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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.

rs1525739

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr7:16850188 (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
C>A / C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.41982 (52716/125568, TOPMED)
C=0.4152 (12833/30906, GnomAD)
C=0.342 (1714/5008, 1000G) (+ 2 more)
C=0.491 (1893/3854, ALSPAC)
C=0.469 (1740/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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 7 NC_000007.14:g.16850188C>A
GRCh38.p7 chr 7 NC_000007.14:g.16850188C>G
GRCh37.p13 chr 7 NC_000007.13:g.16889812C>A
GRCh37.p13 chr 7 NC_000007.13:g.16889812C>G
LOC100287613 pseudogene NG_023341.2:g.814G>T
LOC100287613 pseudogene NG_023341.2:g.814G>C
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 C=0.41982 G=0.58018
The Genome Aggregation Database Global Study-wide 30906 C=0.4152 G=0.5843, A=0.0005
The Genome Aggregation Database European Sub 18466 C=0.4516 G=0.5484, A=0.0000
The Genome Aggregation Database African Sub 8698 C=0.370 G=0.629, A=0.002
The Genome Aggregation Database East Asian Sub 1620 C=0.177 G=0.823, A=0.000
The Genome Aggregation Database Other Sub 982 C=0.43 G=0.57, A=0.00
The Genome Aggregation Database American Sub 838 C=0.50 G=0.50, A=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 C=0.49 G=0.51, A=0.00
1000Genomes Global Study-wide 5008 C=0.342 G=0.657, A=0.001
1000Genomes African Sub 1322 C=0.350 G=0.646, A=0.004
1000Genomes East Asian Sub 1008 C=0.195 G=0.805, A=0.000
1000Genomes Europe Sub 1006 C=0.468 G=0.532, A=0.000
1000Genomes South Asian Sub 978 C=0.25 G=0.75, A=0.00
1000Genomes American Sub 694 C=0.48 G=0.51, A=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.491 G=0.509
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.469 G=0.531
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 Note
GRCh38.p7 chr 7 NC_000007.14:g.16...

NC_000007.14:g.16850188C=

NC_000007.14:g.16...

NC_000007.14:g.16850188C>A

NC_000007.14:g.16...

NC_000007.14:g.16850188C>G

GRCh37.p13 chr 7 NC_000007.13:g.16...

NC_000007.13:g.16889812C=

NC_000007.13:g.16...

NC_000007.13:g.16889812C>A

NC_000007.13:g.16...

NC_000007.13:g.16889812C>G

LOC100287613 pseudogene NG_023341.2:g.814G= NG_023341.2:g.814G>T NG_023341.2:g.814G>C
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#.

56 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2365288 Oct 23, 2000 (88)
2 SC_JCM ss5936986 Feb 20, 2003 (111)
3 PERLEGEN ss24382180 Sep 20, 2004 (123)
4 ABI ss44827165 Mar 14, 2006 (126)
5 AFFY ss66407756 Nov 30, 2006 (127)
6 PERLEGEN ss69006898 May 17, 2007 (127)
7 AFFY ss76162610 Dec 06, 2007 (129)
8 KRIBB_YJKIM ss81525182 Dec 14, 2007 (130)
9 BCMHGSC_JDW ss93636528 Mar 24, 2008 (129)
10 BGI ss105498842 Feb 03, 2009 (130)
11 1000GENOMES ss111593537 Jan 25, 2009 (130)
12 1000GENOMES ss113386394 Jan 25, 2009 (130)
13 ILLUMINA-UK ss115956279 Feb 14, 2009 (130)
14 ENSEMBL ss142702728 Dec 01, 2009 (131)
15 GMI ss158088789 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss162086806 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss163725668 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss166204756 Jul 04, 2010 (132)
19 AFFY ss172680719 Jul 04, 2010 (132)
20 BUSHMAN ss203009755 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss208138525 Jul 04, 2010 (132)
22 1000GENOMES ss222932884 Jul 14, 2010 (132)
23 1000GENOMES ss233867954 Jul 15, 2010 (132)
24 1000GENOMES ss240844129 Jul 15, 2010 (132)
25 GMI ss279203021 May 04, 2012 (137)
26 GMI ss285582130 Apr 25, 2013 (138)
27 PJP ss294020340 May 09, 2011 (134)
28 TISHKOFF ss559833971 Apr 25, 2013 (138)
29 SSMP ss654184159 Apr 25, 2013 (138)
30 EVA-GONL ss983993751 Aug 21, 2014 (142)
31 JMKIDD_LAB ss1074397269 Aug 21, 2014 (142)
32 1000GENOMES ss1324089039 Aug 21, 2014 (142)
33 1000GENOMES ss1324089040 Aug 21, 2014 (142)
34 DDI ss1431041893 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1582089594 Apr 01, 2015 (144)
36 EVA_DECODE ss1593560357 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1617655570 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1660649603 Apr 01, 2015 (144)
39 EVA_MGP ss1711156138 Apr 01, 2015 (144)
40 EVA_SVP ss1712934526 Apr 01, 2015 (144)
41 HAMMER_LAB ss1804887885 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1927240624 Feb 12, 2016 (147)
43 GENOMED ss1970635340 Jul 19, 2016 (147)
44 JJLAB ss2024294739 Sep 14, 2016 (149)
45 USC_VALOUEV ss2152491361 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2291994042 Dec 20, 2016 (150)
47 TOPMED ss2460832142 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2626636461 Nov 08, 2017 (151)
49 GRF ss2708143888 Nov 08, 2017 (151)
50 GNOMAD ss2850207054 Nov 08, 2017 (151)
51 SWEGEN ss3000692097 Nov 08, 2017 (151)
52 ILLUMINA ss3022711575 Nov 08, 2017 (151)
53 BIOINF_KMB_FNS_UNIBA ss3025941654 Nov 08, 2017 (151)
54 CSHL ss3347457803 Nov 08, 2017 (151)
55 TOPMED ss3523511455 Nov 08, 2017 (151)
56 TOPMED ss3523511456 Nov 08, 2017 (151)
57 1000Genomes NC_000007.13 - 16889812 Jul 20, 2018 (151)
58 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 16889812 Jul 20, 2018 (151)
59 The Genome Aggregation Database NC_000007.13 - 16889812 Jul 20, 2018 (151)
60 Trans-Omics for Precision Medicine NC_000007.14 - 16850188 Jul 20, 2018 (151)
61 UK 10K study - Twins NC_000007.13 - 16889812 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)
rs17642204 Oct 08, 2004 (123)
rs57948013 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss66407756, ss76162610, ss93636528, ss111593537, ss113386394, ss115956279, ss162086806, ss163725668, ss166204756, ss172680719, ss203009755, ss208138525, ss279203021, ss285582130, ss294020340, ss1593560357, ss1712934526 NC_000007.12:16856336:C= NC_000007.14:16850187:C= (self)
36022559, 20078983, 190834812, 20078983, ss222932884, ss233867954, ss240844129, ss559833971, ss654184159, ss983993751, ss1074397269, ss1324089039, ss1324089040, ss1431041893, ss1582089594, ss1617655570, ss1660649603, ss1711156138, ss1804887885, ss1927240624, ss1970635340, ss2024294739, ss2152491361, ss2460832142, ss2626636461, ss2708143888, ss2850207054, ss3000692097, ss3022711575, ss3347457803 NC_000007.13:16889811:C= NC_000007.14:16850187:C= (self)
359267270, ss2291994042, ss3025941654, ss3523511455, ss3523511456 NC_000007.14:16850187:C= NC_000007.14:16850187:C= (self)
ss2365288, ss5936986, ss24382180, ss44827165, ss69006898, ss81525182, ss105498842, ss142702728, ss158088789 NT_007819.17:16879811:C= NC_000007.14:16850187:C= (self)
36022559, 190834812, ss1324089039, ss2850207054 NC_000007.13:16889811:C>A NC_000007.14:16850187:C>A (self)
ss2291994042, ss3523511455 NC_000007.14:16850187:C>A NC_000007.14:16850187:C>A (self)
ss66407756, ss76162610, ss93636528, ss111593537, ss113386394, ss115956279, ss162086806, ss163725668, ss166204756, ss172680719, ss203009755, ss208138525, ss279203021, ss285582130, ss294020340, ss1593560357, ss1712934526 NC_000007.12:16856336:C>G NC_000007.14:16850187:C>G (self)
36022559, 20078983, 190834812, 20078983, ss222932884, ss233867954, ss240844129, ss559833971, ss654184159, ss983993751, ss1074397269, ss1324089040, ss1431041893, ss1582089594, ss1617655570, ss1660649603, ss1711156138, ss1804887885, ss1927240624, ss1970635340, ss2024294739, ss2152491361, ss2460832142, ss2626636461, ss2708143888, ss2850207054, ss3000692097, ss3022711575, ss3347457803 NC_000007.13:16889811:C>G NC_000007.14:16850187:C>G (self)
359267270, ss2291994042, ss3025941654, ss3523511456 NC_000007.14:16850187:C>G NC_000007.14:16850187:C>G (self)
ss2365288, ss5936986, ss24382180, ss44827165, ss69006898, ss81525182, ss105498842, ss142702728, ss158088789 NT_007819.17:16879811:C>G NC_000007.14:16850187:C>G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs1525739
PMID Title Author Year Journal
23386860 Exploring genome-wide - dietary heme iron intake interactions and the risk of type 2 diabetes. Pasquale LR et al. 2013 Frontiers in genetics

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