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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs10007934

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:136903447 (GRCh38.p14) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.077124 (20414/264690, TOPMED)
A=0.074688 (13402/179440, ALFA)
A=0.083270 (11668/140122, GnomAD) (+ 15 more)
A=0.0612 (392/6404, 1000G_30x)
A=0.0607 (304/5008, 1000G)
A=0.0967 (433/4480, Estonian)
A=0.0688 (265/3854, ALSPAC)
A=0.0698 (259/3708, TWINSUK)
A=0.0369 (77/2084, HGDP_Stanford)
A=0.0834 (130/1558, HapMap)
A=0.090 (90/998, GoNL)
A=0.080 (48/600, NorthernSweden)
A=0.088 (19/216, Qatari)
G=0.48 (21/44, SGDP_PRJ)
A=0.10 (4/40, GENOME_DK)
A=0.08 (2/26, Ancient Sardinia)
G=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC02511 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 179440 G=0.925312 A=0.074688
European Sub 157652 G=0.923382 A=0.076618
African Sub 6674 G=0.9091 A=0.0909
African Others Sub 256 G=0.898 A=0.102
African American Sub 6418 G=0.9095 A=0.0905
Asian Sub 400 G=1.000 A=0.000
East Asian Sub 292 G=1.000 A=0.000
Other Asian Sub 108 G=1.000 A=0.000
Latin American 1 Sub 740 G=0.923 A=0.077
Latin American 2 Sub 2662 G=0.9666 A=0.0334
South Asian Sub 5012 G=0.9785 A=0.0215
Other Sub 6300 G=0.9267 A=0.0733


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 G=0.922876 A=0.077124
Allele Frequency Aggregator Total Global 179440 G=0.925312 A=0.074688
Allele Frequency Aggregator European Sub 157652 G=0.923382 A=0.076618
Allele Frequency Aggregator African Sub 6674 G=0.9091 A=0.0909
Allele Frequency Aggregator Other Sub 6300 G=0.9267 A=0.0733
Allele Frequency Aggregator South Asian Sub 5012 G=0.9785 A=0.0215
Allele Frequency Aggregator Latin American 2 Sub 2662 G=0.9666 A=0.0334
Allele Frequency Aggregator Latin American 1 Sub 740 G=0.923 A=0.077
Allele Frequency Aggregator Asian Sub 400 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 140122 G=0.916730 A=0.083270
gnomAD - Genomes European Sub 75888 G=0.91734 A=0.08266
gnomAD - Genomes African Sub 41982 G=0.90167 A=0.09833
gnomAD - Genomes American Sub 13648 G=0.94219 A=0.05781
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=0.9073 A=0.0927
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9209 A=0.0791
1000Genomes_30x Global Study-wide 6404 G=0.9388 A=0.0612
1000Genomes_30x African Sub 1786 G=0.8914 A=0.1086
1000Genomes_30x Europe Sub 1266 G=0.8942 A=0.1058
1000Genomes_30x South Asian Sub 1202 G=0.9900 A=0.0100
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.947 A=0.053
1000Genomes Global Study-wide 5008 G=0.9393 A=0.0607
1000Genomes African Sub 1322 G=0.8880 A=0.1120
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.8926 A=0.1074
1000Genomes South Asian Sub 978 G=0.990 A=0.010
1000Genomes American Sub 694 G=0.945 A=0.055
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9033 A=0.0967
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9312 A=0.0688
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9302 A=0.0698
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 G=0.9631 A=0.0369
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 G=0.998 A=0.002
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 G=0.978 A=0.022
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 G=0.943 A=0.057
HGDP-CEPH-db Supplement 1 Europe Sub 320 G=0.909 A=0.091
HGDP-CEPH-db Supplement 1 Africa Sub 242 G=0.930 A=0.070
HGDP-CEPH-db Supplement 1 America Sub 216 G=0.995 A=0.005
HGDP-CEPH-db Supplement 1 Oceania Sub 72 G=1.00 A=0.00
HapMap Global Study-wide 1558 G=0.9166 A=0.0834
HapMap African Sub 692 G=0.902 A=0.098
HapMap American Sub 600 G=0.932 A=0.068
HapMap Europe Sub 176 G=0.881 A=0.119
HapMap Asian Sub 90 G=1.00 A=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.910 A=0.090
Northern Sweden ACPOP Study-wide 600 G=0.920 A=0.080
Qatari Global Study-wide 216 G=0.912 A=0.088
SGDP_PRJ Global Study-wide 44 G=0.48 A=0.52
The Danish reference pan genome Danish Study-wide 40 G=0.90 A=0.10
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 26 G=0.92 A=0.08
Siberian Global Study-wide 2 G=0.5 A=0.5
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.p14 chr 4 NC_000004.12:g.136903447G>A
GRCh37.p13 chr 4 NC_000004.11:g.137824601G>A
Gene: LINC02511, long intergenic non-protein coding RNA 2511 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC02511 transcript NR_149105.1: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

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
GRCh38.p14 chr 4 NC_000004.12:g.136903447= NC_000004.12:g.136903447G>A
GRCh37.p13 chr 4 NC_000004.11:g.137824601= NC_000004.11:g.137824601G>A
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#.

95 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss13853942 Dec 05, 2003 (119)
2 ILLUMINA ss66792657 Nov 29, 2006 (127)
3 ILLUMINA ss66864091 Nov 29, 2006 (127)
4 ILLUMINA ss66933332 Nov 29, 2006 (127)
5 ILLUMINA ss70356040 May 16, 2007 (127)
6 ILLUMINA ss70459447 May 25, 2008 (130)
7 ILLUMINA ss70980017 May 16, 2007 (127)
8 ILLUMINA ss75826342 Dec 07, 2007 (129)
9 AFFY ss76527508 Dec 07, 2007 (129)
10 KRIBB_YJKIM ss84888866 Dec 15, 2007 (130)
11 1000GENOMES ss108379978 Jan 23, 2009 (130)
12 ILLUMINA ss121252275 Dec 01, 2009 (131)
13 ILLUMINA ss152539977 Dec 01, 2009 (131)
14 ILLUMINA ss159103314 Dec 01, 2009 (131)
15 ILLUMINA ss159850964 Dec 01, 2009 (131)
16 ILLUMINA ss169208137 Jul 04, 2010 (132)
17 ILLUMINA ss169498333 Jul 04, 2010 (132)
18 1000GENOMES ss221240211 Jul 14, 2010 (132)
19 1000GENOMES ss232619319 Jul 14, 2010 (132)
20 GMI ss285015415 Apr 25, 2013 (138)
21 ILLUMINA ss479154553 May 04, 2012 (137)
22 ILLUMINA ss479156241 May 04, 2012 (137)
23 ILLUMINA ss479470482 Sep 08, 2015 (146)
24 ILLUMINA ss484378492 May 04, 2012 (137)
25 ILLUMINA ss536564733 Sep 08, 2015 (146)
26 TISHKOFF ss557885579 Apr 25, 2013 (138)
27 ILLUMINA ss778343679 Sep 08, 2015 (146)
28 ILLUMINA ss782635530 Sep 08, 2015 (146)
29 ILLUMINA ss783605077 Sep 08, 2015 (146)
30 ILLUMINA ss825325771 Jul 19, 2016 (147)
31 ILLUMINA ss831885611 Sep 08, 2015 (146)
32 ILLUMINA ss832616110 Jul 13, 2019 (153)
33 ILLUMINA ss833798314 Sep 08, 2015 (146)
34 EVA-GONL ss980732830 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1071999690 Aug 21, 2014 (142)
36 1000GENOMES ss1312018130 Aug 21, 2014 (142)
37 EVA_GENOME_DK ss1580798794 Apr 01, 2015 (144)
38 EVA_DECODE ss1590243541 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1611277524 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1654271557 Apr 01, 2015 (144)
41 EVA_SVP ss1712709622 Apr 01, 2015 (144)
42 ILLUMINA ss1752499243 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1923974544 Feb 12, 2016 (147)
44 GENOMED ss1969883348 Jul 19, 2016 (147)
45 JJLAB ss2022573771 Sep 14, 2016 (149)
46 USC_VALOUEV ss2150705469 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2267562664 Dec 20, 2016 (150)
48 ILLUMINA ss2634183034 Nov 08, 2017 (151)
49 GNOMAD ss2815842695 Nov 08, 2017 (151)
50 SWEGEN ss2995638894 Nov 08, 2017 (151)
51 BIOINF_KMB_FNS_UNIBA ss3025063660 Nov 08, 2017 (151)
52 CSHL ss3345986551 Nov 08, 2017 (151)
53 ILLUMINA ss3629074728 Oct 12, 2018 (152)
54 ILLUMINA ss3632115455 Oct 12, 2018 (152)
55 ILLUMINA ss3633350263 Oct 12, 2018 (152)
56 ILLUMINA ss3634069828 Oct 12, 2018 (152)
57 ILLUMINA ss3634972230 Oct 12, 2018 (152)
58 ILLUMINA ss3635752395 Oct 12, 2018 (152)
59 ILLUMINA ss3636678986 Oct 12, 2018 (152)
60 ILLUMINA ss3637504953 Oct 12, 2018 (152)
61 ILLUMINA ss3638513953 Oct 12, 2018 (152)
62 ILLUMINA ss3639259187 Oct 12, 2018 (152)
63 ILLUMINA ss3639651474 Oct 12, 2018 (152)
64 ILLUMINA ss3640679524 Oct 12, 2018 (152)
65 ILLUMINA ss3641168436 Oct 12, 2018 (152)
66 ILLUMINA ss3641465356 Oct 12, 2018 (152)
67 ILLUMINA ss3643463226 Oct 12, 2018 (152)
68 EGCUT_WGS ss3663545413 Jul 13, 2019 (153)
69 EVA_DECODE ss3713160020 Jul 13, 2019 (153)
70 ACPOP ss3731654050 Jul 13, 2019 (153)
71 ILLUMINA ss3745272467 Jul 13, 2019 (153)
72 ILLUMINA ss3772766934 Jul 13, 2019 (153)
73 PACBIO ss3784876361 Jul 13, 2019 (153)
74 PACBIO ss3790310545 Jul 13, 2019 (153)
75 PACBIO ss3795186081 Jul 13, 2019 (153)
76 KHV_HUMAN_GENOMES ss3805633926 Jul 13, 2019 (153)
77 EVA ss3828835644 Apr 26, 2020 (154)
78 EVA ss3837865721 Apr 26, 2020 (154)
79 EVA ss3843305410 Apr 26, 2020 (154)
80 HGDP ss3847766152 Apr 26, 2020 (154)
81 SGDP_PRJ ss3860165427 Apr 26, 2020 (154)
82 EVA ss3985097897 Apr 26, 2021 (155)
83 EVA ss4017170690 Apr 26, 2021 (155)
84 TOPMED ss4633776363 Apr 26, 2021 (155)
85 1000G_HIGH_COVERAGE ss5261199335 Oct 13, 2022 (156)
86 EVA ss5314993675 Oct 13, 2022 (156)
87 EVA ss5352621334 Oct 13, 2022 (156)
88 HUGCELL_USP ss5459738452 Oct 13, 2022 (156)
89 1000G_HIGH_COVERAGE ss5543388929 Oct 13, 2022 (156)
90 SANFORD_IMAGENETICS ss5636200040 Oct 13, 2022 (156)
91 EVA ss5799628134 Oct 13, 2022 (156)
92 YY_MCH ss5805582600 Oct 13, 2022 (156)
93 EVA ss5844782878 Oct 13, 2022 (156)
94 EVA ss5865706378 Oct 13, 2022 (156)
95 EVA ss5964601962 Oct 13, 2022 (156)
96 1000Genomes NC_000004.11 - 137824601 Oct 12, 2018 (152)
97 1000Genomes_30x NC_000004.12 - 136903447 Oct 13, 2022 (156)
98 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 137824601 Oct 12, 2018 (152)
99 Genetic variation in the Estonian population NC_000004.11 - 137824601 Oct 12, 2018 (152)
100 The Danish reference pan genome NC_000004.11 - 137824601 Apr 26, 2020 (154)
101 gnomAD - Genomes NC_000004.12 - 136903447 Apr 26, 2021 (155)
102 Genome of the Netherlands Release 5 NC_000004.11 - 137824601 Apr 26, 2020 (154)
103 HGDP-CEPH-db Supplement 1 NC_000004.10 - 138044051 Apr 26, 2020 (154)
104 HapMap NC_000004.12 - 136903447 Apr 26, 2020 (154)
105 Northern Sweden NC_000004.11 - 137824601 Jul 13, 2019 (153)
106 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000004.11 - 137824601 Apr 26, 2021 (155)
107 Qatari NC_000004.11 - 137824601 Apr 26, 2020 (154)
108 SGDP_PRJ NC_000004.11 - 137824601 Apr 26, 2020 (154)
109 Siberian NC_000004.11 - 137824601 Apr 26, 2020 (154)
110 TopMed NC_000004.12 - 136903447 Apr 26, 2021 (155)
111 UK 10K study - Twins NC_000004.11 - 137824601 Oct 12, 2018 (152)
112 ALFA NC_000004.12 - 136903447 Apr 26, 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)
rs60362576 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3639259187, ss3639651474 NC_000004.9:138182205:G:A NC_000004.12:136903446:G:A (self)
444044, ss76527508, ss108379978, ss285015415, ss479154553, ss825325771, ss1590243541, ss1712709622, ss3643463226, ss3847766152 NC_000004.10:138044050:G:A NC_000004.12:136903446:G:A (self)
23501246, 13067478, 9283661, 6963733, 5789244, 4938915, 323824, 6016474, 12182407, 3221823, 13067478, ss221240211, ss232619319, ss479156241, ss479470482, ss484378492, ss536564733, ss557885579, ss778343679, ss782635530, ss783605077, ss831885611, ss832616110, ss833798314, ss980732830, ss1071999690, ss1312018130, ss1580798794, ss1611277524, ss1654271557, ss1752499243, ss1923974544, ss1969883348, ss2022573771, ss2150705469, ss2634183034, ss2815842695, ss2995638894, ss3345986551, ss3629074728, ss3632115455, ss3633350263, ss3634069828, ss3634972230, ss3635752395, ss3636678986, ss3637504953, ss3638513953, ss3640679524, ss3641168436, ss3641465356, ss3663545413, ss3731654050, ss3745272467, ss3772766934, ss3784876361, ss3790310545, ss3795186081, ss3828835644, ss3837865721, ss3860165427, ss3985097897, ss4017170690, ss5314993675, ss5352621334, ss5636200040, ss5799628134, ss5844782878, ss5964601962 NC_000004.11:137824600:G:A NC_000004.12:136903446:G:A (self)
30914864, 166473345, 2718647, 471153919, 14452101218, ss2267562664, ss3025063660, ss3713160020, ss3805633926, ss3843305410, ss4633776363, ss5261199335, ss5459738452, ss5543388929, ss5805582600, ss5865706378 NC_000004.12:136903446:G:A NC_000004.12:136903446:G:A (self)
ss13853942 NT_016354.16:62319731:G:A NC_000004.12:136903446:G:A (self)
ss66792657, ss66864091, ss66933332, ss70356040, ss70459447, ss70980017, ss75826342, ss84888866, ss121252275, ss152539977, ss159103314, ss159850964, ss169208137, ss169498333 NT_016354.19:62372321:G:A NC_000004.12:136903446:G:A (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 rs10007934

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.post761+d5e8e07