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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.

rs4421048

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr4:55079914 (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>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.009143 (2420/264690, TOPMED)
A=0.002944 (740/251332, GnomAD_exome)
A=0.008548 (1199/140262, GnomAD) (+ 17 more)
A=0.003212 (390/121406, ExAC)
A=0.00505 (210/41598, ALFA)
A=0.00006 (1/16760, 8.3KJPN)
A=0.00800 (104/13006, GO-ESP)
A=0.0072 (36/5008, 1000G)
A=0.0000 (0/3854, ALSPAC)
A=0.0005 (2/3708, TWINSUK)
A=0.0003 (1/2930, KOREAN)
A=0.0000 (0/1832, Korea1K)
A=0.003 (3/998, GoNL)
A=0.000 (0/600, NorthernSweden)
A=0.004 (2/558, SGDP_PRJ)
A=0.009 (5/534, MGP)
A=0.009 (2/216, Qatari)
A=0.000 (0/214, Vietnamese)
A=0.00 (0/56, Siberian)
A=0.00 (0/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
KDR : 3 Prime UTR Variant
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 4 NC_000004.12:g.55079914A>G
GRCh38.p13 chr 4 NC_000004.12:g.55079914A>T
GRCh37.p13 chr 4 NC_000004.11:g.55946081A>G
GRCh37.p13 chr 4 NC_000004.11:g.55946081A>T
KDR RefSeqGene (LRG_1198) NG_012004.1:g.50682T>C
KDR RefSeqGene (LRG_1198) NG_012004.1:g.50682T>A
Gene: KDR, kinase insert domain receptor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
KDR transcript NM_002253.4:c.*27= N/A 3 Prime UTR 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

ALFA Allele Frequency (New)
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 41598 A=0.00505 G=0.99495
European Sub 30718 A=0.00114 G=0.99886
African Sub 6358 A=0.0256 G=0.9744
African Others Sub 216 A=0.032 G=0.968
African American Sub 6142 A=0.0254 G=0.9746
Asian Sub 184 A=0.000 G=1.000
East Asian Sub 126 A=0.000 G=1.000
Other Asian Sub 58 A=0.00 G=1.00
Latin American 1 Sub 168 A=0.006 G=0.994
Latin American 2 Sub 700 A=0.001 G=0.999
South Asian Sub 114 A=0.000 G=1.000
Other Sub 3356 A=0.0030 G=0.9970


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 A=0.009143 G=0.990857
gnomAD - Exomes Global Study-wide 251332 A=0.002944 G=0.997056
gnomAD - Exomes European Sub 135274 A=0.000658 G=0.999342
gnomAD - Exomes Asian Sub 49010 A=0.00004 G=0.99996
gnomAD - Exomes American Sub 34590 A=0.00437 G=0.99563
gnomAD - Exomes African Sub 16256 A=0.02559 G=0.97441
gnomAD - Exomes Ashkenazi Jewish Sub 10072 A=0.00496 G=0.99504
gnomAD - Exomes Other Sub 6130 A=0.0052 G=0.9948
gnomAD - Genomes Global Study-wide 140262 A=0.008548 G=0.991452
gnomAD - Genomes European Sub 75964 A=0.00068 G=0.99932
gnomAD - Genomes African Sub 42024 A=0.02510 G=0.97490
gnomAD - Genomes American Sub 13662 A=0.00483 G=0.99517
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.0048 G=0.9952
gnomAD - Genomes East Asian Sub 3134 A=0.0000 G=1.0000
gnomAD - Genomes Other Sub 2154 A=0.0046 G=0.9954
ExAC Global Study-wide 121406 A=0.003212 G=0.996788
ExAC Europe Sub 73352 A=0.00094 G=0.99906
ExAC Asian Sub 25166 A=0.00004 G=0.99996
ExAC American Sub 11574 A=0.00553 G=0.99447
ExAC African Sub 10406 A=0.02412 G=0.97588
ExAC Other Sub 908 A=0.006 G=0.994
8.3KJPN JAPANESE Study-wide 16760 A=0.00006 G=0.99994
GO Exome Sequencing Project Global Study-wide 13006 A=0.00800 G=0.99200
GO Exome Sequencing Project European American Sub 8600 A=0.0002 G=0.9998
GO Exome Sequencing Project African American Sub 4406 A=0.0232 G=0.9768
1000Genomes Global Study-wide 5008 A=0.0072 G=0.9928
1000Genomes African Sub 1322 A=0.0242 G=0.9758
1000Genomes East Asian Sub 1008 A=0.0000 G=1.0000
1000Genomes Europe Sub 1006 A=0.0000 G=1.0000
1000Genomes South Asian Sub 978 A=0.000 G=1.000
1000Genomes American Sub 694 A=0.006 G=0.994
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.0000 G=1.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.0005 G=0.9995
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0003 G=0.9997, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.0000 G=1.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.003 G=0.997
Northern Sweden ACPOP Study-wide 600 A=0.000 G=1.000
SGDP_PRJ Global Study-wide 558 A=0.004 G=0.996
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.009 G=0.991
Qatari Global Study-wide 216 A=0.009 G=0.991
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.000 G=1.000
Siberian Global Study-wide 56 A=0.00 G=1.00
The Danish reference pan genome Danish Study-wide 40 A=0.00 G=1.00
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= G T
GRCh38.p13 chr 4 NC_000004.12:g.55079914= NC_000004.12:g.55079914A>G NC_000004.12:g.55079914A>T
GRCh37.p13 chr 4 NC_000004.11:g.55946081= NC_000004.11:g.55946081A>G NC_000004.11:g.55946081A>T
KDR RefSeqGene (LRG_1198) NG_012004.1:g.50682= NG_012004.1:g.50682T>C NG_012004.1:g.50682T>A
KDR transcript NM_002253.4:c.*27= NM_002253.4:c.*27T>C NM_002253.4:c.*27T>A
KDR transcript NM_002253.3:c.*27= NM_002253.3:c.*27T>C NM_002253.3:c.*27T>A
KDR transcript NM_002253.2:c.*27= NM_002253.2:c.*27T>C NM_002253.2:c.*27T>A
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#.

93 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss5917842 Feb 20, 2003 (111)
2 WI_SSAHASNP ss14312151 Dec 05, 2003 (119)
3 CSHL-HAPMAP ss16996391 Feb 27, 2004 (120)
4 SSAHASNP ss22060067 Apr 05, 2004 (121)
5 HGSV ss77172457 Dec 06, 2007 (129)
6 HGSV ss78072204 Dec 06, 2007 (129)
7 HGSV ss78577881 Dec 06, 2007 (129)
8 BCMHGSC_JDW ss92585368 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss98823456 Feb 04, 2009 (130)
10 BGI ss105827179 Feb 04, 2009 (130)
11 1000GENOMES ss112252352 Jan 25, 2009 (130)
12 1000GENOMES ss113065821 Jan 25, 2009 (130)
13 ILLUMINA-UK ss116992316 Feb 14, 2009 (130)
14 ENSEMBL ss134695999 Dec 01, 2009 (131)
15 ENSEMBL ss139614445 Dec 01, 2009 (131)
16 GMI ss157264123 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss162115057 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss163445758 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss166583343 Jul 04, 2010 (132)
20 ILLUMINA ss168900644 Jul 04, 2010 (132)
21 BUSHMAN ss198510483 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss206256310 Jul 04, 2010 (132)
23 1000GENOMES ss220918810 Jul 14, 2010 (132)
24 1000GENOMES ss232387621 Jul 14, 2010 (132)
25 1000GENOMES ss239681848 Jul 15, 2010 (132)
26 BL ss253137072 May 09, 2011 (134)
27 GMI ss277713499 May 04, 2012 (137)
28 GMI ss284907045 Apr 25, 2013 (138)
29 PJP ss293070420 May 09, 2011 (134)
30 ILLUMINA ss479716673 May 04, 2012 (137)
31 ILLUMINA ss484832387 May 04, 2012 (137)
32 1000GENOMES ss490887579 May 04, 2012 (137)
33 ILLUMINA ss533220650 Sep 08, 2015 (146)
34 TISHKOFF ss557508769 Apr 25, 2013 (138)
35 SSMP ss651304943 Apr 25, 2013 (138)
36 NHLBI-ESP ss712594913 Apr 25, 2013 (138)
37 ILLUMINA ss779167889 Aug 21, 2014 (142)
38 ILLUMINA ss781050847 Aug 21, 2014 (142)
39 ILLUMINA ss834633015 Aug 21, 2014 (142)
40 EVA-GONL ss980101013 Aug 21, 2014 (142)
41 JMKIDD_LAB ss1071526847 Aug 21, 2014 (142)
42 1000GENOMES ss1309691498 Aug 21, 2014 (142)
43 DDI ss1429878937 Apr 01, 2015 (144)
44 EVA_GENOME_DK ss1580550225 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1610063719 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1653057752 Apr 01, 2015 (144)
47 EVA_EXAC ss1687495488 Apr 01, 2015 (144)
48 EVA_MGP ss1711059799 Apr 01, 2015 (144)
49 HAMMER_LAB ss1801430393 Sep 08, 2015 (146)
50 WEILL_CORNELL_DGM ss1923340182 Feb 12, 2016 (147)
51 GENOMED ss1966658495 Feb 12, 2016 (147)
52 JJLAB ss2022253682 Sep 14, 2016 (149)
53 USC_VALOUEV ss2150378824 Dec 20, 2016 (150)
54 HUMAN_LONGEVITY ss2262859912 Dec 20, 2016 (150)
55 TOPMED ss2430510443 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2625626132 Nov 08, 2017 (151)
57 ILLUMINA ss2634118682 Nov 08, 2017 (151)
58 GRF ss2705844055 Nov 08, 2017 (151)
59 GNOMAD ss2734512872 Nov 08, 2017 (151)
60 GNOMAD ss2747239022 Nov 08, 2017 (151)
61 GNOMAD ss2809184163 Nov 08, 2017 (151)
62 SWEGEN ss2994682328 Nov 08, 2017 (151)
63 BIOINF_KMB_FNS_UNIBA ss3024897979 Nov 08, 2017 (151)
64 CSHL ss3345708475 Nov 08, 2017 (151)
65 TOPMED ss3428800488 Nov 08, 2017 (151)
66 ILLUMINA ss3628964106 Oct 12, 2018 (152)
67 ILLUMINA ss3632055424 Oct 12, 2018 (152)
68 ILLUMINA ss3638486399 Oct 12, 2018 (152)
69 OMUKHERJEE_ADBS ss3646307593 Oct 12, 2018 (152)
70 URBANLAB ss3647726527 Oct 12, 2018 (152)
71 EVA_DECODE ss3712030544 Jul 13, 2019 (153)
72 ACPOP ss3731137651 Jul 13, 2019 (153)
73 EVA ss3761783788 Jul 13, 2019 (153)
74 PACBIO ss3784710868 Jul 13, 2019 (153)
75 PACBIO ss3790168980 Jul 13, 2019 (153)
76 PACBIO ss3795044088 Jul 13, 2019 (153)
77 KHV_HUMAN_GENOMES ss3804919148 Jul 13, 2019 (153)
78 EVA ss3824016422 Apr 26, 2020 (154)
79 EVA ss3828532662 Apr 26, 2020 (154)
80 EVA ss3837703680 Apr 26, 2020 (154)
81 EVA ss3843139755 Apr 26, 2020 (154)
82 SGDP_PRJ ss3858922998 Apr 26, 2020 (154)
83 KRGDB ss3905160445 Apr 26, 2020 (154)
84 KOGIC ss3954167499 Apr 26, 2020 (154)
85 FSA-LAB ss3984283443 Apr 26, 2021 (155)
86 FSA-LAB ss3984283444 Apr 26, 2021 (155)
87 EVA ss3986027547 Apr 26, 2021 (155)
88 EVA ss3986280028 Apr 26, 2021 (155)
89 TOPMED ss4613503524 Apr 26, 2021 (155)
90 TOMMO_GENOMICS ss5165667931 Apr 26, 2021 (155)
91 CPQ_GEN_INCA ss5236854812 Apr 26, 2021 (155)
92 CPQ_GEN_INCA ss5236860054 Apr 26, 2021 (155)
93 EVA ss5237182001 Apr 26, 2021 (155)
94 1000Genomes NC_000004.11 - 55946081 Oct 12, 2018 (152)
95 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 55946081 Oct 12, 2018 (152)
96 ExAC NC_000004.11 - 55946081 Oct 12, 2018 (152)
97 The Danish reference pan genome NC_000004.11 - 55946081 Apr 26, 2020 (154)
98 gnomAD - Genomes NC_000004.12 - 55079914 Apr 26, 2021 (155)
99 gnomAD - Exomes NC_000004.11 - 55946081 Jul 13, 2019 (153)
100 GO Exome Sequencing Project NC_000004.11 - 55946081 Oct 12, 2018 (152)
101 Genome of the Netherlands Release 5 NC_000004.11 - 55946081 Apr 26, 2020 (154)
102 KOREAN population from KRGDB NC_000004.11 - 55946081 Apr 26, 2020 (154)
103 Korean Genome Project NC_000004.12 - 55079914 Apr 26, 2020 (154)
104 Medical Genome Project healthy controls from Spanish population NC_000004.11 - 55946081 Apr 26, 2020 (154)
105 Northern Sweden NC_000004.11 - 55946081 Jul 13, 2019 (153)
106 Qatari NC_000004.11 - 55946081 Apr 26, 2020 (154)
107 SGDP_PRJ NC_000004.11 - 55946081 Apr 26, 2020 (154)
108 Siberian NC_000004.11 - 55946081 Apr 26, 2020 (154)
109 8.3KJPN NC_000004.11 - 55946081 Apr 26, 2021 (155)
110 TopMed NC_000004.12 - 55079914 Apr 26, 2021 (155)
111 UK 10K study - Twins NC_000004.11 - 55946081 Oct 12, 2018 (152)
112 A Vietnamese Genetic Variation Database NC_000004.11 - 55946081 Jul 13, 2019 (153)
113 ALFA NC_000004.12 - 55079914 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77172457, ss78072204, ss78577881 NC_000004.9:55787008:A:G NC_000004.12:55079913:A:G (self)
ss92585368, ss112252352, ss113065821, ss116992316, ss162115057, ss163445758, ss166583343, ss198510483, ss206256310, ss253137072, ss277713499, ss284907045, ss293070420, ss484832387 NC_000004.10:55640837:A:G NC_000004.12:55079913:A:G (self)
21084971, 11734703, 7459782, 6715164, 3616019, 474647, 5173526, 12337839, 175559, 4422516, 5382112, 10939978, 2895178, 23637238, 11734703, 2576729, ss220918810, ss232387621, ss239681848, ss479716673, ss490887579, ss533220650, ss557508769, ss651304943, ss712594913, ss779167889, ss781050847, ss834633015, ss980101013, ss1071526847, ss1309691498, ss1429878937, ss1580550225, ss1610063719, ss1653057752, ss1687495488, ss1711059799, ss1801430393, ss1923340182, ss1966658495, ss2022253682, ss2150378824, ss2430510443, ss2625626132, ss2634118682, ss2705844055, ss2734512872, ss2747239022, ss2809184163, ss2994682328, ss3345708475, ss3628964106, ss3632055424, ss3638486399, ss3646307593, ss3731137651, ss3761783788, ss3784710868, ss3790168980, ss3795044088, ss3824016422, ss3828532662, ss3837703680, ss3858922998, ss3905160445, ss3984283443, ss3984283444, ss3986027547, ss3986280028, ss5165667931, ss5236854812, ss5236860054 NC_000004.11:55946080:A:G NC_000004.12:55079913:A:G (self)
149455614, 10545500, 281821446, 450881080, 6603076665, ss2262859912, ss3024897979, ss3428800488, ss3647726527, ss3712030544, ss3804919148, ss3843139755, ss3954167499, ss4613503524, ss5237182001 NC_000004.12:55079913:A:G NC_000004.12:55079913:A:G (self)
ss14312151, ss16996391, ss22060067 NT_022853.14:3285963:A:G NC_000004.12:55079913:A:G (self)
ss5917842, ss98823456, ss105827179, ss134695999, ss139614445, ss157264123, ss168900644 NT_022853.15:3285963:A:G NC_000004.12:55079913:A:G (self)
12337839, ss3905160445 NC_000004.11:55946080:A:T NC_000004.12:55079913: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 rs4421048

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