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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.

rs7518025

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:99600959 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.395266 (104623/264690, TOPMED)
T=0.435858 (94351/216472, ALFA)
T=0.409113 (57257/139954, GnomAD) (+ 17 more)
T=0.02118 (355/16760, 8.3KJPN)
T=0.2885 (1445/5008, 1000G)
T=0.4346 (1947/4480, Estonian)
T=0.4590 (1769/3854, ALSPAC)
T=0.4628 (1716/3708, TWINSUK)
T=0.0229 (67/2922, KOREAN)
T=0.2817 (587/2084, HGDP_Stanford)
T=0.2849 (539/1892, HapMap)
T=0.0218 (40/1832, Korea1K)
T=0.480 (479/998, GoNL)
T=0.388 (233/600, NorthernSweden)
C=0.399 (103/258, SGDP_PRJ)
T=0.389 (84/216, Qatari)
T=0.052 (11/212, Vietnamese)
T=0.28 (16/58, Ancient Sardinia)
T=0.45 (18/40, GENOME_DK)
C=0.36 (8/22, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.99600959C>T
GRCh37.p13 chr 1 NC_000001.10:g.100066515C>T
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 (New)
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 216472 C=0.564142 T=0.435858
European Sub 188962 C=0.548893 T=0.451107
African Sub 7094 C=0.6271 T=0.3729
African Others Sub 264 C=0.686 T=0.314
African American Sub 6830 C=0.6249 T=0.3751
Asian Sub 746 C=0.948 T=0.052
East Asian Sub 600 C=0.953 T=0.047
Other Asian Sub 146 C=0.925 T=0.075
Latin American 1 Sub 842 C=0.562 T=0.438
Latin American 2 Sub 6908 C=0.7015 T=0.2985
South Asian Sub 5040 C=0.7575 T=0.2425
Other Sub 6880 C=0.5971 T=0.4029


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 264690 C=0.604734 T=0.395266
gnomAD - Genomes Global Study-wide 139954 C=0.590887 T=0.409113
gnomAD - Genomes European Sub 75832 C=0.55426 T=0.44574
gnomAD - Genomes African Sub 41886 C=0.62474 T=0.37526
gnomAD - Genomes American Sub 13634 C=0.60635 T=0.39365
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.5837 T=0.4163
gnomAD - Genomes East Asian Sub 3128 C=0.9588 T=0.0412
gnomAD - Genomes Other Sub 2152 C=0.6008 T=0.3992
8.3KJPN JAPANESE Study-wide 16760 C=0.97882 T=0.02118
1000Genomes Global Study-wide 5008 C=0.7115 T=0.2885
1000Genomes African Sub 1322 C=0.6558 T=0.3442
1000Genomes East Asian Sub 1008 C=0.9524 T=0.0476
1000Genomes Europe Sub 1006 C=0.5348 T=0.4652
1000Genomes South Asian Sub 978 C=0.789 T=0.211
1000Genomes American Sub 694 C=0.614 T=0.386
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5654 T=0.4346
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.5410 T=0.4590
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.5372 T=0.4628
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9771 T=0.0229
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.7183 T=0.2817
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.923 T=0.077
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.790 T=0.210
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.526 T=0.474
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.575 T=0.425
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.711 T=0.289
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.764 T=0.236
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.43 T=0.57
HapMap Global Study-wide 1892 C=0.7151 T=0.2849
HapMap American Sub 770 C=0.721 T=0.279
HapMap African Sub 692 C=0.655 T=0.345
HapMap Asian Sub 254 C=0.969 T=0.031
HapMap Europe Sub 176 C=0.562 T=0.438
Korean Genome Project KOREAN Study-wide 1832 C=0.9782 T=0.0218
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.520 T=0.480
Northern Sweden ACPOP Study-wide 600 C=0.612 T=0.388
SGDP_PRJ Global Study-wide 258 C=0.399 T=0.601
Qatari Global Study-wide 216 C=0.611 T=0.389
A Vietnamese Genetic Variation Database Global Study-wide 212 C=0.948 T=0.052
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 58 C=0.72 T=0.28
The Danish reference pan genome Danish Study-wide 40 C=0.55 T=0.45
Siberian Global Study-wide 22 C=0.36 T=0.64
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
GRCh38.p13 chr 1 NC_000001.11:g.99600959= NC_000001.11:g.99600959C>T
GRCh37.p13 chr 1 NC_000001.10:g.100066515= NC_000001.10:g.100066515C>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#.

99 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss11353580 Jul 11, 2003 (116)
2 ILLUMINA ss65773377 Oct 13, 2006 (127)
3 ILLUMINA ss70930871 May 26, 2008 (130)
4 ILLUMINA ss71532470 May 16, 2007 (127)
5 ILLUMINA ss75634112 Dec 07, 2007 (129)
6 HGSV ss81282285 Dec 16, 2007 (130)
7 HGSV ss84760299 Dec 16, 2007 (130)
8 BCMHGSC_JDW ss87656611 Mar 23, 2008 (129)
9 1000GENOMES ss108453807 Jan 23, 2009 (130)
10 1000GENOMES ss110891259 Jan 25, 2009 (130)
11 ILLUMINA-UK ss118919287 Feb 15, 2009 (130)
12 ENSEMBL ss138045121 Dec 01, 2009 (131)
13 ILLUMINA ss154427206 Dec 01, 2009 (131)
14 ILLUMINA ss159602321 Dec 01, 2009 (131)
15 ILLUMINA ss160883619 Dec 01, 2009 (131)
16 COMPLETE_GENOMICS ss163739405 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss164869388 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss166904899 Jul 04, 2010 (132)
19 ILLUMINA ss174393701 Jul 04, 2010 (132)
20 BUSHMAN ss198832910 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss205276889 Jul 04, 2010 (132)
22 1000GENOMES ss218548713 Jul 14, 2010 (132)
23 1000GENOMES ss230656785 Jul 14, 2010 (132)
24 1000GENOMES ss238323753 Jul 15, 2010 (132)
25 BL ss253316049 May 09, 2011 (134)
26 GMI ss275945361 May 04, 2012 (137)
27 GMI ss284105707 Apr 25, 2013 (138)
28 PJP ss290580525 May 09, 2011 (134)
29 ILLUMINA ss481578705 May 04, 2012 (137)
30 ILLUMINA ss481608542 May 04, 2012 (137)
31 ILLUMINA ss482579795 Sep 08, 2015 (146)
32 ILLUMINA ss485584336 May 04, 2012 (137)
33 ILLUMINA ss537476622 Sep 08, 2015 (146)
34 TISHKOFF ss554480762 Apr 25, 2013 (138)
35 SSMP ss648254023 Apr 25, 2013 (138)
36 ILLUMINA ss778604580 Sep 08, 2015 (146)
37 ILLUMINA ss783237772 Sep 08, 2015 (146)
38 ILLUMINA ss784191699 Sep 08, 2015 (146)
39 ILLUMINA ss832498300 Sep 08, 2015 (146)
40 ILLUMINA ss833113319 Jul 12, 2019 (153)
41 ILLUMINA ss834061908 Sep 08, 2015 (146)
42 EVA-GONL ss975483121 Aug 21, 2014 (142)
43 JMKIDD_LAB ss1068127797 Aug 21, 2014 (142)
44 1000GENOMES ss1292108188 Aug 21, 2014 (142)
45 DDI ss1425911029 Apr 01, 2015 (144)
46 EVA_GENOME_DK ss1574271706 Apr 01, 2015 (144)
47 EVA_DECODE ss1584861437 Apr 01, 2015 (144)
48 EVA_UK10K_ALSPAC ss1600817232 Apr 01, 2015 (144)
49 EVA_UK10K_TWINSUK ss1643811265 Apr 01, 2015 (144)
50 EVA_SVP ss1712357160 Apr 01, 2015 (144)
51 ILLUMINA ss1751859120 Sep 08, 2015 (146)
52 HAMMER_LAB ss1794807828 Sep 08, 2015 (146)
53 WEILL_CORNELL_DGM ss1918682714 Feb 12, 2016 (147)
54 GENOMED ss1966820817 Jul 19, 2016 (147)
55 JJLAB ss2019862873 Sep 14, 2016 (149)
56 USC_VALOUEV ss2147881569 Dec 20, 2016 (150)
57 HUMAN_LONGEVITY ss2165032217 Dec 20, 2016 (150)
58 TOPMED ss2327382997 Dec 20, 2016 (150)
59 SYSTEMSBIOZJU ss2624442846 Nov 08, 2017 (151)
60 ILLUMINA ss2632553637 Nov 08, 2017 (151)
61 GRF ss2697808903 Nov 08, 2017 (151)
62 ILLUMINA ss2710678278 Nov 08, 2017 (151)
63 GNOMAD ss2758639176 Nov 08, 2017 (151)
64 SWEGEN ss2987305862 Nov 08, 2017 (151)
65 BIOINF_KMB_FNS_UNIBA ss3023695027 Nov 08, 2017 (151)
66 TOPMED ss3084653269 Nov 08, 2017 (151)
67 CSHL ss3343595993 Nov 08, 2017 (151)
68 ILLUMINA ss3626165313 Oct 11, 2018 (152)
69 ILLUMINA ss3630587813 Oct 11, 2018 (152)
70 ILLUMINA ss3632903290 Oct 11, 2018 (152)
71 ILLUMINA ss3633598288 Oct 11, 2018 (152)
72 ILLUMINA ss3634339262 Oct 11, 2018 (152)
73 ILLUMINA ss3635291898 Oct 11, 2018 (152)
74 ILLUMINA ss3636016817 Oct 11, 2018 (152)
75 ILLUMINA ss3637042354 Oct 11, 2018 (152)
76 ILLUMINA ss3637775460 Oct 11, 2018 (152)
77 ILLUMINA ss3640046622 Oct 11, 2018 (152)
78 ILLUMINA ss3642785645 Oct 11, 2018 (152)
79 EGCUT_WGS ss3655390968 Jul 12, 2019 (153)
80 EVA_DECODE ss3687367370 Jul 12, 2019 (153)
81 ACPOP ss3727314184 Jul 12, 2019 (153)
82 ILLUMINA ss3744640231 Jul 12, 2019 (153)
83 EVA ss3746574287 Jul 12, 2019 (153)
84 ILLUMINA ss3772141468 Jul 12, 2019 (153)
85 PACBIO ss3783495936 Jul 12, 2019 (153)
86 PACBIO ss3789140969 Jul 12, 2019 (153)
87 PACBIO ss3794013813 Jul 12, 2019 (153)
88 KHV_HUMAN_GENOMES ss3799575046 Jul 12, 2019 (153)
89 EVA ss3826326650 Apr 25, 2020 (154)
90 EVA ss3836553601 Apr 25, 2020 (154)
91 EVA ss3841961598 Apr 25, 2020 (154)
92 HGDP ss3847343747 Apr 25, 2020 (154)
93 SGDP_PRJ ss3849477827 Apr 25, 2020 (154)
94 KRGDB ss3894555897 Apr 25, 2020 (154)
95 KOGIC ss3945091569 Apr 25, 2020 (154)
96 EVA ss3984814985 Apr 25, 2021 (155)
97 EVA ss4016927699 Apr 25, 2021 (155)
98 TOPMED ss4460702360 Apr 25, 2021 (155)
99 TOMMO_GENOMICS ss5145313792 Apr 25, 2021 (155)
100 1000Genomes NC_000001.10 - 100066515 Oct 11, 2018 (152)
101 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 100066515 Oct 11, 2018 (152)
102 Genetic variation in the Estonian population NC_000001.10 - 100066515 Oct 11, 2018 (152)
103 The Danish reference pan genome NC_000001.10 - 100066515 Apr 25, 2020 (154)
104 gnomAD - Genomes NC_000001.11 - 99600959 Apr 25, 2021 (155)
105 Genome of the Netherlands Release 5 NC_000001.10 - 100066515 Apr 25, 2020 (154)
106 HGDP-CEPH-db Supplement 1 NC_000001.9 - 99839103 Apr 25, 2020 (154)
107 HapMap NC_000001.11 - 99600959 Apr 25, 2020 (154)
108 KOREAN population from KRGDB NC_000001.10 - 100066515 Apr 25, 2020 (154)
109 Korean Genome Project NC_000001.11 - 99600959 Apr 25, 2020 (154)
110 Northern Sweden NC_000001.10 - 100066515 Jul 12, 2019 (153)
111 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 100066515 Apr 25, 2021 (155)
112 Qatari NC_000001.10 - 100066515 Apr 25, 2020 (154)
113 SGDP_PRJ NC_000001.10 - 100066515 Apr 25, 2020 (154)
114 Siberian NC_000001.10 - 100066515 Apr 25, 2020 (154)
115 8.3KJPN NC_000001.10 - 100066515 Apr 25, 2021 (155)
116 TopMed NC_000001.11 - 99600959 Apr 25, 2021 (155)
117 UK 10K study - Twins NC_000001.10 - 100066515 Oct 11, 2018 (152)
118 A Vietnamese Genetic Variation Database NC_000001.10 - 100066515 Jul 12, 2019 (153)
119 ALFA NC_000001.11 - 99600959 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)
rs61308865 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81282285, ss84760299 NC_000001.8:99778535:C:T NC_000001.11:99600958:C:T (self)
21639, ss87656611, ss108453807, ss110891259, ss118919287, ss163739405, ss164869388, ss166904899, ss198832910, ss205276889, ss253316049, ss275945361, ss284105707, ss290580525, ss481578705, ss1584861437, ss1712357160, ss3642785645, ss3847343747 NC_000001.9:99839102:C:T NC_000001.11:99600958:C:T (self)
2871771, 1584181, 1129216, 1629005, 687215, 1733291, 599049, 40912, 724644, 1494807, 397923, 3283099, 1584181, 341258, ss218548713, ss230656785, ss238323753, ss481608542, ss482579795, ss485584336, ss537476622, ss554480762, ss648254023, ss778604580, ss783237772, ss784191699, ss832498300, ss833113319, ss834061908, ss975483121, ss1068127797, ss1292108188, ss1425911029, ss1574271706, ss1600817232, ss1643811265, ss1751859120, ss1794807828, ss1918682714, ss1966820817, ss2019862873, ss2147881569, ss2327382997, ss2624442846, ss2632553637, ss2697808903, ss2710678278, ss2758639176, ss2987305862, ss3343595993, ss3626165313, ss3630587813, ss3632903290, ss3633598288, ss3634339262, ss3635291898, ss3636016817, ss3637042354, ss3637775460, ss3640046622, ss3655390968, ss3727314184, ss3744640231, ss3746574287, ss3772141468, ss3783495936, ss3789140969, ss3794013813, ss3826326650, ss3836553601, ss3849477827, ss3894555897, ss3984814985, ss4016927699, ss5145313792 NC_000001.10:100066514:C:T NC_000001.11:99600958:C:T (self)
20300569, 136598, 1469570, 15310297, 24308695, 7034274849, ss2165032217, ss3023695027, ss3084653269, ss3687367370, ss3799575046, ss3841961598, ss3945091569, ss4460702360 NC_000001.11:99600958:C:T NC_000001.11:99600958:C:T (self)
ss11353580 NT_028050.12:940185:C:T NC_000001.11:99600958:C:T (self)
ss65773377, ss70930871, ss71532470, ss75634112, ss138045121, ss154427206, ss159602321, ss160883619, ss174393701 NT_032977.9:70038432:C:T NC_000001.11:99600958: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 rs7518025

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