Name: rs34287831
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.

rs34287831

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:1131009 (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: dupT
Variation Type: Indel Insertion and Deletion
Frequency: T=0.475405 (125835/264690, TOPMED)
T=0.485656 (67819/139644, GnomAD)
T=0.43453 (12278/28256, 14KJPN) (+ 11 more)
T=0.43687 (7321/16758, 8.3KJPN)
T=0.46345 (7569/16332, ALFA)
T=0.4861 (3113/6404, 1000G_30x)
T=0.4832 (2420/5008, 1000G)
T=0.4558 (2042/4480, Estonian)
T=0.3918 (1510/3854, ALSPAC)
T=0.4008 (1486/3708, TWINSUK)
T=0.4410 (807/1830, Korea1K)
T=0.413 (412/998, GoNL)
T=0.402 (241/600, NorthernSweden)
T=0.38 (15/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC124903820 : 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	16332	T=0.46345	TT=0.53655
European	Sub	12080	T=0.42550	TT=0.57450
African	Sub	2816	T=0.6562	TT=0.3438
African Others	Sub	108	T=0.741	TT=0.259
African American	Sub	2708	T=0.6529	TT=0.3471
Asian	Sub	108	T=0.472	TT=0.528
East Asian	Sub	84	T=0.49	TT=0.51
Other Asian	Sub	24	T=0.42	TT=0.58
Latin American 1	Sub	146	T=0.473	TT=0.527
Latin American 2	Sub	610	T=0.311	TT=0.689
South Asian	Sub	94	T=0.38	TT=0.62
Other	Sub	478	T=0.492	TT=0.508

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	- No frequency provided	dupT=0.524595
gnomAD - Genomes	Global	Study-wide	139644	- No frequency provided	dupT=0.514344
gnomAD - Genomes	European	Sub	75578	- No frequency provided	dupT=0.57419
gnomAD - Genomes	African	Sub	41900	- No frequency provided	dupT=0.35554
gnomAD - Genomes	American	Sub	13610	- No frequency provided	dupT=0.64702
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	- No frequency provided	dupT=0.5850
gnomAD - Genomes	East Asian	Sub	3092	- No frequency provided	dupT=0.5233
gnomAD - Genomes	Other	Sub	2148	- No frequency provided	dupT=0.5438
14KJPN	JAPANESE	Study-wide	28256	- No frequency provided	dupT=0.56547
8.3KJPN	JAPANESE	Study-wide	16758	- No frequency provided	dupT=0.56313
Allele Frequency Aggregator	Total	Global	16332	T=0.46345	dupT=0.53655
Allele Frequency Aggregator	European	Sub	12080	T=0.42550	dupT=0.57450
Allele Frequency Aggregator	African	Sub	2816	T=0.6562	dupT=0.3438
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.311	dupT=0.689
Allele Frequency Aggregator	Other	Sub	478	T=0.492	dupT=0.508
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.473	dupT=0.527
Allele Frequency Aggregator	Asian	Sub	108	T=0.472	dupT=0.528
Allele Frequency Aggregator	South Asian	Sub	94	T=0.38	dupT=0.62
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupT=0.5139
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupT=0.2861
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupT=0.6066
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupT=0.5774
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupT=0.5504
1000Genomes_30x	American	Sub	980	- No frequency provided	dupT=0.688
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupT=0.5168
1000Genomes	African	Sub	1322	- No frequency provided	dupT=0.2912
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupT=0.5476
1000Genomes	Europe	Sub	1006	- No frequency provided	dupT=0.6014
1000Genomes	South Asian	Sub	978	- No frequency provided	dupT=0.579
1000Genomes	American	Sub	694	- No frequency provided	dupT=0.692
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupT=0.5442
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	dupT=0.6082
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	dupT=0.5992
Korean Genome Project	KOREAN	Study-wide	1830	- No frequency provided	dupT=0.5590
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupT=0.587
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupT=0.598
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	dupT=0.62

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.1131009dup
GRCh37.p13 chr 1	NC_000001.10:g.1066389dup

Gene: LOC124903820, uncharacterized LOC124903820 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC124903820 transcript variant X2	XR_007065351.1:n.	N/A	Intron Variant
LOC124903820 transcript variant X1	XR_007065350.1:n.	N/A	Genic Upstream Transcript Variant

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	T=	dupT
GRCh38.p14 chr 1	NC_000001.11:g.1131009=	NC_000001.11:g.1131009dup
GRCh37.p13 chr 1	NC_000001.10:g.1066389=	NC_000001.10:g.1066389dup

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#.

55 SubSNP, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss41070105	Mar 13, 2006 (126)
2	HUMANGENOME_JCVI	ss95218995	Feb 04, 2009 (130)
3	GMI	ss229263759	May 09, 2011 (138)
4	BL	ss255892857	May 09, 2011 (138)
5	PJP	ss294562416	May 09, 2011 (135)
6	1000GENOMES	ss325997192	May 09, 2011 (138)
7	1000GENOMES	ss325997358	May 09, 2011 (138)
8	1000GENOMES	ss325997789	May 09, 2011 (138)
9	1000GENOMES	ss498764004	May 04, 2012 (138)
10	LUNTER	ss550899298	Apr 25, 2013 (138)
11	LUNTER	ss550903266	Apr 25, 2013 (138)
12	LUNTER	ss552739261	Apr 25, 2013 (138)
13	TISHKOFF	ss553747952	Apr 25, 2013 (138)
14	SSMP	ss663107342	Apr 01, 2015 (144)
15	BILGI_BIOE	ss666080119	Apr 25, 2013 (138)
16	EVA-GONL	ss974772139	Aug 21, 2014 (142)
17	1000GENOMES	ss1367645864	Aug 21, 2014 (142)
18	DDI	ss1536213991	Apr 01, 2015 (144)
19	EVA_GENOME_DK	ss1573868731	Apr 01, 2015 (144)
20	EVA_DECODE	ss1584132061	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1700146516	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1700155063	Apr 01, 2015 (144)
23	HAMMER_LAB	ss1793717250	Sep 08, 2015 (146)
24	JJLAB	ss2030297893	Sep 14, 2016 (149)
25	SYSTEMSBIOZJU	ss2624265579	Nov 08, 2017 (151)
26	GNOMAD	ss2750673385	Nov 08, 2017 (151)
27	SWEGEN	ss2986154580	Nov 08, 2017 (151)
28	MCHAISSO	ss3063573624	Nov 08, 2017 (151)
29	MCHAISSO	ss3065282698	Nov 08, 2017 (151)
30	BEROUKHIMLAB	ss3644051584	Oct 11, 2018 (152)
31	BIOINF_KMB_FNS_UNIBA	ss3645022520	Oct 11, 2018 (152)
32	URBANLAB	ss3646581971	Oct 11, 2018 (152)
33	EGCUT_WGS	ss3654265695	Jul 12, 2019 (153)
34	EVA_DECODE	ss3685998276	Jul 12, 2019 (153)
35	ACPOP	ss3726718824	Jul 12, 2019 (153)
36	PACBIO	ss3783303060	Jul 12, 2019 (153)
37	PACBIO	ss3788980835	Jul 12, 2019 (153)
38	PACBIO	ss3793853386	Jul 12, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3798747084	Jul 12, 2019 (153)
40	EVA	ss3825982683	Apr 25, 2020 (154)
41	EVA	ss3836379037	Apr 25, 2020 (154)
42	EVA	ss3841783065	Apr 25, 2020 (154)
43	KOGIC	ss3943636659	Apr 25, 2020 (154)
44	TOPMED	ss4436524361	Apr 25, 2021 (155)
45	TOMMO_GENOMICS	ss5142067549	Apr 25, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5240874094	Oct 12, 2022 (156)
47	HUGCELL_USP	ss5442120793	Oct 12, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5512503039	Oct 12, 2022 (156)
49	SANFORD_IMAGENETICS	ss5624755681	Oct 12, 2022 (156)
50	TOMMO_GENOMICS	ss5666212336	Oct 12, 2022 (156)
51	YY_MCH	ss5800246454	Oct 12, 2022 (156)
52	EVA	ss5831423070	Oct 12, 2022 (156)
53	EVA	ss5848749812	Oct 12, 2022 (156)
54	EVA	ss5906715506	Oct 12, 2022 (156)
55	EVA	ss5936587912	Oct 12, 2022 (156)
56	1000Genomes	NC_000001.10 - 1066389	Oct 11, 2018 (152)
57	1000Genomes_30x	NC_000001.11 - 1131009	Oct 12, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 1066389	Oct 11, 2018 (152)
59	Genetic variation in the Estonian population	NC_000001.10 - 1066389	Oct 11, 2018 (152)
60	The Danish reference pan genome	NC_000001.10 - 1066389	Apr 25, 2020 (154)
61	gnomAD - Genomes	NC_000001.11 - 1131009	Apr 25, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000001.10 - 1066389	Apr 25, 2020 (154)
63	Korean Genome Project	NC_000001.11 - 1131009	Apr 25, 2020 (154)
64	Northern Sweden	NC_000001.10 - 1066389	Jul 12, 2019 (153)
65	8.3KJPN	NC_000001.10 - 1066389	Apr 25, 2021 (155)
66	14KJPN	NC_000001.11 - 1131009	Oct 12, 2022 (156)
67	TopMed	NC_000001.11 - 1131009	Apr 25, 2021 (155)
68	UK 10K study - Twins	NC_000001.10 - 1066389	Oct 11, 2018 (152)
69	ALFA	NC_000001.11 - 1131009	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).

Associated ID	History Updated (Build)
rs140634183	May 15, 2013 (138)
rs141532946	Sep 17, 2011 (135)
rs145549192	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss255892857, ss325997192, ss325997358, ss325997789, ss550899298, ss550903266, ss552739261, ss1584132061	NC_000001.9:1056251::T	NC_000001.11:1131008:T:TT	(self)
ss294562416	NC_000001.9:1056252::T	NC_000001.11:1131008:T:TT	(self)
15997, 5251, 3943, 120356, 2413, 3689, 36856, 5251, ss498764004, ss663107342, ss666080119, ss974772139, ss1367645864, ss1536213991, ss1573868731, ss1700146516, ss1700155063, ss1793717250, ss2030297893, ss2624265579, ss2750673385, ss2986154580, ss3644051584, ss3654265695, ss3726718824, ss3783303060, ss3788980835, ss3793853386, ss3825982683, ss3836379037, ss5142067549, ss5624755681, ss5831423070, ss5936587912	NC_000001.10:1066388::T	NC_000001.11:1131008:T:TT	(self)
ss553747952	NC_000001.10:1066389::T	NC_000001.11:1131008:T:TT	(self)
28974, 145647, 14660, 49440, 130696, ss3063573624, ss3065282698, ss3645022520, ss3646581971, ss3685998276, ss3798747084, ss3841783065, ss3943636659, ss4436524361, ss5240874094, ss5442120793, ss5512503039, ss5666212336, ss5800246454, ss5848749812, ss5906715506	NC_000001.11:1131008::T	NC_000001.11:1131008:T:TT	(self)
7390448574	NC_000001.11:1131008:T:TT	NC_000001.11:1131008:T:TT	(self)
ss229263759	NT_004350.19:545020::T	NC_000001.11:1131008:T:TT	(self)
ss41070105, ss95218995	NT_004350.19:545021::T	NC_000001.11:1131008:T:TT	(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 rs34287831

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

rs34287831