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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.

rs1175546

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:3777345 (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=0.146704 (38831/264690, TOPMED)
T=0.167019 (23413/140182, GnomAD)
T=0.20201 (3816/18890, ALFA) (+ 11 more)
T=0.00006 (1/16760, 8.3KJPN)
T=0.0887 (444/5008, 1000G)
T=0.2625 (1176/4480, Estonian)
T=0.2447 (943/3854, ALSPAC)
T=0.2362 (876/3708, TWINSUK)
T=0.240 (240/998, GoNL)
T=0.180 (108/600, NorthernSweden)
T=0.120 (26/216, Qatari)
C=0.446 (50/112, SGDP_PRJ)
T=0.17 (7/40, GENOME_DK)
C=0.41 (9/22, 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.3777345C>T
GRCh37.p13 chr 1 NC_000001.10:g.3693909C>T
Vel blood group RefSeqGene (LRG_827) NG_033869.1:g.9585C>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
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 18890 C=0.79799 T=0.20201
European Sub 14286 C=0.75710 T=0.24290
African Sub 2946 C=0.9504 T=0.0496
African Others Sub 114 C=0.991 T=0.009
African American Sub 2832 C=0.9488 T=0.0512
Asian Sub 112 C=0.991 T=0.009
East Asian Sub 86 C=0.99 T=0.01
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 146 C=0.822 T=0.178
Latin American 2 Sub 610 C=0.897 T=0.103
South Asian Sub 98 C=0.91 T=0.09
Other Sub 692 C=0.854 T=0.146


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=0.853296 T=0.146704
gnomAD - Genomes Global Study-wide 140182 C=0.832981 T=0.167019
gnomAD - Genomes European Sub 75888 C=0.75275 T=0.24725
gnomAD - Genomes African Sub 42036 C=0.95647 T=0.04353
gnomAD - Genomes American Sub 13654 C=0.87652 T=0.12348
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.7647 T=0.2353
gnomAD - Genomes East Asian Sub 3128 C=0.9990 T=0.0010
gnomAD - Genomes Other Sub 2152 C=0.8378 T=0.1622
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 T=0.00006
1000Genomes Global Study-wide 5008 C=0.9113 T=0.0887
1000Genomes African Sub 1322 C=0.9849 T=0.0151
1000Genomes East Asian Sub 1008 C=0.9980 T=0.0020
1000Genomes Europe Sub 1006 C=0.7922 T=0.2078
1000Genomes South Asian Sub 978 C=0.865 T=0.135
1000Genomes American Sub 694 C=0.883 T=0.117
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.7375 T=0.2625
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7553 T=0.2447
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7638 T=0.2362
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.760 T=0.240
Northern Sweden ACPOP Study-wide 600 C=0.820 T=0.180
Qatari Global Study-wide 216 C=0.880 T=0.120
SGDP_PRJ Global Study-wide 112 C=0.446 T=0.554
The Danish reference pan genome Danish Study-wide 40 C=0.82 T=0.17
Siberian Global Study-wide 22 C=0.41 T=0.59
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.3777345= NC_000001.11:g.3777345C>T
GRCh37.p13 chr 1 NC_000001.10:g.3693909= NC_000001.10:g.3693909C>T
Vel blood group RefSeqGene (LRG_827) NG_033869.1:g.9585= NG_033869.1:g.9585C>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#.

40 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1618050 Oct 18, 2000 (87)
2 SC_JCM ss2637443 Nov 08, 2000 (89)
3 SC_JCM ss3961806 Sep 28, 2001 (100)
4 SC_SNP ss12992560 Dec 05, 2003 (119)
5 BCMHGSC_JDW ss87174158 Mar 23, 2008 (129)
6 1000GENOMES ss107948884 Jan 22, 2009 (130)
7 ENSEMBL ss137763445 Dec 01, 2009 (131)
8 COMPLETE_GENOMICS ss163737406 Jul 04, 2010 (132)
9 1000GENOMES ss230404007 Jul 14, 2010 (132)
10 PJP ss290498232 May 09, 2011 (134)
11 SSMP ss647536210 Apr 25, 2013 (138)
12 EVA-GONL ss974796078 Aug 21, 2014 (142)
13 JMKIDD_LAB ss1067627044 Aug 21, 2014 (142)
14 1000GENOMES ss1289450410 Aug 21, 2014 (142)
15 DDI ss1425692840 Apr 01, 2015 (144)
16 EVA_GENOME_DK ss1573859962 Apr 01, 2015 (144)
17 EVA_DECODE ss1584154857 Apr 01, 2015 (144)
18 EVA_UK10K_ALSPAC ss1599426678 Apr 01, 2015 (144)
19 EVA_UK10K_TWINSUK ss1642420711 Apr 01, 2015 (144)
20 WEILL_CORNELL_DGM ss1917991622 Feb 12, 2016 (147)
21 JJLAB ss2019511911 Sep 14, 2016 (149)
22 USC_VALOUEV ss2147502328 Dec 20, 2016 (150)
23 HUMAN_LONGEVITY ss2159571994 Dec 20, 2016 (150)
24 TOPMED ss2321727001 Dec 20, 2016 (150)
25 GNOMAD ss2750968806 Nov 08, 2017 (151)
26 SWEGEN ss2986200796 Nov 08, 2017 (151)
27 BIOINF_KMB_FNS_UNIBA ss3023519575 Nov 08, 2017 (151)
28 TOPMED ss3067119016 Nov 08, 2017 (151)
29 CSHL ss3343288745 Nov 08, 2017 (151)
30 EGCUT_WGS ss3654301940 Jul 12, 2019 (153)
31 EVA_DECODE ss3686046546 Jul 12, 2019 (153)
32 ACPOP ss3726739703 Jul 12, 2019 (153)
33 EVA ss3745754852 Jul 12, 2019 (153)
34 KHV_HUMAN_GENOMES ss3798776618 Jul 12, 2019 (153)
35 EVA ss3825993811 Apr 25, 2020 (154)
36 EVA ss3836384030 Apr 25, 2020 (154)
37 EVA ss3841788191 Apr 25, 2020 (154)
38 SGDP_PRJ ss3848068886 Apr 25, 2020 (154)
39 TOPMED ss4437295362 Apr 25, 2021 (155)
40 TOMMO_GENOMICS ss5142200293 Apr 25, 2021 (155)
41 1000Genomes NC_000001.10 - 3693909 Oct 11, 2018 (152)
42 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 3693909 Oct 11, 2018 (152)
43 Genetic variation in the Estonian population NC_000001.10 - 3693909 Oct 11, 2018 (152)
44 The Danish reference pan genome NC_000001.10 - 3693909 Apr 25, 2020 (154)
45 gnomAD - Genomes NC_000001.11 - 3777345 Apr 25, 2021 (155)
46 Genome of the Netherlands Release 5 NC_000001.10 - 3693909 Apr 25, 2020 (154)
47 Northern Sweden NC_000001.10 - 3693909 Jul 12, 2019 (153)
48 Qatari NC_000001.10 - 3693909 Apr 25, 2020 (154)
49 SGDP_PRJ NC_000001.10 - 3693909 Apr 25, 2020 (154)
50 Siberian NC_000001.10 - 3693909 Apr 25, 2020 (154)
51 8.3KJPN NC_000001.10 - 3693909 Apr 25, 2021 (155)
52 TopMed NC_000001.11 - 3777345 Apr 25, 2021 (155)
53 UK 10K study - Twins NC_000001.10 - 3693909 Oct 11, 2018 (152)
54 ALFA NC_000001.11 - 3777345 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss87174158, ss107948884, ss163737406, ss290498232, ss1584154857 NC_000001.9:3683768:C:T NC_000001.11:3777344:C:T (self)
118399, 52862, 40188, 1367196, 22706, 24568, 33552, 85866, 18682, 169600, 52862, ss230404007, ss647536210, ss974796078, ss1067627044, ss1289450410, ss1425692840, ss1573859962, ss1599426678, ss1642420711, ss1917991622, ss2019511911, ss2147502328, ss2321727001, ss2750968806, ss2986200796, ss3343288745, ss3654301940, ss3726739703, ss3745754852, ss3825993811, ss3836384030, ss3848068886, ss5142200293 NC_000001.10:3693908:C:T NC_000001.11:3777344:C:T (self)
855107, 561089, 901697, 2631916789, ss2159571994, ss3023519575, ss3067119016, ss3686046546, ss3798776618, ss3841788191, ss4437295362 NC_000001.11:3777344:C:T NC_000001.11:3777344:C:T (self)
ss12992560 NT_004321.15:1000683:C:T NC_000001.11:3777344:C:T (self)
ss1618050, ss2637443, ss3961806, ss137763445 NT_004350.19:3172540:C:T NC_000001.11:3777344: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 rs1175546

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