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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 Aliases 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.

rs2062595

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr1:15748633 (GRCh38.p12) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.15929 (20002/125568, TOPMED)
T=0.1510 (4735/31358, GnomAD)
T=0.152 (760/5008, 1000G) (+ 5 more)
T=0.187 (836/4480, Estonian)
T=0.238 (917/3854, ALSPAC)
T=0.243 (902/3708, TWINSUK)
T=0.18 (108/600, NorthernSweden)
T=0.01 (2/216, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC25A34-AS1 : 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.p12 chr 1 NC_000001.11:g.15748633C>T
GRCh37.p13 chr 1 NC_000001.10:g.16075128C>T
Gene: SLC25A34-AS1, SLC25A34 and TMEM82 antisense RNA 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC25A34-AS1 transcript NR_149050.1: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

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 125568 C=0.84071 T=0.15929
gnomAD - Genomes Global Study-wide 31358 C=0.8490 T=0.1510
gnomAD - Genomes European Sub 18880 C=0.7979 T=0.2021
gnomAD - Genomes African Sub 8694 C=0.964 T=0.036
gnomAD - Genomes East Asian Sub 1560 C=0.980 T=0.020
gnomAD - Genomes Other Sub 1086 C=0.792 T=0.208
gnomAD - Genomes American Sub 848 C=0.67 T=0.33
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.78 T=0.22
1000Genomes Global Study-wide 5008 C=0.848 T=0.152
1000Genomes African Sub 1322 C=0.991 T=0.009
1000Genomes East Asian Sub 1008 C=0.976 T=0.024
1000Genomes Europe Sub 1006 C=0.783 T=0.217
1000Genomes South Asian Sub 978 C=0.66 T=0.34
1000Genomes American Sub 694 C=0.74 T=0.26
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.813 T=0.187
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.762 T=0.238
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.757 T=0.243
Northern Sweden ACPOP Study-wide 600 C=0.82 T=0.18
A Vietnamese Genetic Variation Database Global Study-wide 216 C=0.99 T=0.01
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= T Note
GRCh38.p12 chr 1 NC_000001.11:g.15748633= NC_000001.11:g.15748633C>T
GRCh37.p13 chr 1 NC_000001.10:g.16075128= NC_000001.10:g.16075128C>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#.

75 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2973884 Apr 12, 2001 (94)
2 ABI ss43907454 Mar 15, 2006 (126)
3 AFFY ss66486679 Dec 02, 2006 (127)
4 ILLUMINA ss67221035 Dec 02, 2006 (127)
5 ILLUMINA ss67615327 Dec 02, 2006 (127)
6 ILLUMINA ss68195355 Dec 12, 2006 (127)
7 PERLEGEN ss68759548 May 18, 2007 (127)
8 ILLUMINA ss70699330 May 24, 2008 (130)
9 ILLUMINA ss71265226 May 18, 2007 (127)
10 ILLUMINA ss75594319 Dec 06, 2007 (129)
11 AFFY ss76307865 Dec 06, 2007 (129)
12 HGSV ss77209896 Dec 06, 2007 (129)
13 KRIBB_YJKIM ss83961505 Dec 14, 2007 (130)
14 BCMHGSC_JDW ss87246822 Mar 23, 2008 (129)
15 HUMANGENOME_JCVI ss99188927 Feb 04, 2009 (130)
16 1000GENOMES ss108015319 Jan 22, 2009 (130)
17 ENSEMBL ss137811903 Dec 01, 2009 (131)
18 ENSEMBL ss139196015 Dec 01, 2009 (131)
19 ILLUMINA ss153839303 Dec 01, 2009 (131)
20 ILLUMINA ss159354839 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss166143400 Jul 04, 2010 (132)
22 ILLUMINA ss173081319 Jul 04, 2010 (132)
23 AFFY ss173206309 Jul 04, 2010 (132)
24 1000GENOMES ss230439193 Jul 14, 2010 (132)
25 1000GENOMES ss238152304 Jul 15, 2010 (132)
26 GMI ss275728104 May 04, 2012 (137)
27 GMI ss284006316 Apr 25, 2013 (138)
28 PJP ss290699153 May 09, 2011 (134)
29 ILLUMINA ss479680860 May 04, 2012 (137)
30 ILLUMINA ss482120376 May 04, 2012 (137)
31 ILLUMINA ss533190559 Sep 08, 2015 (146)
32 TISHKOFF ss553830914 Apr 25, 2013 (138)
33 SSMP ss647599615 Apr 25, 2013 (138)
34 ILLUMINA ss778659793 Sep 08, 2015 (146)
35 ILLUMINA ss781041855 Sep 08, 2015 (146)
36 ILLUMINA ss832866756 Jul 12, 2019 (153)
37 ILLUMINA ss834117932 Sep 08, 2015 (146)
38 EVA-GONL ss974889406 Aug 21, 2014 (142)
39 JMKIDD_LAB ss1067694010 Aug 21, 2014 (142)
40 1000GENOMES ss1289812256 Aug 21, 2014 (142)
41 DDI ss1425724008 Apr 01, 2015 (144)
42 EVA_GENOME_DK ss1573906888 Apr 01, 2015 (144)
43 EVA_DECODE ss1584246621 Apr 01, 2015 (144)
44 EVA_UK10K_ALSPAC ss1599613396 Apr 01, 2015 (144)
45 EVA_UK10K_TWINSUK ss1642607429 Apr 01, 2015 (144)
46 EVA_SVP ss1712313617 Apr 01, 2015 (144)
47 WEILL_CORNELL_DGM ss1918092702 Feb 12, 2016 (147)
48 GENOMED ss1966691534 Jul 19, 2016 (147)
49 JJLAB ss2019559966 Sep 14, 2016 (149)
50 USC_VALOUEV ss2147559204 Dec 20, 2016 (150)
51 HUMAN_LONGEVITY ss2160296224 Dec 20, 2016 (150)
52 TOPMED ss2322464479 Dec 20, 2016 (150)
53 ILLUMINA ss2632481995 Nov 08, 2017 (151)
54 ILLUMINA ss2632481996 Nov 08, 2017 (151)
55 GRF ss2697460395 Nov 08, 2017 (151)
56 GNOMAD ss2752000319 Nov 08, 2017 (151)
57 SWEGEN ss2986360674 Nov 08, 2017 (151)
58 BIOINF_KMB_FNS_UNIBA ss3023544156 Nov 08, 2017 (151)
59 TOPMED ss3069468383 Nov 08, 2017 (151)
60 CSHL ss3343335048 Nov 08, 2017 (151)
61 ILLUMINA ss3626034137 Oct 11, 2018 (152)
62 ILLUMINA ss3630520141 Oct 11, 2018 (152)
63 ILLUMINA ss3637739354 Oct 11, 2018 (152)
64 ILLUMINA ss3638890827 Oct 11, 2018 (152)
65 ILLUMINA ss3639758146 Oct 11, 2018 (152)
66 ILLUMINA ss3640975488 Oct 11, 2018 (152)
67 ILLUMINA ss3641269346 Oct 11, 2018 (152)
68 ILLUMINA ss3642753021 Oct 11, 2018 (152)
69 ILLUMINA ss3643812018 Oct 11, 2018 (152)
70 URBANLAB ss3646607792 Oct 11, 2018 (152)
71 EGCUT_WGS ss3654447968 Jul 12, 2019 (153)
72 EVA_DECODE ss3686230612 Jul 12, 2019 (153)
73 ACPOP ss3726820310 Jul 12, 2019 (153)
74 EVA ss3745870333 Jul 12, 2019 (153)
75 KHV_HUMAN_GENOMES ss3798891527 Jul 12, 2019 (153)
76 1000Genomes NC_000001.10 - 16075128 Oct 11, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 16075128 Oct 11, 2018 (152)
78 Genetic variation in the Estonian population NC_000001.10 - 16075128 Oct 11, 2018 (152)
79 gnomAD - Genomes NC_000001.10 - 16075128 Jul 12, 2019 (153)
80 Northern Sweden NC_000001.10 - 16075128 Jul 12, 2019 (153)
81 TopMed NC_000001.11 - 15748633 Oct 11, 2018 (152)
82 UK 10K study - Twins NC_000001.10 - 16075128 Oct 11, 2018 (152)
83 A Vietnamese Genetic Variation Database NC_000001.10 - 16075128 Jul 12, 2019 (153)
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)
rs58163354 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77209896, ss3638890827, ss3639758146, ss3643812018 NC_000001.8:15820433:C:T NC_000001.11:15748632:C:T (self)
ss66486679, ss76307865, ss87246822, ss108015319, ss166143400, ss173206309, ss275728104, ss284006316, ss290699153, ss482120376, ss1584246621, ss1712313617, ss3642753021 NC_000001.9:15947714:C:T NC_000001.11:15748632:C:T (self)
492852, 258474, 186216, 1335101, 105175, 258474, 55230, ss230439193, ss238152304, ss479680860, ss533190559, ss553830914, ss647599615, ss778659793, ss781041855, ss832866756, ss834117932, ss974889406, ss1067694010, ss1289812256, ss1425724008, ss1573906888, ss1599613396, ss1642607429, ss1918092702, ss1966691534, ss2019559966, ss2147559204, ss2322464479, ss2632481995, ss2632481996, ss2697460395, ss2752000319, ss2986360674, ss3343335048, ss3626034137, ss3630520141, ss3637739354, ss3640975488, ss3641269346, ss3654447968, ss3726820310, ss3745870333 NC_000001.10:16075127:C:T NC_000001.11:15748632:C:T (self)
2458435, ss2160296224, ss3023544156, ss3069468383, ss3646607792, ss3686230612, ss3798891527 NC_000001.11:15748632:C:T NC_000001.11:15748632:C:T (self)
ss2973884, ss43907454, ss67221035, ss67615327, ss68195355, ss68759548, ss70699330, ss71265226, ss75594319, ss83961505, ss99188927, ss137811903, ss139196015, ss153839303, ss159354839, ss173081319 NT_004610.19:2755215:C:T NC_000001.11:15748632: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 rs2062595

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.post308+0fe9b3b