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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.

rs1048488

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:825532 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.285320 (39938/139976, GnomAD)
C=0.16193 (2714/16760, 8.3KJPN)
C=0.3024 (2702/8936, ALFA) (+ 12 more)
C=0.2660 (1332/5008, 1000G)
C=0.1518 (585/3854, ALSPAC)
C=0.1578 (585/3708, TWINSUK)
C=0.1631 (478/2930, KOREAN)
C=0.3043 (574/1886, HapMap)
C=0.1643 (301/1832, Korea1K)
C=0.173 (173/998, GoNL)
C=0.148 (89/600, NorthernSweden)
C=0.166 (88/530, SGDP_PRJ)
C=0.241 (52/216, Qatari)
C=0.085 (18/212, Vietnamese)
C=0.05 (2/40, GENOME_DK)
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.825532C>A
GRCh38.p13 chr 1 NC_000001.11:g.825532C>T
GRCh37.p13 chr 1 NC_000001.10:g.760912C>A
GRCh37.p13 chr 1 NC_000001.10:g.760912C>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

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 8936 C=0.3024 A=0.0000, T=0.6976
European Sub 7030 C=0.2215 A=0.0000, T=0.7785
African Sub 1238 C=0.7649 A=0.0000, T=0.2351
African Others Sub 62 C=0.85 A=0.00, T=0.15
African American Sub 1176 C=0.7602 A=0.0000, T=0.2398
Asian Sub 14 C=0.21 A=0.00, T=0.79
East Asian Sub 12 C=0.25 A=0.00, T=0.75
Other Asian Sub 2 C=0.0 A=0.0, T=1.0
Latin American 1 Sub 36 C=0.64 A=0.00, T=0.36
Latin American 2 Sub 90 C=0.44 A=0.00, T=0.56
South Asian Sub 2 C=1.0 A=0.0, T=0.0
Other Sub 526 C=0.247 A=0.000, T=0.753


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
gnomAD - Genomes Global Study-wide 139976 C=0.285320 T=0.714680
gnomAD - Genomes European Sub 75820 C=0.17998 T=0.82002
gnomAD - Genomes African Sub 41914 C=0.52169 T=0.47831
gnomAD - Genomes American Sub 13642 C=0.20943 T=0.79057
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=0.2158 T=0.7842
gnomAD - Genomes East Asian Sub 3130 C=0.1026 T=0.8974
gnomAD - Genomes Other Sub 2152 C=0.2472 T=0.7528
8.3KJPN JAPANESE Study-wide 16760 C=0.16193 T=0.83807
Allele Frequency Aggregator Total Global 8936 C=0.3024 A=0.0000, T=0.6976
Allele Frequency Aggregator European Sub 7030 C=0.2215 A=0.0000, T=0.7785
Allele Frequency Aggregator African Sub 1238 C=0.7649 A=0.0000, T=0.2351
Allele Frequency Aggregator Other Sub 526 C=0.247 A=0.000, T=0.753
Allele Frequency Aggregator Latin American 2 Sub 90 C=0.44 A=0.00, T=0.56
Allele Frequency Aggregator Latin American 1 Sub 36 C=0.64 A=0.00, T=0.36
Allele Frequency Aggregator Asian Sub 14 C=0.21 A=0.00, T=0.79
Allele Frequency Aggregator South Asian Sub 2 C=1.0 A=0.0, T=0.0
1000Genomes Global Study-wide 5008 C=0.2660 T=0.7340
1000Genomes African Sub 1322 C=0.5552 T=0.4448
1000Genomes East Asian Sub 1008 C=0.1161 T=0.8839
1000Genomes Europe Sub 1006 C=0.1600 T=0.8400
1000Genomes South Asian Sub 978 C=0.189 T=0.811
1000Genomes American Sub 694 C=0.195 T=0.805
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.1518 T=0.8482
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.1578 T=0.8422
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.1631 T=0.8369
HapMap Global Study-wide 1886 C=0.3043 T=0.6957
HapMap American Sub 764 C=0.205 T=0.795
HapMap African Sub 692 C=0.523 T=0.477
HapMap Asian Sub 254 C=0.118 T=0.882
HapMap Europe Sub 176 C=0.142 T=0.858
Korean Genome Project KOREAN Study-wide 1832 C=0.1643 T=0.8357
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.173 T=0.827
Northern Sweden ACPOP Study-wide 600 C=0.148 T=0.852
SGDP_PRJ Global Study-wide 530 C=0.166 T=0.834
Qatari Global Study-wide 216 C=0.241 T=0.759
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.085 T=0.915
The Danish reference pan genome Danish Study-wide 40 C=0.05 T=0.95
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 C= A T
GRCh38.p13 chr 1 NC_000001.11:g.825532= NC_000001.11:g.825532C>A NC_000001.11:g.825532C>T
GRCh37.p13 chr 1 NC_000001.10:g.760912= NC_000001.10:g.760912C>A NC_000001.10:g.760912C>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#.

68 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss4358500 Mar 26, 2002 (103)
2 SC_JCM ss6040318 Feb 20, 2003 (111)
3 WI_SSAHASNP ss11348776 Jul 11, 2003 (117)
4 ILLUMINA ss75004583 Dec 07, 2007 (129)
5 HGSV ss78852399 Dec 07, 2007 (129)
6 BCMHGSC_JDW ss87155773 Mar 23, 2008 (129)
7 HUMANGENOME_JCVI ss97913205 Feb 04, 2009 (130)
8 BGI ss105111678 Dec 01, 2009 (131)
9 1000GENOMES ss107938275 Jan 22, 2009 (130)
10 1000GENOMES ss109937276 Jan 24, 2009 (130)
11 ILLUMINA-UK ss118438281 Feb 14, 2009 (130)
12 KRIBB_YJKIM ss119380166 Dec 01, 2009 (131)
13 ENSEMBL ss137752234 Dec 01, 2009 (131)
14 ENSEMBL ss138897564 Dec 01, 2009 (131)
15 GMI ss154522359 Dec 01, 2009 (131)
16 ILLUMINA ss170151194 Jul 04, 2010 (132)
17 BUSHMAN ss197885432 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss205161238 Jul 04, 2010 (132)
19 1000GENOMES ss218190389 Jul 14, 2010 (132)
20 1000GENOMES ss230395469 Jul 14, 2010 (132)
21 1000GENOMES ss238114976 Jul 15, 2010 (132)
22 BL ss252864114 May 09, 2011 (134)
23 GMI ss275680797 May 04, 2012 (137)
24 GMI ss283987383 Apr 25, 2013 (138)
25 PJP ss290493782 May 09, 2011 (134)
26 ILLUMINA ss536609952 Sep 08, 2015 (146)
27 TISHKOFF ss553710388 Apr 25, 2013 (138)
28 SSMP ss647516153 Apr 25, 2013 (138)
29 EVA-GONL ss974769293 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1067612337 Aug 21, 2014 (142)
31 1000GENOMES ss1289339032 Aug 21, 2014 (142)
32 DDI ss1425684826 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1573851142 Apr 01, 2015 (144)
34 EVA_DECODE ss1584129454 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1599378343 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1642372376 Apr 01, 2015 (144)
37 EVA_SVP ss1712305458 Apr 01, 2015 (144)
38 HAMMER_LAB ss1793705724 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1917960267 Feb 12, 2016 (147)
40 GENOMED ss1966667322 Jul 19, 2016 (147)
41 JJLAB ss2019498401 Sep 14, 2016 (149)
42 TOPMED ss2321502949 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2624264760 Nov 08, 2017 (151)
44 GRF ss2697374589 Nov 08, 2017 (151)
45 GNOMAD ss2750637726 Nov 08, 2017 (151)
46 SWEGEN ss2986148904 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3023513710 Nov 08, 2017 (151)
48 TOPMED ss3066397790 Nov 08, 2017 (151)
49 CSHL ss3343272530 Nov 08, 2017 (151)
50 ILLUMINA ss3626006482 Oct 11, 2018 (152)
51 ILLUMINA ss3637732360 Oct 11, 2018 (152)
52 ILLUMINA ss3642746661 Oct 11, 2018 (152)
53 URBANLAB ss3646581199 Oct 11, 2018 (152)
54 EVA_DECODE ss3685992031 Jul 12, 2019 (153)
55 ACPOP ss3726716325 Jul 12, 2019 (153)
56 EVA ss3745720902 Jul 12, 2019 (153)
57 PACBIO ss3783302121 Jul 12, 2019 (153)
58 PACBIO ss3788979991 Jul 12, 2019 (153)
59 PACBIO ss3793852527 Jul 12, 2019 (153)
60 KHV_HUMAN_GENOMES ss3798743507 Jul 12, 2019 (153)
61 EVA ss3825981445 Apr 25, 2020 (154)
62 EVA ss3836378389 Apr 25, 2020 (154)
63 EVA ss3841782390 Apr 25, 2020 (154)
64 SGDP_PRJ ss3847995210 Apr 25, 2020 (154)
65 KRGDB ss3892835577 Apr 25, 2020 (154)
66 KOGIC ss3943629382 Apr 25, 2020 (154)
67 EVA ss4016889035 Apr 25, 2021 (155)
68 TOMMO_GENOMICS ss5142051703 Apr 25, 2021 (155)
69 1000Genomes NC_000001.10 - 760912 Oct 11, 2018 (152)
70 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 760912 Oct 11, 2018 (152)
71 The Danish reference pan genome NC_000001.10 - 760912 Apr 25, 2020 (154)
72 gnomAD - Genomes NC_000001.11 - 825532 Apr 25, 2021 (155)
73 Genome of the Netherlands Release 5 NC_000001.10 - 760912 Apr 25, 2020 (154)
74 HapMap NC_000001.11 - 825532 Apr 25, 2020 (154)
75 KOREAN population from KRGDB NC_000001.10 - 760912 Apr 25, 2020 (154)
76 Korean Genome Project NC_000001.11 - 825532 Apr 25, 2020 (154)
77 Northern Sweden NC_000001.10 - 760912 Jul 12, 2019 (153)
78 Qatari NC_000001.10 - 760912 Apr 25, 2020 (154)
79 SGDP_PRJ NC_000001.10 - 760912 Apr 25, 2020 (154)
80 8.3KJPN NC_000001.10 - 760912 Apr 25, 2021 (155)
81 UK 10K study - Twins NC_000001.10 - 760912 Oct 11, 2018 (152)
82 A Vietnamese Genetic Variation Database NC_000001.10 - 760912 Jul 12, 2019 (153)
83 ALFA NC_000001.11 - 825532 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)
rs3175776 Jul 03, 2002 (106)
rs4081590 Dec 16, 2002 (110)
rs7515682 Aug 27, 2003 (117)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
397932652 NC_000001.11:825531:C:A NC_000001.11:825531:C:A
ss78852399 NC_000001.8:800774:C:T NC_000001.11:825531:C:T (self)
ss87155773, ss107938275, ss109937276, ss118438281, ss197885432, ss205161238, ss252864114, ss275680797, ss283987383, ss290493782, ss1584129454, ss1712305458, ss3642746661 NC_000001.9:750774:C:T NC_000001.11:825531:C:T (self)
3753, 239, 1358376, 365, 12971, 1190, 2197, 12190, 21010, 239, 48, ss218190389, ss230395469, ss238114976, ss536609952, ss553710388, ss647516153, ss974769293, ss1067612337, ss1289339032, ss1425684826, ss1573851142, ss1599378343, ss1642372376, ss1793705724, ss1917960267, ss1966667322, ss2019498401, ss2321502949, ss2624264760, ss2697374589, ss2750637726, ss2986148904, ss3343272530, ss3626006482, ss3637732360, ss3726716325, ss3745720902, ss3783302121, ss3788979991, ss3793852527, ss3825981445, ss3836378389, ss3847995210, ss3892835577, ss4016889035, ss5142051703 NC_000001.10:760911:C:T NC_000001.11:825531:C:T (self)
63120, 49, 7383, 397932652, ss3023513710, ss3066397790, ss3646581199, ss3685992031, ss3798743507, ss3841782390, ss3943629382 NC_000001.11:825531:C:T NC_000001.11:825531:C:T (self)
ss4358500, ss6040318, ss75004583, ss97913205, ss105111678, ss119380166, ss137752234, ss138897564, ss154522359, ss170151194 NT_004350.19:239543:C:T NC_000001.11:825531:C:T (self)
ss11348776 NT_034471.3:239543:C:T NC_000001.11:825531:C: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 rs1048488

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