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dbSNP Short Genetic Variations

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.

rs12565727

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr1:10973025 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.30838 (38723/125568, TOPMED)
G=0.3163 (9761/30864, GnomAD)
G=0.326 (1635/5008, 1000G) (+ 3 more)
G=0.248 (1111/4480, Estonian)
G=0.229 (881/3854, ALSPAC)
G=0.219 (812/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C1orf127 : Intron Variant
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.p12 chr 1 NC_000001.11:g.10973025A>G
GRCh37.p13 chr 1 NC_000001.10:g.11033082A>G
Gene: C1orf127, chromosome 1 open reading frame 127 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
C1orf127 transcript variant 1 NM_001170754.1:c. N/A Intron Variant
C1orf127 transcript variant X1 XM_017000373.1:c. N/A Genic Upstream Transcript Variant
C1orf127 transcript variant X2 XM_024453349.1:c. N/A Genic Upstream Transcript 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 A=0.69162 G=0.30838
gnomAD - Genomes Global Study-wide 30864 A=0.6837 G=0.3163
gnomAD - Genomes European Sub 18428 A=0.7466 G=0.2534
gnomAD - Genomes African Sub 8696 A=0.537 G=0.463
gnomAD - Genomes East Asian Sub 1618 A=0.690 G=0.310
gnomAD - Genomes Other Sub 982 A=0.73 G=0.27
gnomAD - Genomes American Sub 838 A=0.73 G=0.27
gnomAD - Genomes Ashkenazi Jewish Sub 302 A=0.74 G=0.26
1000Genomes Global Study-wide 5008 A=0.674 G=0.326
1000Genomes African Sub 1322 A=0.467 G=0.533
1000Genomes East Asian Sub 1008 A=0.710 G=0.290
1000Genomes Europe Sub 1006 A=0.762 G=0.238
1000Genomes South Asian Sub 978 A=0.79 G=0.21
1000Genomes American Sub 694 A=0.73 G=0.27
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.752 G=0.248
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.771 G=0.229
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.781 G=0.219
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 A= G Note
GRCh38.p12 chr 1 NC_000001.11:g.10973025A= NC_000001.11:g.10973025A>G
GRCh37.p13 chr 1 NC_000001.10:g.11033082A= NC_000001.10:g.11033082A>G
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#.

59 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss19852486 Feb 28, 2004 (120)
2 ABI ss41071623 Mar 14, 2006 (126)
3 ILLUMINA ss75090533 Dec 06, 2007 (129)
4 1000GENOMES ss107989945 Jan 22, 2009 (130)
5 1000GENOMES ss110051427 Jan 24, 2009 (130)
6 KRIBB_YJKIM ss119793877 Dec 01, 2009 (131)
7 GMI ss154632956 Dec 01, 2009 (131)
8 ILLUMINA ss160282956 Dec 01, 2009 (131)
9 ENSEMBL ss161157667 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss163070560 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss163822545 Jul 04, 2010 (132)
12 ILLUMINA ss172158962 Jul 04, 2010 (132)
13 BUSHMAN ss198014456 Jul 04, 2010 (132)
14 1000GENOMES ss218235121 Jul 14, 2010 (132)
15 1000GENOMES ss230425638 Jul 14, 2010 (132)
16 1000GENOMES ss238140842 Jul 15, 2010 (132)
17 BL ss252914264 May 09, 2011 (134)
18 GMI ss275712839 May 04, 2012 (137)
19 ILLUMINA ss480348577 Sep 08, 2015 (146)
20 ILLUMINA ss536795143 Sep 08, 2015 (146)
21 TISHKOFF ss553793505 Apr 25, 2013 (138)
22 SSMP ss647573196 Apr 25, 2013 (138)
23 EVA-GONL ss974854170 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1067667882 Aug 21, 2014 (142)
25 1000GENOMES ss1289675727 Aug 21, 2014 (142)
26 DDI ss1425711417 Apr 01, 2015 (144)
27 EVA_GENOME_DK ss1573886439 Apr 01, 2015 (144)
28 EVA_DECODE ss1584212356 Apr 01, 2015 (144)
29 EVA_UK10K_ALSPAC ss1599544611 Apr 01, 2015 (144)
30 EVA_UK10K_TWINSUK ss1642538644 Apr 01, 2015 (144)
31 EVA_SVP ss1712311029 Apr 01, 2015 (144)
32 HAMMER_LAB ss1793899666 Sep 08, 2015 (146)
33 WEILL_CORNELL_DGM ss1918053251 Feb 12, 2016 (147)
34 ILLUMINA ss1945984528 Feb 12, 2016 (147)
35 ILLUMINA ss1958240863 Feb 12, 2016 (147)
36 GENOMED ss1966684085 Jul 19, 2016 (147)
37 JJLAB ss2019540760 Sep 14, 2016 (149)
38 ILLUMINA ss2094952878 Dec 20, 2016 (150)
39 USC_VALOUEV ss2147538089 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2160034933 Dec 20, 2016 (150)
41 TOPMED ss2322192692 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2624286787 Nov 08, 2017 (151)
43 ILLUMINA ss2632476992 Nov 08, 2017 (151)
44 GRF ss2697434262 Nov 08, 2017 (151)
45 ILLUMINA ss2710665590 Nov 08, 2017 (151)
46 GNOMAD ss2751603812 Nov 08, 2017 (151)
47 AFFY ss2985498770 Nov 08, 2017 (151)
48 SWEGEN ss2986293776 Nov 08, 2017 (151)
49 ILLUMINA ss3021053881 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3023534693 Nov 08, 2017 (151)
51 TOPMED ss3068552387 Nov 08, 2017 (151)
52 CSHL ss3343316561 Nov 08, 2017 (151)
53 ILLUMINA ss3625525054 Oct 11, 2018 (152)
54 ILLUMINA ss3626025619 Oct 11, 2018 (152)
55 ILLUMINA ss3635982846 Oct 11, 2018 (152)
56 ILLUMINA ss3637737189 Oct 11, 2018 (152)
57 ILLUMINA ss3642751075 Oct 11, 2018 (152)
58 ILLUMINA ss3644480379 Oct 11, 2018 (152)
59 ILLUMINA ss3651377813 Oct 11, 2018 (152)
60 1000Genomes NC_000001.10 - 11033082 Oct 11, 2018 (152)
61 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 11033082 Oct 11, 2018 (152)
62 Genetic variation in the Estonian population NC_000001.10 - 11033082 Oct 11, 2018 (152)
63 gnomAD - Genomes NC_000001.10 - 11033082 Oct 11, 2018 (152)
64 TopMed NC_000001.11 - 10973025 Oct 11, 2018 (152)
65 UK 10K study - Twins NC_000001.10 - 11033082 Oct 11, 2018 (152)
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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss107989945, ss110051427, ss160282956, ss163070560, ss163822545, ss198014456, ss252914264, ss275712839, ss1584212356, ss1712311029, ss3642751075 NC_000001.9:10955668:A= NC_000001.11:10973024:A= (self)
351534, 182678, 132467, 1003011, 182678, ss218235121, ss230425638, ss238140842, ss480348577, ss536795143, ss553793505, ss647573196, ss974854170, ss1067667882, ss1289675727, ss1425711417, ss1573886439, ss1599544611, ss1642538644, ss1793899666, ss1918053251, ss1945984528, ss1958240863, ss1966684085, ss2019540760, ss2094952878, ss2147538089, ss2322192692, ss2624286787, ss2632476992, ss2697434262, ss2710665590, ss2751603812, ss2985498770, ss2986293776, ss3021053881, ss3343316561, ss3625525054, ss3626025619, ss3635982846, ss3637737189, ss3644480379, ss3651377813 NC_000001.10:11033081:A= NC_000001.11:10973024:A= (self)
1745965, ss2160034933, ss3023534693, ss3068552387 NC_000001.11:10973024:A= NC_000001.11:10973024:A= (self)
ss19852486 NT_021937.16:5160140:A= NC_000001.11:10973024:A= (self)
ss41071623, ss75090533, ss119793877, ss154632956, ss161157667, ss172158962 NT_021937.19:7037813:A= NC_000001.11:10973024:A= (self)
ss107989945, ss110051427, ss160282956, ss163070560, ss163822545, ss198014456, ss252914264, ss275712839, ss1584212356, ss1712311029, ss3642751075 NC_000001.9:10955668:A>G NC_000001.11:10973024:A>G (self)
351534, 182678, 132467, 1003011, 182678, ss218235121, ss230425638, ss238140842, ss480348577, ss536795143, ss553793505, ss647573196, ss974854170, ss1067667882, ss1289675727, ss1425711417, ss1573886439, ss1599544611, ss1642538644, ss1793899666, ss1918053251, ss1945984528, ss1958240863, ss1966684085, ss2019540760, ss2094952878, ss2147538089, ss2322192692, ss2624286787, ss2632476992, ss2697434262, ss2710665590, ss2751603812, ss2985498770, ss2986293776, ss3021053881, ss3343316561, ss3625525054, ss3626025619, ss3635982846, ss3637737189, ss3644480379, ss3651377813 NC_000001.10:11033081:A>G NC_000001.11:10973024:A>G (self)
1745965, ss2160034933, ss3023534693, ss3068552387 NC_000001.11:10973024:A>G NC_000001.11:10973024:A>G (self)
ss19852486 NT_021937.16:5160140:A>G NC_000001.11:10973024:A>G (self)
ss41071623, ss75090533, ss119793877, ss154632956, ss161157667, ss172158962 NT_021937.19:7037813:A>G NC_000001.11:10973024:A>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 rs12565727
PMID Title Author Year Journal
26001114 Evaluation of DNA variants associated with androgenetic alopecia and their potential to predict male pattern baldness. MarciƄska M et al. 2015 PloS one

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.post58+e54ea20