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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.

rs4403648

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83376263 (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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.165953 (22086/133086, ALFA)
C=0.05024 (842/16760, 8.3KJPN)
C=0.1300 (651/5008, 1000G) (+ 13 more)
C=0.2071 (798/3854, ALSPAC)
C=0.2087 (774/3708, TWINSUK)
C=0.0637 (186/2922, KOREAN)
C=0.1169 (221/1890, HapMap)
C=0.1496 (170/1136, Daghestan)
C=0.197 (197/998, GoNL)
C=0.248 (149/600, NorthernSweden)
C=0.083 (18/216, Qatari)
C=0.090 (19/212, Vietnamese)
A=0.464 (51/110, SGDP_PRJ)
C=0.30 (12/40, GENOME_DK)
A=0.50 (8/16, Siberian)
C=0.50 (8/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC107985037 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

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 133086 A=0.834047 C=0.165953, G=0.000000, T=0.000000
European Sub 112410 A=0.823815 C=0.176185, G=0.000000, T=0.000000
African Sub 8136 A=0.9079 C=0.0921, G=0.0000, T=0.0000
African Others Sub 296 A=0.926 C=0.074, G=0.000, T=0.000
African American Sub 7840 A=0.9073 C=0.0927, G=0.0000, T=0.0000
Asian Sub 308 A=0.935 C=0.065, G=0.000, T=0.000
East Asian Sub 220 A=0.955 C=0.045, G=0.000, T=0.000
Other Asian Sub 88 A=0.89 C=0.11, G=0.00, T=0.00
Latin American 1 Sub 652 A=0.768 C=0.232, G=0.000, T=0.000
Latin American 2 Sub 5948 A=0.9213 C=0.0787, G=0.0000, T=0.0000
South Asian Sub 152 A=0.947 C=0.053, G=0.000, T=0.000
Other Sub 5480 A=0.8385 C=0.1615, G=0.0000, T=0.0000


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
8.3KJPN JAPANESE Study-wide 16760 A=0.94976 C=0.05024
1000Genomes Global Study-wide 5008 A=0.8700 C=0.1300
1000Genomes African Sub 1322 A=0.8752 C=0.1248
1000Genomes East Asian Sub 1008 A=0.9236 C=0.0764
1000Genomes Europe Sub 1006 A=0.7992 C=0.2008
1000Genomes South Asian Sub 978 A=0.846 C=0.154
1000Genomes American Sub 694 A=0.919 C=0.081
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7929 C=0.2071
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.7913 C=0.2087
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9363 C=0.0637
HapMap Global Study-wide 1890 A=0.8831 C=0.1169
HapMap American Sub 768 A=0.876 C=0.124
HapMap African Sub 692 A=0.909 C=0.091
HapMap Asian Sub 254 A=0.933 C=0.067
HapMap Europe Sub 176 A=0.739 C=0.261
Genome-wide autozygosity in Daghestan Global Study-wide 1136 A=0.8504 C=0.1496
Genome-wide autozygosity in Daghestan Daghestan Sub 628 A=0.858 C=0.142
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.854 C=0.146
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.869 C=0.131
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.824 C=0.176
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=0.84 C=0.16
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.75 C=0.25
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.803 C=0.197
Northern Sweden ACPOP Study-wide 600 A=0.752 C=0.248
Qatari Global Study-wide 216 A=0.917 C=0.083
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.910 C=0.090
SGDP_PRJ Global Study-wide 110 A=0.464 C=0.536
The Danish reference pan genome Danish Study-wide 40 A=0.70 C=0.30
Siberian Global Study-wide 16 A=0.50 C=0.50
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.83376263A>C
GRCh38.p13 chr 1 NC_000001.11:g.83376263A>G
GRCh38.p13 chr 1 NC_000001.11:g.83376263A>T
GRCh37.p13 chr 1 NC_000001.10:g.83841946A>C
GRCh37.p13 chr 1 NC_000001.10:g.83841946A>G
GRCh37.p13 chr 1 NC_000001.10:g.83841946A>T
Gene: LOC107985037, uncharacterized LOC107985037 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985037 transcript XR_001738121.1:n. N/A Intron Variant
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
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= C G T
GRCh38.p13 chr 1 NC_000001.11:g.83376263= NC_000001.11:g.83376263A>C NC_000001.11:g.83376263A>G NC_000001.11:g.83376263A>T
GRCh37.p13 chr 1 NC_000001.10:g.83841946= NC_000001.10:g.83841946A>C NC_000001.10:g.83841946A>G NC_000001.10:g.83841946A>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#.

76 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5886371 Feb 20, 2003 (111)
2 SC_JCM ss13504714 Dec 05, 2003 (123)
3 SSAHASNP ss20525244 Apr 05, 2004 (123)
4 PERLEGEN ss23145061 Sep 21, 2004 (124)
5 ILLUMINA ss75073776 Dec 07, 2007 (129)
6 HUMANGENOME_JCVI ss99223626 Feb 05, 2009 (130)
7 ILLUMINA-UK ss118851259 Feb 14, 2009 (130)
8 KRIBB_YJKIM ss119476156 Dec 01, 2009 (131)
9 ENSEMBL ss131819153 Dec 01, 2009 (131)
10 ILLUMINA ss160677520 Dec 01, 2009 (131)
11 ILLUMINA ss173727921 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss205325249 Jul 04, 2010 (132)
13 1000GENOMES ss230613246 Jul 14, 2010 (132)
14 1000GENOMES ss238291201 Jul 15, 2010 (132)
15 GMI ss275904011 May 04, 2012 (137)
16 PJP ss290551205 May 09, 2011 (134)
17 ILLUMINA ss480939698 May 04, 2012 (137)
18 ILLUMINA ss480959259 May 04, 2012 (137)
19 ILLUMINA ss481924545 Sep 08, 2015 (146)
20 ILLUMINA ss485264823 May 04, 2012 (137)
21 ILLUMINA ss537233641 Sep 08, 2015 (146)
22 TISHKOFF ss554363243 Apr 25, 2013 (138)
23 SSMP ss648177772 Apr 25, 2013 (138)
24 ILLUMINA ss778535534 Aug 21, 2014 (142)
25 ILLUMINA ss783078336 Aug 21, 2014 (142)
26 ILLUMINA ss784036013 Aug 21, 2014 (142)
27 ILLUMINA ss832336606 Apr 01, 2015 (144)
28 ILLUMINA ss833992105 Aug 21, 2014 (142)
29 EVA-GONL ss975367588 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1068044352 Aug 21, 2014 (142)
31 1000GENOMES ss1291676605 Aug 21, 2014 (142)
32 HAMMER_LAB ss1397251793 Sep 08, 2015 (146)
33 DDI ss1425876984 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1574192867 Apr 01, 2015 (144)
35 EVA_DECODE ss1584741210 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1600584585 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1643578618 Apr 01, 2015 (144)
38 EVA_SVP ss1712348449 Apr 01, 2015 (144)
39 ILLUMINA ss1751935406 Sep 08, 2015 (146)
40 WEILL_CORNELL_DGM ss1918570899 Feb 12, 2016 (147)
41 JJLAB ss2019805736 Sep 14, 2016 (149)
42 USC_VALOUEV ss2147822750 Dec 20, 2016 (150)
43 TOPMED ss2326439940 Dec 20, 2016 (150)
44 ILLUMINA ss2632540037 Nov 08, 2017 (151)
45 GRF ss2697745697 Nov 08, 2017 (151)
46 GNOMAD ss2757387360 Nov 08, 2017 (151)
47 SWEGEN ss2987129423 Nov 08, 2017 (151)
48 TOPMED ss3081788541 Nov 08, 2017 (151)
49 TOPMED ss3081788542 Nov 08, 2017 (151)
50 TOPMED ss3081788543 Nov 08, 2017 (151)
51 CSHL ss3343544955 Nov 08, 2017 (151)
52 ILLUMINA ss3626140563 Oct 11, 2018 (152)
53 ILLUMINA ss3630574892 Oct 11, 2018 (152)
54 ILLUMINA ss3632898774 Oct 11, 2018 (152)
55 ILLUMINA ss3633593605 Oct 11, 2018 (152)
56 ILLUMINA ss3634333519 Oct 11, 2018 (152)
57 ILLUMINA ss3635287315 Oct 11, 2018 (152)
58 ILLUMINA ss3636010746 Oct 11, 2018 (152)
59 ILLUMINA ss3637037760 Oct 11, 2018 (152)
60 ILLUMINA ss3637768414 Oct 11, 2018 (152)
61 ILLUMINA ss3640040880 Oct 11, 2018 (152)
62 ILLUMINA ss3642779254 Oct 11, 2018 (152)
63 URBANLAB ss3646706508 Oct 11, 2018 (152)
64 ILLUMINA ss3651432932 Oct 11, 2018 (152)
65 EVA_DECODE ss3687154307 Jul 12, 2019 (153)
66 ACPOP ss3727218870 Jul 12, 2019 (153)
67 ILLUMINA ss3744634484 Jul 12, 2019 (153)
68 EVA ss3746442285 Jul 12, 2019 (153)
69 ILLUMINA ss3772135783 Jul 12, 2019 (153)
70 KHV_HUMAN_GENOMES ss3799448771 Jul 12, 2019 (153)
71 EVA ss3826272282 Apr 25, 2020 (154)
72 SGDP_PRJ ss3849255282 Apr 25, 2020 (154)
73 KRGDB ss3894307128 Apr 25, 2020 (154)
74 TOPMED ss4456763762 Apr 25, 2021 (155)
75 TOPMED ss4456763763 Apr 25, 2021 (155)
76 TOMMO_GENOMICS ss5144821882 Apr 25, 2021 (155)
77 1000Genomes NC_000001.10 - 83841946 Oct 11, 2018 (152)
78 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 83841946 Oct 11, 2018 (152)
79 Genome-wide autozygosity in Daghestan NC_000001.9 - 83614534 Apr 25, 2020 (154)
80 The Danish reference pan genome NC_000001.10 - 83841946 Apr 25, 2020 (154)
81 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 17111866 (NC_000001.11:83376262:A:C 23341/140120)
Row 17111867 (NC_000001.11:83376262:A:T 2/140154)

- Apr 25, 2021 (155)
82 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 17111866 (NC_000001.11:83376262:A:C 23341/140120)
Row 17111867 (NC_000001.11:83376262:A:T 2/140154)

- Apr 25, 2021 (155)
83 Genome of the Netherlands Release 5 NC_000001.10 - 83841946 Apr 25, 2020 (154)
84 HapMap NC_000001.11 - 83376263 Apr 25, 2020 (154)
85 KOREAN population from KRGDB NC_000001.10 - 83841946 Apr 25, 2020 (154)
86 Northern Sweden NC_000001.10 - 83841946 Jul 12, 2019 (153)
87 Qatari NC_000001.10 - 83841946 Apr 25, 2020 (154)
88 SGDP_PRJ NC_000001.10 - 83841946 Apr 25, 2020 (154)
89 Siberian NC_000001.10 - 83841946 Apr 25, 2020 (154)
90 8.3KJPN NC_000001.10 - 83841946 Apr 25, 2021 (155)
91 TopMed

Submission ignored due to conflicting rows:
Row 20370097 (NC_000001.11:83376262:A:C 41833/264690)
Row 20370098 (NC_000001.11:83376262:A:G 4/264690)

- Apr 25, 2021 (155)
92 TopMed

Submission ignored due to conflicting rows:
Row 20370097 (NC_000001.11:83376262:A:C 41833/264690)
Row 20370098 (NC_000001.11:83376262:A:G 4/264690)

- Apr 25, 2021 (155)
93 UK 10K study - Twins NC_000001.10 - 83841946 Oct 11, 2018 (152)
94 A Vietnamese Genetic Variation Database NC_000001.10 - 83841946 Jul 12, 2019 (153)
95 ALFA NC_000001.11 - 83376263 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)
rs9701436 Sep 24, 2004 (123)
rs17842720 Dec 02, 2004 (124)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
13132, ss118851259, ss160677520, ss205325249, ss275904011, ss290551205, ss480939698, ss1397251793, ss1584741210, ss1712348449, ss3642779254 NC_000001.9:83614533:A:C NC_000001.11:83376262:A:C (self)
2424108, 1328305, 1583845, 574376, 1484522, 503735, 612829, 1272262, 339104, 2791189, 1328305, 284966, ss230613246, ss238291201, ss480959259, ss481924545, ss485264823, ss537233641, ss554363243, ss648177772, ss778535534, ss783078336, ss784036013, ss832336606, ss833992105, ss975367588, ss1068044352, ss1291676605, ss1425876984, ss1574192867, ss1600584585, ss1643578618, ss1751935406, ss1918570899, ss2019805736, ss2147822750, ss2326439940, ss2632540037, ss2697745697, ss2757387360, ss2987129423, ss3343544955, ss3626140563, ss3630574892, ss3632898774, ss3633593605, ss3634333519, ss3635287315, ss3636010746, ss3637037760, ss3637768414, ss3640040880, ss3651432932, ss3727218870, ss3744634484, ss3746442285, ss3772135783, ss3826272282, ss3849255282, ss3894307128, ss5144821882 NC_000001.10:83841945:A:C NC_000001.11:83376262:A:C (self)
113222, 12830226, 10509308815, ss3081788541, ss3646706508, ss3687154307, ss3799448771, ss4456763762 NC_000001.11:83376262:A:C NC_000001.11:83376262:A:C (self)
ss13504714, ss20525244 NT_026943.13:8662119:A:C NC_000001.11:83376262:A:C (self)
ss5886371, ss23145061, ss75073776, ss99223626, ss119476156, ss131819153, ss173727921 NT_032977.9:53813863:A:C NC_000001.11:83376262:A:C (self)
12830226, 10509308815, ss3081788542, ss4456763763 NC_000001.11:83376262:A:G NC_000001.11:83376262:A:G (self)
10509308815, ss3081788543 NC_000001.11:83376262:A:T NC_000001.11:83376262:A: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 rs4403648

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.post629+eb05767