=0.2966
Korean Genome Project KOREAN Study-wide 1832 G=0.7260 C=0.2740
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.627 C=0.373
Northern Sweden ACPOP Study-wide 600 G=0.603 C=0.397
SGDP_PRJ Global Study-wide 284 G=0.373 C=0.627
Qatari Global Study-wide 216 G=0.685 C=0.315
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.762 C=0.238
HapMap Global Study-wide 208 G=0.904 C=0.096
HapMap African Sub 120 G=0.967 C=0.033
HapMap Asian Sub 88 G=0.82 C=0.18
The Danish reference pan genome Danish Study-wide 40 G=0.60 C=0.40
Siberian Global Study-wide 22 G=0.32 C=0.68
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 C
GRCh38.p13 chr 3 NC_000003.12:g.176750090= NC_000003.12:g.176750090G>A NC_000003.12:g.176750090G>C
GRCh37.p13 chr 3 NC_000003.11:g.176467878= NC_000003.11:g.176467878G>A NC_000003.11:g.176467878G>C
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#.

63 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1459603 Oct 05, 2000 (86)
2 SSAHASNP ss21994911 Apr 05, 2004 (121)
3 PERLEGEN ss24673634 Sep 20, 2004 (123)
4 ABI ss44390014 Mar 15, 2006 (126)
5 ILLUMINA ss65713996 Oct 16, 2006 (127)
6 PERLEGEN ss68883698 May 17, 2007 (127)
7 AFFY ss76728359 Dec 08, 2007 (130)
8 HUMANGENOME_JCVI ss96078279 Feb 06, 2009 (130)
9 BGI ss104016896 Dec 01, 2009 (131)
10 1000GENOMES ss112721300 Jan 25, 2009 (130)
11 ILLUMINA ss120244568 Dec 01, 2009 (131)
12 ENSEMBL ss133167507 Dec 01, 2009 (131)
13 GMI ss156543339 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss162855782 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss206183394 Jul 04, 2010 (132)
16 1000GENOMES ss220601071 Jul 14, 2010 (132)
17 1000GENOMES ss232158080 Jul 14, 2010 (132)
18 1000GENOMES ss239501760 Jul 15, 2010 (132)
19 GMI ss277470755 May 04, 2012 (137)
20 GMI ss284800417 Apr 25, 2013 (138)
21 PJP ss292980945 May 09, 2011 (134)
22 TISHKOFF ss557140702 Apr 25, 2013 (138)
23 SSMP ss650885924 Apr 25, 2013 (138)
24 EVA-GONL ss979494711 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1071084829 Aug 21, 2014 (142)
26 1000GENOMES ss1307416569 Aug 21, 2014 (142)
27 DDI ss1429684452 Apr 01, 2015 (144)
28 EVA_GENOME_DK ss1580311470 Apr 01, 2015 (144)
29 EVA_DECODE ss1588990209 Apr 01, 2015 (144)
30 EVA_UK10K_ALSPAC ss1608880846 Apr 01, 2015 (144)
31 EVA_UK10K_TWINSUK ss1651874879 Apr 01, 2015 (144)
32 EVA_SVP ss1712634184 Apr 01, 2015 (144)
33 HAMMER_LAB ss1800495827 Sep 08, 2015 (146)
34 WEILL_CORNELL_DGM ss1922715556 Feb 12, 2016 (147)
35 GENOMED ss1969599036 Jul 19, 2016 (147)
36 JJLAB ss2021933457 Sep 14, 2016 (149)
37 USC_VALOUEV ss2150031085 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2258464763 Dec 20, 2016 (150)
39 TOPMED ss2425864329 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2625466022 Nov 08, 2017 (151)
41 GRF ss2705453239 Nov 08, 2017 (151)
42 GNOMAD ss2802742788 Nov 08, 2017 (151)
43 SWEGEN ss2993699982 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3024735391 Nov 08, 2017 (151)
45 CSHL ss3345411744 Nov 08, 2017 (151)
46 TOPMED ss3413815796 Nov 08, 2017 (151)
47 URBANLAB ss3647594047 Oct 12, 2018 (152)
48 EGCUT_WGS ss3661654202 Jul 13, 2019 (153)
49 EVA_DECODE ss3710895934 Jul 13, 2019 (153)
50 ACPOP ss3730625273 Jul 13, 2019 (153)
51 EVA ss3761078830 Jul 13, 2019 (153)
52 PACBIO ss3784546504 Jul 13, 2019 (153)
53 PACBIO ss3790026857 Jul 13, 2019 (153)
54 PACBIO ss3794901530 Jul 13, 2019 (153)
55 KHV_HUMAN_GENOMES ss3804216164 Jul 13, 2019 (153)
56 EVA ss3828237008 Apr 25, 2020 (154)
57 EVA ss3837551263 Apr 25, 2020 (154)
58 EVA ss3842983528 Apr 25, 2020 (154)
59 SGDP_PRJ ss3857636468 Apr 25, 2020 (154)
60 KRGDB ss3903711566 Apr 25, 2020 (154)
61 KOGIC ss3953009245 Apr 25, 2020 (154)
62 TOPMED ss4594633827 Apr 26, 2021 (155)
63 TOMMO_GENOMICS ss5163003100 Apr 26, 2021 (155)
64 1000Genomes NC_000003.11 - 176467878 Oct 12, 2018 (152)
65 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 176467878 Oct 12, 2018 (152)
66 Genetic variation in the Estonian population NC_000003.11 - 176467878 Oct 12, 2018 (152)
67 The Danish reference pan genome NC_000003.11 - 176467878 Apr 25, 2020 (154)
68 gnomAD - Genomes NC_000003.12 - 176750090 Apr 26, 2021 (155)
69 Genome of the Netherlands Release 5 NC_000003.11 - 176467878 Apr 25, 2020 (154)
70 HapMap NC_000003.12 - 176750090 Apr 25, 2020 (154)
71 KOREAN population from KRGDB NC_000003.11 - 176467878 Apr 25, 2020 (154)
72 Korean Genome Project NC_000003.12 - 176750090 Apr 25, 2020 (154)
73 Northern Sweden NC_000003.11 - 176467878 Jul 13, 2019 (153)
74 Qatari NC_000003.11 - 176467878 Apr 25, 2020 (154)
75 SGDP_PRJ NC_000003.11 - 176467878 Apr 25, 2020 (154)
76 Siberian NC_000003.11 - 176467878 Apr 25, 2020 (154)
77 8.3KJPN NC_000003.11 - 176467878 Apr 26, 2021 (155)
78 TopMed NC_000003.12 - 176750090 Apr 26, 2021 (155)
79 UK 10K study - Twins NC_000003.11 - 176467878 Oct 12, 2018 (152)
80 A Vietnamese Genetic Variation Database NC_000003.11 - 176467878 Jul 13, 2019 (153)
81 ALFA NC_000003.12 - 176750090 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)
rs17645849 Oct 07, 2004 (123)
rs56617219 May 27, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
10888960, ss3903711566 NC_000003.11:176467877:G:A NC_000003.12:176750089:G:A (self)
ss76728359, ss112721300, ss162855782, ss206183394, ss277470755, ss284800417, ss292980945, ss1588990209, ss1712634184 NC_000003.10:177950571:G:C NC_000003.12:176750089:G:C (self)
18728741, 10435982, 7392450, 6476409, 4588205, 10888960, 3910138, 4757486, 9653448, 2547439, 20972407, 10435982, 2283933, ss220601071, ss232158080, ss239501760, ss557140702, ss650885924, ss979494711, ss1071084829, ss1307416569, ss1429684452, ss1580311470, ss1608880846, ss1651874879, ss1800495827, ss1922715556, ss1969599036, ss2021933457, ss2150031085, ss2425864329, ss2625466022, ss2705453239, ss2802742788, ss2993699982, ss3345411744, ss3661654202, ss3730625273, ss3761078830, ss3784546504, ss3790026857, ss3794901530, ss3828237008, ss3837551263, ss3857636468, ss3903711566, ss5163003100 NC_000003.11:176467877:G:C NC_000003.12:176750089:G:C (self)
133031572, 2516554, 9387246, 270040256, 432011382, 4505436121, ss2258464763, ss3024735391, ss3413815796, ss3647594047, ss3710895934, ss3804216164, ss3842983528, ss3953009245, ss4594633827 NC_000003.12:176750089:G:C NC_000003.12:176750089:G:C (self)
ss21994911 NT_005612.14:82963035:G:C NC_000003.12:176750089:G:C (self)
ss1459603, ss24673634, ss44390014, ss65713996, ss68883698, ss96078279, ss104016896, ss120244568, ss133167507, ss156543339 NT_005612.16:82963023:G:C NC_000003.12:176750089:G:C (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 rs1000021

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