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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.

rs28765502

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:897538 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.365461 (96734/264690, TOPMED)
C=0.377792 (52875/139958, GnomAD)
C=0.34076 (6437/18890, ALFA) (+ 14 more)
C=0.28294 (4742/16760, 8.3KJPN)
C=0.3454 (1730/5008, 1000G)
C=0.2885 (1112/3854, ALSPAC)
C=0.2859 (1060/3708, TWINSUK)
C=0.1659 (486/2930, KOREAN)
C=0.1567 (287/1832, Korea1K)
C=0.292 (291/998, GoNL)
C=0.235 (141/600, NorthernSweden)
T=0.385 (94/244, SGDP_PRJ)
C=0.347 (75/216, Qatari)
C=0.199 (43/216, Vietnamese)
C=0.31 (16/52, Ancient Sardinia)
C=0.35 (14/40, GENOME_DK)
T=0.42 (16/38, 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.897538T>C
GRCh37.p13 chr 1 NC_000001.10:g.832918T>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 T=0.65924 C=0.34076
European Sub 14286 T=0.69789 C=0.30211
African Sub 2946 T=0.4572 C=0.5428
African Others Sub 114 T=0.404 C=0.596
African American Sub 2832 T=0.4594 C=0.5406
Asian Sub 112 T=0.857 C=0.143
East Asian Sub 86 T=0.87 C=0.13
Other Asian Sub 26 T=0.81 C=0.19
Latin American 1 Sub 146 T=0.623 C=0.377
Latin American 2 Sub 610 T=0.707 C=0.293
South Asian Sub 98 T=0.78 C=0.22
Other Sub 692 T=0.639 C=0.361


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 T=0.634539 C=0.365461
gnomAD - Genomes Global Study-wide 139958 T=0.622208 C=0.377792
gnomAD - Genomes European Sub 75754 T=0.69064 C=0.30936
gnomAD - Genomes African Sub 41948 T=0.45344 C=0.54656
gnomAD - Genomes American Sub 13652 T=0.68576 C=0.31424
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.6863 C=0.3137
gnomAD - Genomes East Asian Sub 3130 T=0.8652 C=0.1348
gnomAD - Genomes Other Sub 2152 T=0.6473 C=0.3527
8.3KJPN JAPANESE Study-wide 16760 T=0.71706 C=0.28294
1000Genomes Global Study-wide 5008 T=0.6546 C=0.3454
1000Genomes African Sub 1322 T=0.4100 C=0.5900
1000Genomes East Asian Sub 1008 T=0.8095 C=0.1905
1000Genomes Europe Sub 1006 T=0.7038 C=0.2962
1000Genomes South Asian Sub 978 T=0.753 C=0.247
1000Genomes American Sub 694 T=0.686 C=0.314
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7115 C=0.2885
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7141 C=0.2859
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.8341 C=0.1659
Korean Genome Project KOREAN Study-wide 1832 T=0.8433 C=0.1567
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.708 C=0.292
Northern Sweden ACPOP Study-wide 600 T=0.765 C=0.235
SGDP_PRJ Global Study-wide 244 T=0.385 C=0.615
Qatari Global Study-wide 216 T=0.653 C=0.347
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.801 C=0.199
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 52 T=0.69 C=0.31
The Danish reference pan genome Danish Study-wide 40 T=0.65 C=0.35
Siberian Global Study-wide 38 T=0.42 C=0.58
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 T= C
GRCh38.p13 chr 1 NC_000001.11:g.897538= NC_000001.11:g.897538T>C
GRCh37.p13 chr 1 NC_000001.10:g.832918= NC_000001.10:g.832918T>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#.

50 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss35108074 May 24, 2005 (125)
2 HGSV ss83453930 Dec 14, 2007 (130)
3 HGSV ss85287109 Dec 14, 2007 (130)
4 1000GENOMES ss107938316 Jan 22, 2009 (130)
5 1000GENOMES ss109937836 Jan 24, 2009 (130)
6 ILLUMINA-UK ss118438632 Dec 01, 2009 (131)
7 GMI ss154524368 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss162981102 Jul 04, 2010 (132)
9 COMPLETE_GENOMICS ss165981136 Jul 04, 2010 (132)
10 BUSHMAN ss197885969 Jul 04, 2010 (132)
11 BCM-HGSC-SUB ss205406930 Jul 04, 2010 (132)
12 1000GENOMES ss218190802 Jul 14, 2010 (132)
13 1000GENOMES ss230395745 Jul 14, 2010 (132)
14 1000GENOMES ss238115306 Jul 15, 2010 (132)
15 GMI ss275681629 May 04, 2012 (137)
16 GMI ss283987726 Apr 25, 2013 (138)
17 PJP ss290493952 May 09, 2011 (134)
18 SSMP ss647516828 Apr 25, 2013 (138)
19 EVA-GONL ss974769842 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1067612528 Aug 21, 2014 (142)
21 1000GENOMES ss1289341205 Aug 21, 2014 (142)
22 DDI ss1425685123 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1573851288 Apr 01, 2015 (144)
24 EVA_DECODE ss1584129764 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1599378775 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1642372808 Apr 01, 2015 (144)
27 HAMMER_LAB ss1793709418 Sep 08, 2015 (146)
28 WEILL_CORNELL_DGM ss1917961189 Feb 12, 2016 (147)
29 JJLAB ss2019498605 Sep 14, 2016 (149)
30 USC_VALOUEV ss2147485142 Dec 20, 2016 (150)
31 TOPMED ss2321506860 Dec 20, 2016 (150)
32 GRF ss2697376102 Nov 08, 2017 (151)
33 GNOMAD ss2750645631 Nov 08, 2017 (151)
34 SWEGEN ss2986150536 Nov 08, 2017 (151)
35 BIOINF_KMB_FNS_UNIBA ss3023513772 Nov 08, 2017 (151)
36 TOPMED ss3066412928 Nov 08, 2017 (151)
37 CSHL ss3343273053 Nov 08, 2017 (151)
38 EVA_DECODE ss3685992939 Jul 12, 2019 (153)
39 ACPOP ss3726716698 Jul 12, 2019 (153)
40 EVA ss3745721441 Jul 12, 2019 (153)
41 KHV_HUMAN_GENOMES ss3798744180 Jul 12, 2019 (153)
42 EVA ss3825981600 Apr 25, 2020 (154)
43 EVA ss3836378525 Apr 25, 2020 (154)
44 EVA ss3841782539 Apr 25, 2020 (154)
45 SGDP_PRJ ss3847997224 Apr 25, 2020 (154)
46 KRGDB ss3892839178 Apr 25, 2020 (154)
47 KOGIC ss3943630797 Apr 25, 2020 (154)
48 EVA ss3984774076 Apr 25, 2021 (155)
49 TOPMED ss4436447377 Apr 25, 2021 (155)
50 TOMMO_GENOMICS ss5142055191 Apr 25, 2021 (155)
51 1000Genomes NC_000001.10 - 832918 Oct 11, 2018 (152)
52 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 832918 Oct 11, 2018 (152)
53 The Danish reference pan genome NC_000001.10 - 832918 Apr 25, 2020 (154)
54 gnomAD - Genomes NC_000001.11 - 897538 Apr 25, 2021 (155)
55 Genome of the Netherlands Release 5 NC_000001.10 - 832918 Apr 25, 2020 (154)
56 KOREAN population from KRGDB NC_000001.10 - 832918 Apr 25, 2020 (154)
57 Korean Genome Project NC_000001.11 - 897538 Apr 25, 2020 (154)
58 Northern Sweden NC_000001.10 - 832918 Jul 12, 2019 (153)
59 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 832918 Apr 25, 2021 (155)
60 Qatari NC_000001.10 - 832918 Apr 25, 2020 (154)
61 SGDP_PRJ NC_000001.10 - 832918 Apr 25, 2020 (154)
62 Siberian NC_000001.10 - 832918 Apr 25, 2020 (154)
63 8.3KJPN NC_000001.10 - 832918 Apr 25, 2021 (155)
64 TopMed NC_000001.11 - 897538 Apr 25, 2021 (155)
65 UK 10K study - Twins NC_000001.10 - 832918 Oct 11, 2018 (152)
66 A Vietnamese Genetic Variation Database NC_000001.10 - 832918 Jul 12, 2019 (153)
67 ALFA NC_000001.11 - 897538 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)
rs56773068 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35108074, ss83453930, ss85287109 NC_000001.8:872780:T:C NC_000001.11:897537:T:C (self)
ss107938316, ss109937836, ss118438632, ss162981102, ss165981136, ss197885969, ss205406930, ss275681629, ss283987726, ss290493952, ss1584129764 NC_000001.9:822780:T:C NC_000001.11:897537:T:C (self)
6008, 790, 1358522, 811, 16572, 1563, 3, 3119, 14204, 1496, 24498, 790, 160, ss218190802, ss230395745, ss238115306, ss647516828, ss974769842, ss1067612528, ss1289341205, ss1425685123, ss1573851288, ss1599378775, ss1642372808, ss1793709418, ss1917961189, ss2019498605, ss2147485142, ss2321506860, ss2697376102, ss2750645631, ss2986150536, ss3343273053, ss3726716698, ss3745721441, ss3825981600, ss3836378525, ss3847997224, ss3892839178, ss3984774076, ss5142055191 NC_000001.10:832917:T:C NC_000001.11:897537:T:C (self)
77940, 8798, 25736, 53712, 7447241861, ss3023513772, ss3066412928, ss3685992939, ss3798744180, ss3841782539, ss3943630797, ss4436447377 NC_000001.11:897537:T:C NC_000001.11:897537:T:C (self)
ss154524368 NT_004350.19:311549:T:C NC_000001.11:897537:T: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 rs28765502

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