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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs1425902

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr8:53206654 (GRCh38.p7) 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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.46337 (58184/125568, TOPMED)
G=0.4490 (13880/30912, GnomAD)
G=0.491 (2458/5008, 1000G) (+ 2 more)
G=0.308 (1186/3854, ALSPAC)
G=0.320 (1188/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105375836 : 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.p7 chr 8 NC_000008.11:g.53206654G>A
GRCh38.p7 chr 8 NC_000008.11:g.53206654G>T
GRCh37.p13 chr 8 NC_000008.10:g.54119214G>A
GRCh37.p13 chr 8 NC_000008.10:g.54119214G>T
Gene: LOC105375836, uncharacterized LOC105375836 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105375836 transcript XR_928877.1: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").

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Study Population Group Sample Size Ref Allele Alt Allele
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.46337 A=0.53663
The Genome Aggregation Database Global Study-wide 30912 G=0.4490 A=0.5510
The Genome Aggregation Database European Sub 18466 G=0.3157 A=0.6843
The Genome Aggregation Database African Sub 8710 G=0.768 A=0.232
The Genome Aggregation Database East Asian Sub 1614 G=0.342 A=0.658
The Genome Aggregation Database Other Sub 982 G=0.38 A=0.62
The Genome Aggregation Database American Sub 838 G=0.37 A=0.63
The Genome Aggregation Database Ashkenazi Jewish Sub 302 G=0.40 A=0.60
1000Genomes Global Study-wide 5008 G=0.491 A=0.509
1000Genomes African Sub 1322 G=0.837 A=0.163
1000Genomes East Asian Sub 1008 G=0.291 A=0.709
1000Genomes Europe Sub 1006 G=0.306 A=0.694
1000Genomes South Asian Sub 978 G=0.48 A=0.52
1000Genomes American Sub 694 G=0.41 A=0.59
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.308 A=0.692
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.320 A=0.680
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 G= A T Note
GRCh38.p7 chr 8 NC_000008.11:g.53...

NC_000008.11:g.53206654G=

NC_000008.11:g.53...

NC_000008.11:g.53206654G>A

NC_000008.11:g.53...

NC_000008.11:g.53206654G>T

GRCh37.p13 chr 8 NC_000008.10:g.54...

NC_000008.10:g.54119214G=

NC_000008.10:g.54...

NC_000008.10:g.54119214G>A

NC_000008.10:g.54...

NC_000008.10:g.54119214G>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#.

5 Frequency, 96 SubSNP submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2232644 Oct 23, 2000 (88)
2 SC_JCM ss3839143 Sep 28, 2001 (100)
3 SSAHASNP ss22740001 Apr 05, 2004 (121)
4 PERLEGEN ss24072098 Sep 20, 2004 (123)
5 ABI ss44921651 Mar 14, 2006 (126)
6 ILLUMINA ss66576002 Nov 30, 2006 (127)
7 ILLUMINA ss67101564 Nov 30, 2006 (127)
8 ILLUMINA ss67436979 Nov 30, 2006 (127)
9 PERLEGEN ss69048623 May 17, 2007 (127)
10 ILLUMINA ss70431610 May 17, 2007 (127)
11 ILLUMINA ss70616603 May 25, 2008 (130)
12 ILLUMINA ss71164688 May 17, 2007 (127)
13 ILLUMINA ss74948673 Dec 07, 2007 (129)
14 AFFY ss76423245 Dec 08, 2007 (130)
15 HGSV ss77778043 Dec 07, 2007 (129)
16 KRIBB_YJKIM ss83767978 Dec 15, 2007 (130)
17 BCMHGSC_JDW ss93887518 Mar 25, 2008 (129)
18 HUMANGENOME_JCVI ss97873112 Feb 05, 2009 (130)
19 BGI ss105618418 Feb 05, 2009 (130)
20 1000GENOMES ss108027731 Jan 22, 2009 (130)
21 ILLUMINA ss121691370 Dec 01, 2009 (131)
22 ENSEMBL ss134381188 Dec 01, 2009 (131)
23 ENSEMBL ss143473561 Dec 01, 2009 (131)
24 ILLUMINA ss153429569 Dec 01, 2009 (131)
25 GMI ss156372640 Dec 01, 2009 (131)
26 ILLUMINA ss159268387 Dec 01, 2009 (131)
27 ILLUMINA ss160351561 Dec 01, 2009 (131)
28 COMPLETE_GENOMICS ss162405539 Jul 04, 2010 (132)
29 COMPLETE_GENOMICS ss166632571 Jul 04, 2010 (132)
30 ILLUMINA ss170496039 Jul 04, 2010 (132)
31 ILLUMINA ss172492314 Jul 04, 2010 (132)
32 BUSHMAN ss199158229 Jul 04, 2010 (132)
33 BCM-HGSC-SUB ss208494548 Jul 04, 2010 (132)
34 1000GENOMES ss223703601 Jul 14, 2010 (132)
35 1000GENOMES ss234436812 Jul 15, 2010 (132)
36 1000GENOMES ss241293155 Jul 15, 2010 (132)
37 BL ss254336041 May 09, 2011 (134)
38 GMI ss279811300 May 04, 2012 (137)
39 GMI ss285844106 Apr 25, 2013 (138)
40 PJP ss294081958 May 09, 2011 (134)
41 ILLUMINA ss479969231 May 04, 2012 (137)
42 ILLUMINA ss479977739 May 04, 2012 (137)
43 ILLUMINA ss480624139 Sep 08, 2015 (146)
44 ILLUMINA ss484782846 May 04, 2012 (137)
45 ILLUMINA ss536869675 Sep 08, 2015 (146)
46 TISHKOFF ss560746687 Apr 25, 2013 (138)
47 SSMP ss655184423 Apr 25, 2013 (138)
48 ILLUMINA ss778431734 Sep 08, 2015 (146)
49 ILLUMINA ss782838091 Sep 08, 2015 (146)
50 ILLUMINA ss783802802 Sep 08, 2015 (146)
51 ILLUMINA ss825400884 Apr 01, 2015 (144)
52 ILLUMINA ss832091727 Sep 08, 2015 (146)
53 ILLUMINA ss833887202 Sep 08, 2015 (146)
54 EVA-GONL ss985514569 Aug 21, 2014 (142)
55 JMKIDD_LAB ss1075518028 Aug 21, 2014 (142)
56 1000GENOMES ss1329858520 Aug 21, 2014 (142)
57 DDI ss1431510792 Apr 01, 2015 (144)
58 EVA_GENOME_DK ss1582683509 Apr 01, 2015 (144)
59 EVA_DECODE ss1595109310 Apr 01, 2015 (144)
60 EVA_UK10K_ALSPAC ss1620637230 Apr 01, 2015 (144)
61 EVA_UK10K_TWINSUK ss1663631263 Apr 01, 2015 (144)
62 EVA_SVP ss1713036017 Apr 01, 2015 (144)
63 ILLUMINA ss1752734947 Sep 08, 2015 (146)
64 HAMMER_LAB ss1805533383 Sep 08, 2015 (146)
65 WEILL_CORNELL_DGM ss1928801477 Feb 12, 2016 (147)
66 GENOMED ss1970979131 Jul 19, 2016 (147)
67 JJLAB ss2025101006 Sep 14, 2016 (149)
68 ILLUMINA ss2095210167 Dec 20, 2016 (150)
69 USC_VALOUEV ss2153327777 Dec 20, 2016 (150)
70 HUMAN_LONGEVITY ss2303105804 Dec 20, 2016 (150)
71 TOPMED ss2472940900 Dec 20, 2016 (150)
72 SYSTEMSBIOZJU ss2627031324 Nov 08, 2017 (151)
73 ILLUMINA ss2634746224 Nov 08, 2017 (151)
74 GRF ss2709096006 Nov 08, 2017 (151)
75 GNOMAD ss2866791570 Nov 08, 2017 (151)
76 AFFY ss2986082208 Nov 08, 2017 (151)
77 SWEGEN ss3003183653 Nov 08, 2017 (151)
78 BIOINF_KMB_FNS_UNIBA ss3026337746 Nov 08, 2017 (151)
79 CSHL ss3348180625 Nov 08, 2017 (151)
80 TOPMED ss3562234522 Nov 08, 2017 (151)
81 TOPMED ss3562234523 Nov 08, 2017 (151)
82 ILLUMINA ss3630059388 Jul 20, 2018 (151)
83 ILLUMINA ss3632645397 Jul 20, 2018 (151)
84 ILLUMINA ss3633500290 Jul 20, 2018 (151)
85 ILLUMINA ss3634227072 Jul 20, 2018 (151)
86 ILLUMINA ss3635171269 Jul 20, 2018 (151)
87 ILLUMINA ss3635905876 Jul 20, 2018 (151)
88 ILLUMINA ss3636908897 Jul 20, 2018 (151)
89 ILLUMINA ss3637659061 Jul 20, 2018 (151)
90 ILLUMINA ss3638759966 Jul 20, 2018 (151)
91 ILLUMINA ss3639382229 Jul 20, 2018 (151)
92 ILLUMINA ss3639720249 Jul 20, 2018 (151)
93 ILLUMINA ss3640878559 Jul 20, 2018 (151)
94 ILLUMINA ss3641227492 Jul 20, 2018 (151)
95 ILLUMINA ss3641525153 Jul 20, 2018 (151)
96 ILLUMINA ss3643690840 Jul 20, 2018 (151)
97 1000Genomes NC_000008.10 - 54119214 Jul 20, 2018 (151)
98 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 54119214 Jul 20, 2018 (151)
99 The Genome Aggregation Database NC_000008.10 - 54119214 Jul 20, 2018 (151)
100 Trans-Omics for Precision Medicine NC_000008.11 - 53206654 Jul 20, 2018 (151)
101 UK 10K study - Twins NC_000008.10 - 54119214 Jul 20, 2018 (151)
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)
rs56553424 May 25, 2008 (130)
rs59895808 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss76423245, ss77778043, ss93887518, ss108027731, ss162405539, ss166632571, ss199158229, ss208494548, ss254336041, ss279811300, ss285844106, ss294081958, ss479969231, ss825400884, ss1595109310, ss1713036017, ss3639382229, ss3639720249, ss3643690840 NC_000008.9:54281766:G= NC_000008.11:53206653:G= (self)
41983145, 23346227, 207419324, 23346227, ss223703601, ss234436812, ss241293155, ss479977739, ss480624139, ss484782846, ss536869675, ss560746687, ss655184423, ss778431734, ss782838091, ss783802802, ss832091727, ss833887202, ss985514569, ss1075518028, ss1329858520, ss1431510792, ss1582683509, ss1620637230, ss1663631263, ss1752734947, ss1805533383, ss1928801477, ss1970979131, ss2025101006, ss2095210167, ss2153327777, ss2472940900, ss2627031324, ss2634746224, ss2709096006, ss2866791570, ss2986082208, ss3003183653, ss3348180625, ss3630059388, ss3632645397, ss3633500290, ss3634227072, ss3635171269, ss3635905876, ss3636908897, ss3637659061, ss3638759966, ss3640878559, ss3641227492, ss3641525153 NC_000008.10:54119213:G= NC_000008.11:53206653:G= (self)
389664925, ss2303105804, ss3026337746, ss3562234522, ss3562234523 NC_000008.11:53206653:G= NC_000008.11:53206653:G= (self)
ss22740001 NT_008183.17:5961761:G= NC_000008.11:53206653:G= (self)
ss2232644, ss3839143, ss24072098, ss44921651, ss66576002, ss67101564, ss67436979, ss69048623, ss70431610, ss70616603, ss71164688, ss74948673, ss83767978, ss97873112, ss105618418, ss121691370, ss134381188, ss143473561, ss153429569, ss156372640, ss159268387, ss160351561, ss170496039, ss172492314 NT_008183.19:5983614:G= NC_000008.11:53206653:G= (self)
ss76423245, ss77778043, ss93887518, ss108027731, ss162405539, ss166632571, ss199158229, ss208494548, ss254336041, ss279811300, ss285844106, ss294081958, ss479969231, ss825400884, ss1595109310, ss1713036017, ss3639382229, ss3639720249, ss3643690840 NC_000008.9:54281766:G>A NC_000008.11:53206653:G>A (self)
41983145, 23346227, 207419324, 23346227, ss223703601, ss234436812, ss241293155, ss479977739, ss480624139, ss484782846, ss536869675, ss560746687, ss655184423, ss778431734, ss782838091, ss783802802, ss832091727, ss833887202, ss985514569, ss1075518028, ss1329858520, ss1431510792, ss1582683509, ss1620637230, ss1663631263, ss1752734947, ss1805533383, ss1928801477, ss1970979131, ss2025101006, ss2095210167, ss2153327777, ss2472940900, ss2627031324, ss2634746224, ss2709096006, ss2866791570, ss2986082208, ss3003183653, ss3348180625, ss3630059388, ss3632645397, ss3633500290, ss3634227072, ss3635171269, ss3635905876, ss3636908897, ss3637659061, ss3638759966, ss3640878559, ss3641227492, ss3641525153 NC_000008.10:54119213:G>A NC_000008.11:53206653:G>A (self)
389664925, ss2303105804, ss3026337746, ss3562234522 NC_000008.11:53206653:G>A NC_000008.11:53206653:G>A (self)
ss22740001 NT_008183.17:5961761:G>A NC_000008.11:53206653:G>A (self)
ss2232644, ss3839143, ss24072098, ss44921651, ss66576002, ss67101564, ss67436979, ss69048623, ss70431610, ss70616603, ss71164688, ss74948673, ss83767978, ss97873112, ss105618418, ss121691370, ss134381188, ss143473561, ss153429569, ss156372640, ss159268387, ss160351561, ss170496039, ss172492314 NT_008183.19:5983614:G>A NC_000008.11:53206653:G>A (self)
ss3562234523 NC_000008.11:53206653:G>T NC_000008.11:53206653:G>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 rs1425902

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: 0.1.4.post833+d3ba21e