Name: rs1857092
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.

rs1857092

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:114311 (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 / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.148525 (39313/264690, TOPMED)
T=0.07301 (2063/28258, 14KJPN)
T=0.07232 (1212/16760, 8.3KJPN) (+ 16 more)
T=0.01585 (249/15712, ALFA)
T=0.1651 (1057/6404, 1000G_30x)
T=0.1637 (820/5008, 1000G)
T=0.0480 (215/4480, Estonian)
T=0.0859 (331/3854, ALSPAC)
T=0.0836 (310/3708, TWINSUK)
T=0.0743 (217/2922, KOREAN)
T=0.0639 (117/1832, Korea1K)
T=0.071 (71/998, GoNL)
T=0.057 (34/600, NorthernSweden)
T=0.181 (39/216, Qatari)
T=0.098 (21/214, Vietnamese)
G=0.393 (44/112, SGDP_PRJ)
T=0.03 (1/40, GENOME_DK)
G=0.5 (2/4, Siberian)
T=0.5 (2/4, 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	15712	G=0.98415	A=0.00000, T=0.01585
European	Sub	12764	G=0.98261	A=0.00000, T=0.01739
African	Sub	1616	G=0.9950	A=0.0000, T=0.0050
African Others	Sub	46	G=1.00	A=0.00, T=0.00
African American	Sub	1570	G=0.9949	A=0.0000, T=0.0051
Asian	Sub	96	G=1.00	A=0.00, T=0.00
East Asian	Sub	72	G=1.00	A=0.00, T=0.00
Other Asian	Sub	24	G=1.00	A=0.00, T=0.00
Latin American 1	Sub	92	G=1.00	A=0.00, T=0.00
Latin American 2	Sub	512	G=1.000	A=0.000, T=0.000
South Asian	Sub	68	G=1.00	A=0.00, T=0.00
Other	Sub	564	G=0.966	A=0.000, T=0.034

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	G=0.851475	T=0.148525
14KJPN	JAPANESE	Study-wide	28258	G=0.92699	T=0.07301
8.3KJPN	JAPANESE	Study-wide	16760	G=0.92768	T=0.07232
Allele Frequency Aggregator	Total	Global	15712	G=0.98415	A=0.00000, T=0.01585
Allele Frequency Aggregator	European	Sub	12764	G=0.98261	A=0.00000, T=0.01739
Allele Frequency Aggregator	African	Sub	1616	G=0.9950	A=0.0000, T=0.0050
Allele Frequency Aggregator	Other	Sub	564	G=0.966	A=0.000, T=0.034
Allele Frequency Aggregator	Latin American 2	Sub	512	G=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	96	G=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	Latin American 1	Sub	92	G=1.00	A=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	68	G=1.00	A=0.00, T=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.8349	T=0.1651
1000Genomes_30x	African	Sub	1786	G=0.6965	T=0.3035
1000Genomes_30x	Europe	Sub	1266	G=0.9115	T=0.0885
1000Genomes_30x	South Asian	Sub	1202	G=0.8311	T=0.1689
1000Genomes_30x	East Asian	Sub	1170	G=0.9128	T=0.0872
1000Genomes_30x	American	Sub	980	G=0.900	T=0.100
1000Genomes	Global	Study-wide	5008	G=0.8363	T=0.1637
1000Genomes	African	Sub	1322	G=0.6967	T=0.3033
1000Genomes	East Asian	Sub	1008	G=0.9137	T=0.0863
1000Genomes	Europe	Sub	1006	G=0.9085	T=0.0915
1000Genomes	South Asian	Sub	978	G=0.831	T=0.169
1000Genomes	American	Sub	694	G=0.892	T=0.108
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9520	T=0.0480
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9141	T=0.0859
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9164	T=0.0836
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9257	T=0.0743
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9361	T=0.0639
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.929	T=0.071
Northern Sweden	ACPOP	Study-wide	600	G=0.943	T=0.057
Qatari	Global	Study-wide	216	G=0.819	T=0.181
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.902	T=0.098
SGDP_PRJ	Global	Study-wide	112	G=0.393	T=0.607
The Danish reference pan genome	Danish	Study-wide	40	G=0.97	T=0.03
Siberian	Global	Study-wide	4	G=0.5	T=0.5

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 20	NC_000020.11:g.114311G>A
GRCh38.p14 chr 20	NC_000020.11:g.114311G>T
GRCh37.p13 chr 20	NC_000020.10:g.94952G>A
GRCh37.p13 chr 20	NC_000020.10:g.94952G>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	G=	A	T
GRCh38.p14 chr 20	NC_000020.11:g.114311=	NC_000020.11:g.114311G>A	NC_000020.11:g.114311G>T
GRCh37.p13 chr 20	NC_000020.10:g.94952=	NC_000020.10:g.94952G>A	NC_000020.10:g.94952G>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#.

59 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2730230	Jan 12, 2001 (92)
2	SC_SNP	ss8364532	Apr 21, 2003 (114)
3	BCM_SSAHASNP	ss10973184	Jul 11, 2003 (116)
4	CSHL-HAPMAP	ss16904749	Feb 27, 2004 (120)
5	PERLEGEN	ss23772461	Sep 20, 2004 (123)
6	HGSV	ss85279834	Dec 15, 2007 (130)
7	BCMHGSC_JDW	ss91611660	Mar 24, 2008 (129)
8	ILLUMINA-UK	ss117452100	Dec 01, 2009 (131)
9	GMI	ss156059219	Dec 01, 2009 (131)
10	ENSEMBL	ss161325332	Dec 01, 2009 (131)
11	BUSHMAN	ss203804049	Jul 04, 2010 (132)
12	1000GENOMES	ss228210703	Jul 14, 2010 (132)
13	1000GENOMES	ss237729985	Jul 15, 2010 (132)
14	1000GENOMES	ss243923498	Jul 15, 2010 (132)
15	GMI	ss283268996	May 04, 2012 (137)
16	PJP	ss292559604	May 09, 2011 (134)
17	TISHKOFF	ss566082561	Apr 25, 2013 (138)
18	SSMP	ss661953485	Apr 25, 2013 (138)
19	EVA-GONL	ss994456926	Aug 21, 2014 (142)
20	JMKIDD_LAB	ss1082009653	Aug 21, 2014 (142)
21	1000GENOMES	ss1363766560	Aug 21, 2014 (142)
22	DDI	ss1428970692	Apr 01, 2015 (144)
23	EVA_GENOME_DK	ss1579402648	Apr 01, 2015 (144)
24	EVA_UK10K_ALSPAC	ss1638249525	Apr 01, 2015 (144)
25	EVA_UK10K_TWINSUK	ss1681243558	Apr 01, 2015 (144)
26	EVA_DECODE	ss1698510488	Apr 01, 2015 (144)
27	HAMMER_LAB	ss1809383677	Sep 08, 2015 (146)
28	WEILL_CORNELL_DGM	ss1937965495	Feb 12, 2016 (147)
29	JJLAB	ss2029757347	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2158311918	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2240714728	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2629376479	Nov 08, 2017 (151)
33	GRF	ss2703983204	Nov 08, 2017 (151)
34	GNOMAD	ss2964604370	Nov 08, 2017 (151)
35	SWEGEN	ss3017744110	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3028710438	Nov 08, 2017 (151)
37	CSHL	ss3352380252	Nov 08, 2017 (151)
38	EGCUT_WGS	ss3684456768	Jul 13, 2019 (153)
39	EVA_DECODE	ss3706405537	Jul 13, 2019 (153)
40	ACPOP	ss3743179048	Jul 13, 2019 (153)
41	EVA	ss3758326285	Jul 13, 2019 (153)
42	KHV_HUMAN_GENOMES	ss3821499192	Jul 13, 2019 (153)
43	EVA	ss3835545017	Apr 27, 2020 (154)
44	SGDP_PRJ	ss3888570626	Apr 27, 2020 (154)
45	KRGDB	ss3938747441	Apr 27, 2020 (154)
46	KOGIC	ss3981678982	Apr 27, 2020 (154)
47	TOPMED	ss5079740926	Apr 27, 2021 (155)
48	TOMMO_GENOMICS	ss5228506380	Apr 27, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5307820959	Oct 13, 2022 (156)
50	EVA	ss5435784067	Oct 13, 2022 (156)
51	HUGCELL_USP	ss5500246308	Oct 13, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5613777577	Oct 13, 2022 (156)
53	SANFORD_IMAGENETICS	ss5662711652	Oct 13, 2022 (156)
54	TOMMO_GENOMICS	ss5787398340	Oct 13, 2022 (156)
55	YY_MCH	ss5817748779	Oct 13, 2022 (156)
56	EVA	ss5845337445	Oct 13, 2022 (156)
57	EVA	ss5853034249	Oct 13, 2022 (156)
58	EVA	ss5922372176	Oct 13, 2022 (156)
59	EVA	ss5957607300	Oct 13, 2022 (156)
60	1000Genomes	NC_000020.10 - 94952	Oct 12, 2018 (152)
61	1000Genomes_30x	NC_000020.11 - 114311	Oct 13, 2022 (156)
62	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 94952	Oct 12, 2018 (152)
63	Genetic variation in the Estonian population	NC_000020.10 - 94952	Oct 12, 2018 (152)
64	The Danish reference pan genome	NC_000020.10 - 94952	Apr 27, 2020 (154)
65	gnomAD - Genomes Submission ignored due to conflicting rows: Row 544385399 (NC_000020.11:114310:G:A 3/140062) Row 544385400 (NC_000020.11:114310:G:T 19460/140028)	-	Apr 27, 2021 (155)
66	gnomAD - Genomes Submission ignored due to conflicting rows: Row 544385399 (NC_000020.11:114310:G:A 3/140062) Row 544385400 (NC_000020.11:114310:G:T 19460/140028)	-	Apr 27, 2021 (155)
67	Genome of the Netherlands Release 5	NC_000020.10 - 94952	Apr 27, 2020 (154)
68	KOREAN population from KRGDB	NC_000020.10 - 94952	Apr 27, 2020 (154)
69	Korean Genome Project	NC_000020.11 - 114311	Apr 27, 2020 (154)
70	Northern Sweden	NC_000020.10 - 94952	Jul 13, 2019 (153)
71	Qatari	NC_000020.10 - 94952	Apr 27, 2020 (154)
72	SGDP_PRJ	NC_000020.10 - 94952	Apr 27, 2020 (154)
73	Siberian	NC_000020.10 - 94952	Apr 27, 2020 (154)
74	8.3KJPN	NC_000020.10 - 94952	Apr 27, 2021 (155)
75	14KJPN	NC_000020.11 - 114311	Oct 13, 2022 (156)
76	TopMed	NC_000020.11 - 114311	Apr 27, 2021 (155)
77	UK 10K study - Twins	NC_000020.10 - 94952	Oct 12, 2018 (152)
78	A Vietnamese Genetic Variation Database	NC_000020.10 - 94952	Jul 13, 2019 (153)
79	ALFA	NC_000020.11 - 114311	Apr 27, 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).

Associated ID	History Updated (Build)
rs17450557	Oct 07, 2004 (123)
rs58707149	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
9078409317	NC_000020.11:114310:G:A	NC_000020.11:114310:G:A	(self)
ss85279834, ss91611660, ss117452100, ss203804049, ss283268996, ss292559604, ss1698510488	NC_000020.9:42951:G:T	NC_000020.11:114310:G:T	(self)
77195933, 42725857, 30195016, 5567587, 19037752, 45924835, 16463913, 20007417, 40587606, 10828272, 86475687, 42725857, 9432443, ss228210703, ss237729985, ss243923498, ss566082561, ss661953485, ss994456926, ss1082009653, ss1363766560, ss1428970692, ss1579402648, ss1638249525, ss1681243558, ss1809383677, ss1937965495, ss2029757347, ss2158311918, ss2629376479, ss2703983204, ss2964604370, ss3017744110, ss3352380252, ss3684456768, ss3743179048, ss3758326285, ss3835545017, ss3888570626, ss3938747441, ss5228506380, ss5435784067, ss5662711652, ss5845337445, ss5957607300	NC_000020.10:94951:G:T	NC_000020.11:114310:G:T	(self)
101303512, 38056983, 121235444, 354849871, 9078409317, ss2240714728, ss3028710438, ss3706405537, ss3821499192, ss3981678982, ss5079740926, ss5307820959, ss5500246308, ss5613777577, ss5787398340, ss5817748779, ss5853034249, ss5922372176	NC_000020.11:114310:G:T	NC_000020.11:114310:G:T	(self)
ss2730230, ss8364532, ss10973184, ss16904749, ss23772461, ss156059219, ss161325332	NT_011387.8:34951:G:T	NC_000020.11:114310:G: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 rs1857092

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

rs1857092