Name: rs4252049
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.

rs4252049

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:160700683 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.434743 (115072/264690, TOPMED)
G=0.460802 (64528/140034, GnomAD)
G=0.18908 (5343/28258, 14KJPN) (+ 10 more)
A=0.47927 (8876/18520, ALFA)
G=0.18795 (3150/16760, 8.3KJPN)
G=0.3501 (2242/6404, 1000G_30x)
G=0.3464 (1735/5008, 1000G)
G=0.2125 (621/2922, KOREAN)
G=0.2085 (382/1832, Korea1K)
A=0.438 (263/600, NorthernSweden)
A=0.390 (117/300, SGDP_PRJ)
G=0.472 (102/216, Qatari)
G=0.47 (19/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PLG : 2KB Upstream 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	18520	A=0.47927	G=0.52073
European	Sub	14152	A=0.41563	G=0.58437
African	Sub	2898	A=0.7063	G=0.2937
African Others	Sub	114	A=0.772	G=0.228
African American	Sub	2784	A=0.7037	G=0.2963
Asian	Sub	112	A=0.777	G=0.223
East Asian	Sub	86	A=0.79	G=0.21
Other Asian	Sub	26	A=0.73	G=0.27
Latin American 1	Sub	146	A=0.541	G=0.459
Latin American 2	Sub	610	A=0.690	G=0.310
South Asian	Sub	98	A=0.69	G=0.31
Other	Sub	504	A=0.579	G=0.421

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	A=0.565257	G=0.434743
gnomAD - Genomes	Global	Study-wide	140034	A=0.539198	G=0.460802
gnomAD - Genomes	European	Sub	75832	A=0.42541	G=0.57459
gnomAD - Genomes	African	Sub	41964	A=0.70441	G=0.29559
gnomAD - Genomes	American	Sub	13644	A=0.62071	G=0.37929
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	A=0.4500	G=0.5500
gnomAD - Genomes	East Asian	Sub	3126	A=0.8125	G=0.1875
gnomAD - Genomes	Other	Sub	2150	A=0.5507	G=0.4493
14KJPN	JAPANESE	Study-wide	28258	A=0.81092	G=0.18908
Allele Frequency Aggregator	Total	Global	18520	A=0.47927	G=0.52073
Allele Frequency Aggregator	European	Sub	14152	A=0.41563	G=0.58437
Allele Frequency Aggregator	African	Sub	2898	A=0.7063	G=0.2937
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.690	G=0.310
Allele Frequency Aggregator	Other	Sub	504	A=0.579	G=0.421
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.541	G=0.459
Allele Frequency Aggregator	Asian	Sub	112	A=0.777	G=0.223
Allele Frequency Aggregator	South Asian	Sub	98	A=0.69	G=0.31
8.3KJPN	JAPANESE	Study-wide	16760	A=0.81205	G=0.18795
1000Genomes_30x	Global	Study-wide	6404	A=0.6499	G=0.3501
1000Genomes_30x	African	Sub	1786	A=0.7408	G=0.2592
1000Genomes_30x	Europe	Sub	1266	A=0.4321	G=0.5679
1000Genomes_30x	South Asian	Sub	1202	A=0.5982	G=0.4018
1000Genomes_30x	East Asian	Sub	1170	A=0.8197	G=0.1803
1000Genomes_30x	American	Sub	980	A=0.627	G=0.373
1000Genomes	Global	Study-wide	5008	A=0.6536	G=0.3464
1000Genomes	African	Sub	1322	A=0.7466	G=0.2534
1000Genomes	East Asian	Sub	1008	A=0.8135	G=0.1865
1000Genomes	Europe	Sub	1006	A=0.4423	G=0.5577
1000Genomes	South Asian	Sub	978	A=0.591	G=0.409
1000Genomes	American	Sub	694	A=0.638	G=0.362
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.7875	G=0.2125
Korean Genome Project	KOREAN	Study-wide	1832	A=0.7915	G=0.2085
Northern Sweden	ACPOP	Study-wide	600	A=0.438	G=0.562
SGDP_PRJ	Global	Study-wide	300	A=0.390	G=0.610
Qatari	Global	Study-wide	216	A=0.528	G=0.472
The Danish reference pan genome	Danish	Study-wide	40	A=0.53	G=0.47

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 6	NC_000006.12:g.160700683A>G
GRCh37.p13 chr 6	NC_000006.11:g.161121715A>G
PLG RefSeqGene (LRG_571)	NG_016200.1:g.3491A>G

Gene: PLG, plasminogen (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
PLG transcript variant 1	NM_000301.5:c.	N/A	Upstream Transcript Variant
PLG transcript variant 2	NM_001168338.1:c.	N/A	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	A=	G
GRCh38.p14 chr 6	NC_000006.12:g.160700683=	NC_000006.12:g.160700683A>G
GRCh37.p13 chr 6	NC_000006.11:g.161121715=	NC_000006.11:g.161121715A>G
PLG RefSeqGene (LRG_571)	NG_016200.1:g.3491=	NG_016200.1:g.3491A>G

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#.

49 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PGA-UW-FHCRC	ss5607850	Feb 20, 2003 (111)
2	CSHL-HAPMAP	ss17146150	Feb 27, 2004 (120)
3	CSHL-HAPMAP	ss17910843	Feb 27, 2004 (120)
4	ABI	ss42709212	Mar 13, 2006 (126)
5	BCMHGSC_JDW	ss93594438	Mar 24, 2008 (129)
6	ENSEMBL	ss142468939	Dec 01, 2009 (147)
7	BCM-HGSC-SUB	ss207869816	Jul 04, 2010 (132)
8	GMI	ss279106108	May 04, 2012 (137)
9	GMI	ss285540916	Apr 25, 2013 (138)
10	1000GENOMES	ss333783394	May 09, 2011 (134)
11	TISHKOFF	ss559670411	Apr 25, 2013 (138)
12	SSMP	ss654013689	Apr 25, 2013 (138)
13	EVA-GONL	ss983732523	Aug 21, 2014 (142)
14	1000GENOMES	ss1323158406	Aug 21, 2014 (142)
15	DDI	ss1430960390	Apr 01, 2015 (144)
16	EVA_GENOME_DK	ss1581985451	Apr 01, 2015 (144)
17	EVA_DECODE	ss1593309321	Apr 01, 2015 (144)
18	HAMMER_LAB	ss1804772660	Sep 08, 2015 (146)
19	WEILL_CORNELL_DGM	ss1926974839	Feb 12, 2016 (147)
20	SYSTEMSBIOZJU	ss2626566997	Nov 08, 2017 (151)
21	GRF	ss2707986100	Nov 08, 2017 (151)
22	GNOMAD	ss2847619753	Nov 08, 2017 (151)
23	SWEGEN	ss3000303740	Nov 08, 2017 (151)
24	CSHL	ss3347330375	Nov 08, 2017 (151)
25	OMUKHERJEE_ADBS	ss3646346461	Oct 12, 2018 (152)
26	ACPOP	ss3734177961	Jul 13, 2019 (153)
27	EVA	ss3765942900	Jul 13, 2019 (153)
28	PACBIO	ss3785678620	Jul 13, 2019 (153)
29	PACBIO	ss3790996580	Jul 13, 2019 (153)
30	PACBIO	ss3795876037	Jul 13, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3809106017	Jul 13, 2019 (153)
32	EVA	ss3830306137	Apr 26, 2020 (154)
33	EVA	ss3838637267	Apr 26, 2020 (154)
34	EVA	ss3844087409	Apr 26, 2020 (154)
35	SGDP_PRJ	ss3866178109	Apr 26, 2020 (154)
36	KRGDB	ss3913169379	Apr 26, 2020 (154)
37	KOGIC	ss3960501264	Apr 26, 2020 (154)
38	TOPMED	ss4729385240	Apr 26, 2021 (155)
39	TOMMO_GENOMICS	ss5180921184	Apr 26, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5271128621	Oct 13, 2022 (156)
41	EVA	ss5370426903	Oct 13, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5558454808	Oct 13, 2022 (156)
43	SANFORD_IMAGENETICS	ss5641938354	Oct 13, 2022 (156)
44	TOMMO_GENOMICS	ss5720090353	Oct 13, 2022 (156)
45	YY_MCH	ss5808150440	Oct 13, 2022 (156)
46	EVA	ss5843294321	Oct 13, 2022 (156)
47	EVA	ss5886852478	Oct 13, 2022 (156)
48	EVA	ss5971001505	Oct 13, 2022 (156)
49	EVA	ss5971001506	Oct 13, 2022 (156)
50	1000Genomes	NC_000006.11 - 161121715	Oct 12, 2018 (152)
51	1000Genomes_30x	NC_000006.12 - 160700683	Oct 13, 2022 (156)
52	The Danish reference pan genome	NC_000006.11 - 161121715	Apr 26, 2020 (154)
53	gnomAD - Genomes	NC_000006.12 - 160700683	Apr 26, 2021 (155)
54	KOREAN population from KRGDB	NC_000006.11 - 161121715	Apr 26, 2020 (154)
55	Korean Genome Project	NC_000006.12 - 160700683	Apr 26, 2020 (154)
56	Northern Sweden	NC_000006.11 - 161121715	Jul 13, 2019 (153)
57	Qatari	NC_000006.11 - 161121715	Apr 26, 2020 (154)
58	SGDP_PRJ	NC_000006.11 - 161121715	Apr 26, 2020 (154)
59	8.3KJPN	NC_000006.11 - 161121715	Apr 26, 2021 (155)
60	14KJPN	NC_000006.12 - 160700683	Oct 13, 2022 (156)
61	TopMed	NC_000006.12 - 160700683	Apr 26, 2021 (155)
62	ALFA	NC_000006.12 - 160700683	Apr 26, 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)
rs77781960	Jul 19, 2016 (147)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss93594438, ss207869816, ss279106108, ss285540916, ss1593309321	NC_000006.10:161041704:A:G	NC_000006.12:160700682:A:G	(self)
35061052, 8150390, 20346773, 7462826, 9016769, 18195089, 38890491, ss333783394, ss559670411, ss654013689, ss983732523, ss1323158406, ss1430960390, ss1581985451, ss1804772660, ss1926974839, ss2626566997, ss2707986100, ss2847619753, ss3000303740, ss3347330375, ss3646346461, ss3734177961, ss3765942900, ss3785678620, ss3790996580, ss3795876037, ss3830306137, ss3838637267, ss3866178109, ss3913169379, ss5180921184, ss5370426903, ss5641938354, ss5843294321, ss5971001505, ss5971001506	NC_000006.11:161121714:A:G	NC_000006.12:160700682:A:G	(self)
45980743, 247490176, 16879265, 53927457, 566762798, 9461276153, ss3809106017, ss3844087409, ss3960501264, ss4729385240, ss5271128621, ss5558454808, ss5720090353, ss5808150440, ss5886852478	NC_000006.12:160700682:A:G	NC_000006.12:160700682:A:G	(self)
ss17146150, ss17910843	NT_007422.12:3409055:A:G	NC_000006.12:160700682:A:G	(self)
ss5607850, ss42709212, ss142468939	NT_025741.15:65291171:A:G	NC_000006.12:160700682:A:G	(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 rs4252049

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

rs4252049