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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.

rs4648360

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:2806780 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.344059 (91069/264690, TOPMED)
T=0.345117 (48355/140112, GnomAD)
T=0.41622 (16940/40700, ALFA) (+ 16 more)
T=0.39928 (6692/16760, 8.3KJPN)
T=0.2736 (1370/5008, 1000G)
T=0.3984 (1785/4480, Estonian)
T=0.4642 (1789/3854, ALSPAC)
T=0.4458 (1653/3708, TWINSUK)
T=0.4242 (1243/2930, KOREAN)
T=0.2442 (460/1884, HapMap)
T=0.4285 (785/1832, Korea1K)
T=0.497 (496/998, GoNL)
T=0.449 (281/626, Chileans)
T=0.407 (244/600, NorthernSweden)
C=0.336 (84/250, SGDP_PRJ)
T=0.333 (72/216, Qatari)
T=0.358 (76/212, Vietnamese)
T=0.45 (18/40, GENOME_DK)
C=0.35 (9/26, 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.2806780C>G
GRCh38.p13 chr 1 NC_000001.11:g.2806780C>T
GRCh37.p13 chr 1 NC_000001.10:g.2723345C>G
GRCh37.p13 chr 1 NC_000001.10:g.2723345C>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 40700 C=0.58378 T=0.41622
European Sub 30930 C=0.54403 T=0.45597
African Sub 4312 C=0.8859 T=0.1141
African Others Sub 158 C=0.949 T=0.051
African American Sub 4154 C=0.8835 T=0.1165
Asian Sub 136 C=0.676 T=0.324
East Asian Sub 108 C=0.685 T=0.315
Other Asian Sub 28 C=0.64 T=0.36
Latin American 1 Sub 262 C=0.615 T=0.385
Latin American 2 Sub 2758 C=0.5457 T=0.4543
South Asian Sub 114 C=0.711 T=0.289
Other Sub 2188 C=0.5823 T=0.4177


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 C=0.655941 T=0.344059
gnomAD - Genomes Global Study-wide 140112 C=0.654883 T=0.345117
gnomAD - Genomes European Sub 75852 C=0.54671 T=0.45329
gnomAD - Genomes African Sub 42012 C=0.88515 T=0.11485
gnomAD - Genomes American Sub 13648 C=0.59313 T=0.40687
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.5018 T=0.4982
gnomAD - Genomes East Asian Sub 3124 C=0.6424 T=0.3576
gnomAD - Genomes Other Sub 2154 C=0.6184 T=0.3816
Allele Frequency Aggregator Total Global 40700 C=0.58378 T=0.41622
Allele Frequency Aggregator European Sub 30930 C=0.54403 T=0.45597
Allele Frequency Aggregator African Sub 4312 C=0.8859 T=0.1141
Allele Frequency Aggregator Latin American 2 Sub 2758 C=0.5457 T=0.4543
Allele Frequency Aggregator Other Sub 2188 C=0.5823 T=0.4177
Allele Frequency Aggregator Latin American 1 Sub 262 C=0.615 T=0.385
Allele Frequency Aggregator Asian Sub 136 C=0.676 T=0.324
Allele Frequency Aggregator South Asian Sub 114 C=0.711 T=0.289
8.3KJPN JAPANESE Study-wide 16760 C=0.60072 T=0.39928
1000Genomes Global Study-wide 5008 C=0.7264 T=0.2736
1000Genomes African Sub 1322 C=0.9516 T=0.0484
1000Genomes East Asian Sub 1008 C=0.6657 T=0.3343
1000Genomes Europe Sub 1006 C=0.5427 T=0.4573
1000Genomes South Asian Sub 978 C=0.755 T=0.245
1000Genomes American Sub 694 C=0.612 T=0.388
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.6016 T=0.3984
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.5358 T=0.4642
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.5542 T=0.4458
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5758 G=0.0000, T=0.4242
HapMap Global Study-wide 1884 C=0.7558 T=0.2442
HapMap American Sub 768 C=0.677 T=0.323
HapMap African Sub 686 C=0.945 T=0.055
HapMap Asian Sub 254 C=0.614 T=0.386
HapMap Europe Sub 176 C=0.568 T=0.432
Korean Genome Project KOREAN Study-wide 1832 C=0.5715 T=0.4285
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.503 T=0.497
Chileans Chilean Study-wide 626 C=0.551 T=0.449
Northern Sweden ACPOP Study-wide 600 C=0.593 T=0.407
SGDP_PRJ Global Study-wide 250 C=0.336 T=0.664
Qatari Global Study-wide 216 C=0.667 T=0.333
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.642 T=0.358
The Danish reference pan genome Danish Study-wide 40 C=0.55 T=0.45
Siberian Global Study-wide 26 C=0.35 T=0.65
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= G T
GRCh38.p13 chr 1 NC_000001.11:g.2806780= NC_000001.11:g.2806780C>G NC_000001.11:g.2806780C>T
GRCh37.p13 chr 1 NC_000001.10:g.2723345= NC_000001.10:g.2723345C>G NC_000001.10:g.2723345C>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#.

85 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6396353 Feb 20, 2003 (111)
2 PERLEGEN ss23839941 Sep 20, 2004 (123)
3 ABI ss43899899 Mar 14, 2006 (126)
4 AFFY ss66216390 Dec 01, 2006 (127)
5 PERLEGEN ss68756458 May 18, 2007 (127)
6 ILLUMINA ss75095705 Dec 07, 2007 (129)
7 AFFY ss76362801 Dec 07, 2007 (129)
8 HGSV ss77414586 Dec 07, 2007 (129)
9 KRIBB_YJKIM ss82076706 Dec 15, 2007 (130)
10 HUMANGENOME_JCVI ss97914967 Feb 03, 2009 (130)
11 1000GENOMES ss107943063 Jan 22, 2009 (130)
12 ENSEMBL ss138987986 Dec 01, 2009 (131)
13 GMI ss154547277 Dec 01, 2009 (131)
14 COMPLETE_GENOMICS ss163723873 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss165997523 Jul 04, 2010 (132)
16 AFFY ss173385910 Jul 04, 2010 (132)
17 ILLUMINA ss173767965 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss205090440 Jul 04, 2010 (132)
19 1000GENOMES ss218197377 Jul 14, 2010 (132)
20 1000GENOMES ss230400396 Jul 14, 2010 (132)
21 1000GENOMES ss238119536 Jul 15, 2010 (132)
22 GMI ss275688032 May 04, 2012 (137)
23 PJP ss290496714 May 09, 2011 (134)
24 ILLUMINA ss410934591 Sep 17, 2011 (135)
25 ILLUMINA ss479833689 May 04, 2012 (137)
26 ILLUMINA ss482305924 May 04, 2012 (137)
27 ILLUMINA ss533318782 Sep 08, 2015 (146)
28 TISHKOFF ss553725608 Apr 25, 2013 (138)
29 SSMP ss647529346 Apr 25, 2013 (138)
30 ILLUMINA ss779660439 Sep 08, 2015 (146)
31 ILLUMINA ss781080074 Sep 08, 2015 (146)
32 ILLUMINA ss835133694 Sep 08, 2015 (146)
33 EVA-GONL ss974785992 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1067621017 Aug 21, 2014 (142)
35 1000GENOMES ss1289412516 Aug 21, 2014 (142)
36 DDI ss1425690028 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1573856649 Apr 01, 2015 (144)
38 EVA_DECODE ss1584145553 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1599407772 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1642401805 Apr 01, 2015 (144)
41 EVA_SVP ss1712306198 Apr 01, 2015 (144)
42 WEILL_CORNELL_DGM ss1917980757 Feb 12, 2016 (147)
43 GENOMED ss1966669651 Jul 19, 2016 (147)
44 JJLAB ss2019506691 Sep 14, 2016 (149)
45 ILLUMINA ss2094840019 Dec 20, 2016 (150)
46 ILLUMINA ss2094949701 Dec 20, 2016 (150)
47 USC_VALOUEV ss2147496487 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2159494595 Dec 20, 2016 (150)
49 TOPMED ss2321650465 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2624269196 Nov 08, 2017 (151)
51 ILLUMINA ss2632467242 Nov 08, 2017 (151)
52 ILLUMINA ss2634995436 Nov 08, 2017 (151)
53 GRF ss2697389915 Nov 08, 2017 (151)
54 GNOMAD ss2750868064 Nov 08, 2017 (151)
55 SWEGEN ss2986185952 Nov 08, 2017 (151)
56 ILLUMINA ss3021046245 Nov 08, 2017 (151)
57 BIOINF_KMB_FNS_UNIBA ss3023517163 Nov 08, 2017 (151)
58 TOPMED ss3066898688 Nov 08, 2017 (151)
59 CSHL ss3343283920 Nov 08, 2017 (151)
60 ILLUMINA ss3626009763 Oct 11, 2018 (152)
61 ILLUMINA ss3630506853 Oct 11, 2018 (152)
62 ILLUMINA ss3637733290 Oct 11, 2018 (152)
63 ILLUMINA ss3641567117 Oct 11, 2018 (152)
64 ILLUMINA ss3642747519 Oct 11, 2018 (152)
65 URBANLAB ss3646585113 Oct 11, 2018 (152)
66 ILLUMINA ss3651368705 Oct 11, 2018 (152)
67 ILLUMINA ss3651368706 Oct 11, 2018 (152)
68 EGCUT_WGS ss3654286922 Jul 12, 2019 (153)
69 EVA_DECODE ss3686028125 Jul 12, 2019 (153)
70 ILLUMINA ss3724989958 Jul 12, 2019 (153)
71 ACPOP ss3726731261 Jul 12, 2019 (153)
72 EVA ss3745742205 Jul 12, 2019 (153)
73 PACBIO ss3783306806 Jul 12, 2019 (153)
74 PACBIO ss3788983869 Jul 12, 2019 (153)
75 PACBIO ss3793856487 Jul 12, 2019 (153)
76 KHV_HUMAN_GENOMES ss3798764860 Jul 12, 2019 (153)
77 EVA ss3825989148 Apr 25, 2020 (154)
78 EVA ss3836381855 Apr 25, 2020 (154)
79 EVA ss3841785956 Apr 25, 2020 (154)
80 SGDP_PRJ ss3848046727 Apr 25, 2020 (154)
81 KRGDB ss3892905905 Apr 25, 2020 (154)
82 KOGIC ss3943670070 Apr 25, 2020 (154)
83 EVA ss4016889698 Apr 25, 2021 (155)
84 TOPMED ss4437008177 Apr 25, 2021 (155)
85 TOMMO_GENOMICS ss5142156513 Apr 25, 2021 (155)
86 1000Genomes NC_000001.10 - 2723345 Oct 11, 2018 (152)
87 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 2723345 Oct 11, 2018 (152)
88 Chileans NC_000001.10 - 2723345 Apr 25, 2020 (154)
89 Genetic variation in the Estonian population NC_000001.10 - 2723345 Oct 11, 2018 (152)
90 The Danish reference pan genome NC_000001.10 - 2723345 Apr 25, 2020 (154)
91 gnomAD - Genomes NC_000001.11 - 2806780 Apr 25, 2021 (155)
92 Genome of the Netherlands Release 5 NC_000001.10 - 2723345 Apr 25, 2020 (154)
93 HapMap NC_000001.11 - 2806780 Apr 25, 2020 (154)
94 KOREAN population from KRGDB NC_000001.10 - 2723345 Apr 25, 2020 (154)
95 Korean Genome Project NC_000001.11 - 2806780 Apr 25, 2020 (154)
96 Northern Sweden NC_000001.10 - 2723345 Jul 12, 2019 (153)
97 Qatari NC_000001.10 - 2723345 Apr 25, 2020 (154)
98 SGDP_PRJ NC_000001.10 - 2723345 Apr 25, 2020 (154)
99 Siberian NC_000001.10 - 2723345 Apr 25, 2020 (154)
100 8.3KJPN NC_000001.10 - 2723345 Apr 25, 2021 (155)
101 TopMed NC_000001.11 - 2806780 Apr 25, 2021 (155)
102 UK 10K study - Twins NC_000001.10 - 2723345 Oct 11, 2018 (152)
103 A Vietnamese Genetic Variation Database NC_000001.10 - 2723345 Jul 12, 2019 (153)
104 ALFA NC_000001.11 - 2806780 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)
rs58567877 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
83299, ss3892905905 NC_000001.10:2723344:C:G NC_000001.11:2806779:C:G (self)
ss77414586 NC_000001.8:2746501:C:T NC_000001.11:2806779:C:T (self)
ss107943063, ss163723873, ss165997523, ss205090440, ss275688032, ss290496714, ss482305924, ss1584145553, ss1712306198, ss2094840019, ss2634995436, ss3642747519 NC_000001.9:2713204:C:T NC_000001.11:2806779:C:T (self)
79462, 32530, 80, 25170, 1363883, 13666, 83299, 16126, 22687, 63707, 12841, 125820, 32530, 6655, ss218197377, ss230400396, ss238119536, ss479833689, ss533318782, ss553725608, ss647529346, ss779660439, ss781080074, ss835133694, ss974785992, ss1067621017, ss1289412516, ss1425690028, ss1573856649, ss1599407772, ss1642401805, ss1917980757, ss1966669651, ss2019506691, ss2094949701, ss2147496487, ss2321650465, ss2624269196, ss2632467242, ss2697389915, ss2750868064, ss2986185952, ss3021046245, ss3343283920, ss3626009763, ss3630506853, ss3637733290, ss3641567117, ss3651368705, ss3651368706, ss3654286922, ss3726731261, ss3745742205, ss3783306806, ss3788983869, ss3793856487, ss3825989148, ss3836381855, ss3848046727, ss3892905905, ss4016889698, ss5142156513 NC_000001.10:2723344:C:T NC_000001.11:2806779:C:T (self)
609075, 1425, 48071, 378049, 614512, 1669584224, ss2159494595, ss3023517163, ss3066898688, ss3646585113, ss3686028125, ss3724989958, ss3798764860, ss3841785956, ss3943670070, ss4437008177 NC_000001.11:2806779:C:T NC_000001.11:2806779:C:T (self)
ss6396353, ss23839941, ss43899899, ss66216390, ss68756458, ss75095705, ss76362801, ss82076706, ss97914967, ss138987986, ss154547277, ss173385910, ss173767965, ss410934591 NT_004350.19:2201976:C:T NC_000001.11:2806779: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 rs4648360

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