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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.

rs6422503

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:266225 (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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.43747 (7332/16760, 8.3KJPN)
C=0.4621 (2630/5692, ALFA)
C=0.4317 (1265/2930, KOREAN) (+ 5 more)
C=0.1086 (199/1832, Korea1K)
C=0.449 (247/550, SGDP_PRJ)
C=0.468 (101/216, Qatari)
C=0.50 (20/40, GENOME_DK)
A=0.50 (20/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC100996442 : Intron 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 1 NC_000001.11:g.266225C>A
GRCh38.p13 chr 1 NC_000001.11:g.266225C>G
GRCh38.p13 chr 1 NC_000001.11:g.266225C>T
GRCh37.p13 chr 1 NC_000001.10:g.235976C>A
GRCh37.p13 chr 1 NC_000001.10:g.235976C>G
GRCh37.p13 chr 1 NC_000001.10:g.235976C>T
Gene: LOC100996442, uncharacterized LOC100996442 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC100996442 transcript variant X12 XR_001737582.2:n. N/A Intron Variant
LOC100996442 transcript variant X4 XR_001737578.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X5 XR_001737579.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X8 XR_001737580.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X11 XR_001737581.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X13 XR_001737583.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X14 XR_001737584.2:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X1 XR_002958514.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X2 XR_002958515.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X3 XR_002958516.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X6 XR_002958517.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X7 XR_002958518.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X9 XR_002958519.1:n. N/A Genic Upstream Transcript Variant
LOC100996442 transcript variant X10 XR_002958520.1:n. N/A Genic Upstream Transcript 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
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 5692 C=0.4621 A=0.5379, G=0.0000, T=0.0000
European Sub 5142 C=0.4769 A=0.5231, G=0.0000, T=0.0000
African Sub 526 C=0.306 A=0.694, G=0.000, T=0.000
African Others Sub 24 C=0.17 A=0.83, G=0.00, T=0.00
African American Sub 502 C=0.313 A=0.687, G=0.000, T=0.000
Asian Sub 0 C=0 A=0, G=0, T=0
East Asian Sub 0 C=0 A=0, G=0, T=0
Other Asian Sub 0 C=0 A=0, G=0, T=0
Latin American 1 Sub 0 C=0 A=0, G=0, T=0
Latin American 2 Sub 4 C=1.0 A=0.0, G=0.0, T=0.0
South Asian Sub 0 C=0 A=0, G=0, T=0
Other Sub 20 C=0.65 A=0.35, G=0.00, T=0.00


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 C=0.43747 A=0.56253
Allele Frequency Aggregator Total Global 5692 C=0.4621 A=0.5379, G=0.0000, T=0.0000
Allele Frequency Aggregator European Sub 5142 C=0.4769 A=0.5231, G=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 526 C=0.306 A=0.694, G=0.000, T=0.000
Allele Frequency Aggregator Other Sub 20 C=0.65 A=0.35, G=0.00, T=0.00
Allele Frequency Aggregator Latin American 2 Sub 4 C=1.0 A=0.0, G=0.0, T=0.0
Allele Frequency Aggregator Latin American 1 Sub 0 C=0 A=0, G=0, T=0
Allele Frequency Aggregator South Asian Sub 0 C=0 A=0, G=0, T=0
Allele Frequency Aggregator Asian Sub 0 C=0 A=0, G=0, T=0
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.4317 A=0.5683
Korean Genome Project KOREAN Study-wide 1832 C=0.1086 A=0.8914
SGDP_PRJ Global Study-wide 550 C=0.449 A=0.551
Qatari Global Study-wide 216 C=0.468 A=0.532
The Danish reference pan genome Danish Study-wide 40 C=0.50 A=0.50
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 G T
GRCh38.p13 chr 1 NC_000001.11:g.266225= NC_000001.11:g.266225C>A NC_000001.11:g.266225C>G NC_000001.11:g.266225C>T
GRCh37.p13 chr 1 NC_000001.10:g.235976= NC_000001.10:g.235976C>A NC_000001.10:g.235976C>G NC_000001.10:g.235976C>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#.

30 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss9903693 Jul 11, 2003 (116)
2 SC_SNP ss11100423 Jul 11, 2003 (116)
3 SC_JCM ss11208256 Jul 11, 2003 (116)
4 SC_SNP ss15441591 Feb 27, 2004 (120)
5 SSAHASNP ss35355613 May 24, 2005 (125)
6 HGSV ss84364884 Dec 15, 2007 (130)
7 BGI ss102713369 Dec 01, 2009 (131)
8 ENSEMBL ss139046100 Dec 01, 2009 (131)
9 GMI ss154521941 Dec 01, 2009 (131)
10 BCM-HGSC-SUB ss205527606 Jul 04, 2010 (132)
11 GMI ss275680090 May 04, 2012 (144)
12 GMI ss283987260 Apr 25, 2013 (144)
13 BILGI_BIOE ss538305607 Apr 25, 2013 (144)
14 DDI ss1425684651 Apr 01, 2015 (144)
15 EVA_GENOME_DK ss1573850857 Apr 01, 2015 (144)
16 WEILL_CORNELL_DGM ss1917958867 Feb 12, 2016 (147)
17 GENOMED ss1966667289 Jul 19, 2016 (147)
18 GRF ss2697373393 Nov 08, 2017 (151)
19 GNOMAD ss2750614341 Nov 08, 2017 (151)
20 SWEGEN ss2986144051 Nov 08, 2017 (151)
21 TOPMED ss3066346866 Nov 08, 2017 (151)
22 CSHL ss3343271811 Nov 08, 2017 (151)
23 URBANLAB ss3646580777 Oct 11, 2018 (152)
24 PACBIO ss3783301630 Jul 12, 2019 (153)
25 PACBIO ss3788979626 Jul 12, 2019 (153)
26 PACBIO ss3793852211 Jul 12, 2019 (153)
27 SGDP_PRJ ss3847987234 Apr 25, 2020 (154)
28 KRGDB ss3892827200 Apr 25, 2020 (154)
29 KOGIC ss3943624818 Apr 25, 2020 (154)
30 TOMMO_GENOMICS ss5142039200 Apr 25, 2021 (155)
31 The Danish reference pan genome NC_000001.10 - 235976 Apr 25, 2020 (154)
32 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 24652 (NC_000001.11:266224:C:A 109003/134866)
Row 24653 (NC_000001.11:266224:C:T 0/134906)

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

Submission ignored due to conflicting rows:
Row 24652 (NC_000001.11:266224:C:A 109003/134866)
Row 24653 (NC_000001.11:266224:C:T 0/134906)

- Apr 25, 2021 (155)
34 KOREAN population from KRGDB NC_000001.10 - 235976 Apr 25, 2020 (154)
35 Korean Genome Project NC_000001.11 - 266225 Apr 25, 2020 (154)
36 Qatari NC_000001.10 - 235976 Apr 25, 2020 (154)
37 SGDP_PRJ NC_000001.10 - 235976 Apr 25, 2020 (154)
38 8.3KJPN NC_000001.10 - 235976 Apr 25, 2021 (155)
39 ALFA NC_000001.11 - 266225 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)
rs58220573 May 26, 2008 (130)
rs201583565 Jul 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss35355613, ss84364884 NC_000001.8:225838:C:A NC_000001.11:266224:C:A (self)
ss205527606, ss275680090, ss283987260 NC_000001.9:225838:C:A NC_000001.11:266224:C:A (self)
1358091, 4594, 797, 4214, 8507, ss538305607, ss1425684651, ss1573850857, ss1917958867, ss1966667289, ss2697373393, ss2750614341, ss2986144051, ss3343271811, ss3783301630, ss3788979626, ss3793852211, ss3847987234, ss3892827200, ss5142039200 NC_000001.10:235975:C:A NC_000001.11:266224:C:A (self)
2819, 1427102875, ss3066346866, ss3646580777, ss3943624818 NC_000001.11:266224:C:A NC_000001.11:266224:C:A (self)
ss15441591, ss102713369, ss139046100, ss154521941 NT_077402.2:225975:C:A NC_000001.11:266224:C:A (self)
ss9903693, ss11100423, ss11208256 NT_077911.1:8558:C:A NC_000001.11:266224:C:A (self)
1427102875 NC_000001.11:266224:C:G NC_000001.11:266224:C:G
1427102875 NC_000001.11:266224:C:T NC_000001.11:266224:C:T
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 rs6422503

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