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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.

rs62101625

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:19004 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.39146 (6167/15754, 8.3KJPN)
A=0.3850 (1045/2714, KOREAN)
G=0.1776 (444/2500, ALFA) (+ 2 more)
A=0.362 (113/312, SGDP_PRJ)
A=0.2 (1/6, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MIR6859-1 : 2KB Upstream Variant
WASH7P : 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.19004A>C
GRCh38.p13 chr 1 NC_000001.11:g.19004A>G
GRCh37.p13 chr 1 NC_000001.10:g.19004A>C
GRCh37.p13 chr 1 NC_000001.10:g.19004A>G
Gene: WASH7P, WASP family homolog 7, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WASH7P transcript NR_024540.1:n. N/A Intron Variant
Gene: MIR6859-1, microRNA 6859-1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR6859-1 transcript NR_106918.1:n. N/A 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 2500 A=0.8224 C=0.0000, G=0.1776
European Sub 1338 A=0.7975 C=0.0000, G=0.2025
African Sub 1004 A=0.8297 C=0.0000, G=0.1703
African Others Sub 38 A=0.79 C=0.00, G=0.21
African American Sub 966 A=0.831 C=0.000, G=0.169
Asian Sub 0 A=0 C=0, G=0
East Asian Sub 0 A=0 C=0, G=0
Other Asian Sub 0 A=0 C=0, G=0
Latin American 1 Sub 14 A=1.00 C=0.00, G=0.00
Latin American 2 Sub 56 A=1.00 C=0.00, G=0.00
South Asian Sub 10 A=1.0 C=0.0, G=0.0
Other Sub 78 A=0.97 C=0.00, G=0.03


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").

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Study Population Group Sample Size Ref Allele Alt Allele
8.3KJPN JAPANESE Study-wide 15754 A=0.39146 G=0.60854
KOREAN population from KRGDB KOREAN Study-wide 2714 A=0.3850 G=0.6150
SGDP_PRJ Global Study-wide 312 A=0.362 G=0.638
The Danish reference pan genome Danish Study-wide 6 A=0.2 G=0.8
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
GRCh38.p13 chr 1 NC_000001.11:g.19004= NC_000001.11:g.19004A>C NC_000001.11:g.19004A>G
GRCh37.p13 chr 1 NC_000001.10:g.19004= NC_000001.10:g.19004A>C NC_000001.10:g.19004A>G
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#.

14 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCMHGSC_JDW ss87152844 Mar 25, 2008 (130)
2 HUMANGENOME_JCVI ss95802272 Feb 13, 2009 (131)
3 BCM-HGSC-SUB ss205555432 Jul 04, 2010 (132)
4 GMI ss275679870 May 04, 2012 (142)
5 EVA_GENOME_DK ss1573850677 Apr 01, 2015 (144)
6 JJLAB ss2019497480 Sep 14, 2016 (149)
7 GNOMAD ss2750602161 Nov 08, 2017 (151)
8 SWEGEN ss2986141530 Nov 08, 2017 (151)
9 TOPMED ss3066317789 Nov 08, 2017 (151)
10 CSHL ss3343271490 Nov 08, 2017 (151)
11 OMUKHERJEE_ADBS ss3646218095 Oct 11, 2018 (152)
12 SGDP_PRJ ss3847983413 Apr 25, 2020 (154)
13 KRGDB ss3892823134 Apr 25, 2020 (154)
14 TOMMO_GENOMICS ss5142031645 Apr 25, 2021 (155)
15 The Danish reference pan genome NC_000001.10 - 19004 Apr 25, 2020 (154)
16 KOREAN population from KRGDB NC_000001.10 - 19004 Apr 25, 2020 (154)
17 SGDP_PRJ NC_000001.10 - 19004 Apr 25, 2020 (154)
18 8.3KJPN NC_000001.10 - 19004 Apr 25, 2021 (155)
19 ALFA NC_000001.11 - 19004 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)
rs62636374 May 23, 2008 (130)
rs71221049 Dec 02, 2009 (131)
rs201619486 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
12796369958 NC_000001.11:19003:A:C NC_000001.11:19003:A:C
ss87152844, ss205555432, ss275679870 NC_000001.9:8866:A:G NC_000001.11:19003:A:G (self)
1357911, 528, 393, 952, ss1573850677, ss2019497480, ss2750602161, ss2986141530, ss3343271490, ss3646218095, ss3847983413, ss3892823134, ss5142031645 NC_000001.10:19003:A:G NC_000001.11:19003:A:G (self)
12796369958, ss3066317789 NC_000001.11:19003:A:G NC_000001.11:19003:A:G (self)
ss95802272 NT_077402.2:9003:A:G NC_000001.11:19003:A:G (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 rs62101625

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