Name: rs1175546
Published: September 21, 2022
License: Open Access

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 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:3777345 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.146704 (38831/264690, TOPMED)
T=0.167019 (23413/140182, GnomAD)
T=0.00004 (1/28258, 14KJPN) (+ 13 more)
T=0.20201 (3816/18890, ALFA)
T=0.00006 (1/16760, 8.3KJPN)
T=0.0865 (554/6404, 1000G_30x)
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

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	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

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
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
14KJPN	JAPANESE	Study-wide	28258	C=0.99996	T=0.00004
Allele Frequency Aggregator	Total	Global	18890	C=0.79799	T=0.20201
Allele Frequency Aggregator	European	Sub	14286	C=0.75710	T=0.24290
Allele Frequency Aggregator	African	Sub	2946	C=0.9504	T=0.0496
Allele Frequency Aggregator	Other	Sub	692	C=0.854	T=0.146
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.897	T=0.103
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.822	T=0.178
Allele Frequency Aggregator	Asian	Sub	112	C=0.991	T=0.009
Allele Frequency Aggregator	South Asian	Sub	98	C=0.91	T=0.09
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99994	T=0.00006
1000Genomes_30x	Global	Study-wide	6404	C=0.9135	T=0.0865
1000Genomes_30x	African	Sub	1786	C=0.9854	T=0.0146
1000Genomes_30x	Europe	Sub	1266	C=0.7923	T=0.2077
1000Genomes_30x	South Asian	Sub	1202	C=0.8710	T=0.1290
1000Genomes_30x	East Asian	Sub	1170	C=0.9983	T=0.0017
1000Genomes_30x	American	Sub	980	C=0.890	T=0.110
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

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 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

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

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.p14 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

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#.

47 SubSNP, 16 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	GNOMAD	ss2750968806	Nov 08, 2017 (151)
25	SWEGEN	ss2986200796	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3023519575	Nov 08, 2017 (151)
27	CSHL	ss3343288745	Nov 08, 2017 (151)
28	EGCUT_WGS	ss3654301940	Jul 12, 2019 (153)
29	EVA_DECODE	ss3686046546	Jul 12, 2019 (153)
30	ACPOP	ss3726739703	Jul 12, 2019 (153)
31	EVA	ss3745754852	Jul 12, 2019 (153)
32	KHV_HUMAN_GENOMES	ss3798776618	Jul 12, 2019 (153)
33	EVA	ss3825993811	Apr 25, 2020 (154)
34	EVA	ss3836384030	Apr 25, 2020 (154)
35	EVA	ss3841788191	Apr 25, 2020 (154)
36	SGDP_PRJ	ss3848068886	Apr 25, 2020 (154)
37	TOPMED	ss4437295362	Apr 25, 2021 (155)
38	TOMMO_GENOMICS	ss5142200293	Apr 25, 2021 (155)
39	1000G_HIGH_COVERAGE	ss5240967154	Oct 13, 2022 (156)
40	EVA	ss5316371680	Oct 13, 2022 (156)
41	HUGCELL_USP	ss5442192980	Oct 13, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5512632395	Oct 13, 2022 (156)
43	SANFORD_IMAGENETICS	ss5624807968	Oct 13, 2022 (156)
44	TOMMO_GENOMICS	ss5666413617	Oct 13, 2022 (156)
45	EVA	ss5831459201	Oct 13, 2022 (156)
46	EVA	ss5906809703	Oct 13, 2022 (156)
47	EVA	ss5936632646	Oct 13, 2022 (156)
48	1000Genomes	NC_000001.10 - 3693909	Oct 11, 2018 (152)
49	1000Genomes_30x	NC_000001.11 - 3777345	Oct 13, 2022 (156)
50	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 3693909	Oct 11, 2018 (152)
51	Genetic variation in the Estonian population	NC_000001.10 - 3693909	Oct 11, 2018 (152)
52	The Danish reference pan genome	NC_000001.10 - 3693909	Apr 25, 2020 (154)
53	gnomAD - Genomes	NC_000001.11 - 3777345	Apr 25, 2021 (155)
54	Genome of the Netherlands Release 5	NC_000001.10 - 3693909	Apr 25, 2020 (154)
55	Northern Sweden	NC_000001.10 - 3693909	Jul 12, 2019 (153)
56	Qatari	NC_000001.10 - 3693909	Apr 25, 2020 (154)
57	SGDP_PRJ	NC_000001.10 - 3693909	Apr 25, 2020 (154)
58	Siberian	NC_000001.10 - 3693909	Apr 25, 2020 (154)
59	8.3KJPN	NC_000001.10 - 3693909	Apr 25, 2021 (155)
60	14KJPN	NC_000001.11 - 3777345	Oct 13, 2022 (156)
61	TopMed	NC_000001.11 - 3777345	Apr 25, 2021 (155)
62	UK 10K study - Twins	NC_000001.10 - 3693909	Oct 11, 2018 (152)
63	ALFA	NC_000001.11 - 3777345	Apr 25, 2021 (155)

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, ss2750968806, ss2986200796, ss3343288745, ss3654301940, ss3726739703, ss3745754852, ss3825993811, ss3836384030, ss3848068886, ss5142200293, ss5316371680, ss5624807968, ss5831459201, ss5936632646	NC_000001.10:3693908:C:T	NC_000001.11:3777344:C:T	(self)
158330, 855107, 250721, 901697, 2631916789, ss2159571994, ss3023519575, ss3686046546, ss3798776618, ss3841788191, ss4437295362, ss5240967154, ss5442192980, ss5512632395, ss5666413617, ss5906809703	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)

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

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1175546