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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.

rs1864449

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:160701731 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.478390 (126625/264690, TOPMED)
T=0.497922 (69718/140018, GnomAD)
C=0.18473 (5220/28258, 14KJPN) (+ 15 more)
T=0.46426 (12951/27896, ALFA)
C=0.18377 (3080/16760, 8.3KJPN)
C=0.3943 (2525/6404, 1000G_30x)
C=0.3896 (1951/5008, 1000G)
T=0.4188 (1614/3854, ALSPAC)
T=0.4121 (1528/3708, TWINSUK)
C=0.2040 (596/2922, KOREAN)
C=0.1987 (364/1832, Korea1K)
T=0.415 (414/998, GoNL)
T=0.438 (263/600, NorthernSweden)
T=0.358 (113/316, SGDP_PRJ)
C=0.495 (107/216, Qatari)
C=0.113 (24/212, Vietnamese)
C=0.47 (19/40, GENOME_DK)
T=0.34 (13/38, Siberian)
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 27988 T=0.46441 C=0.53559
European Sub 20448 T=0.41843 C=0.58157
African Sub 5568 T=0.5860 C=0.4140
African Others Sub 198 T=0.596 C=0.404
African American Sub 5370 T=0.5857 C=0.4143
Asian Sub 112 T=0.768 C=0.232
East Asian Sub 86 T=0.78 C=0.22
Other Asian Sub 26 T=0.73 C=0.27
Latin American 1 Sub 146 T=0.486 C=0.514
Latin American 2 Sub 610 T=0.682 C=0.318
South Asian Sub 98 T=0.69 C=0.31
Other Sub 1006 T=0.5348 C=0.4652


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 T=0.521610 C=0.478390
gnomAD - Genomes Global Study-wide 140018 T=0.497922 C=0.502078
gnomAD - Genomes European Sub 75834 T=0.42453 C=0.57547
gnomAD - Genomes African Sub 41934 T=0.57638 C=0.42362
gnomAD - Genomes American Sub 13654 T=0.60151 C=0.39849
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=0.4404 C=0.5596
gnomAD - Genomes East Asian Sub 3128 T=0.8242 C=0.1758
gnomAD - Genomes Other Sub 2148 T=0.5126 C=0.4874
14KJPN JAPANESE Study-wide 28258 T=0.81527 C=0.18473
Allele Frequency Aggregator Total Global 27896 T=0.46426 C=0.53574
Allele Frequency Aggregator European Sub 20372 T=0.41802 C=0.58198
Allele Frequency Aggregator African Sub 5568 T=0.5860 C=0.4140
Allele Frequency Aggregator Other Sub 990 T=0.536 C=0.464
Allele Frequency Aggregator Latin American 2 Sub 610 T=0.682 C=0.318
Allele Frequency Aggregator Latin American 1 Sub 146 T=0.486 C=0.514
Allele Frequency Aggregator Asian Sub 112 T=0.768 C=0.232
Allele Frequency Aggregator South Asian Sub 98 T=0.69 C=0.31
8.3KJPN JAPANESE Study-wide 16760 T=0.81623 C=0.18377
1000Genomes_30x Global Study-wide 6404 T=0.6057 C=0.3943
1000Genomes_30x African Sub 1786 T=0.5873 C=0.4127
1000Genomes_30x Europe Sub 1266 T=0.4305 C=0.5695
1000Genomes_30x South Asian Sub 1202 T=0.5998 C=0.4002
1000Genomes_30x East Asian Sub 1170 T=0.8265 C=0.1735
1000Genomes_30x American Sub 980 T=0.609 C=0.391
1000Genomes Global Study-wide 5008 T=0.6104 C=0.3896
1000Genomes African Sub 1322 T=0.5915 C=0.4085
1000Genomes East Asian Sub 1008 T=0.8185 C=0.1815
1000Genomes Europe Sub 1006 T=0.4404 C=0.5596
1000Genomes South Asian Sub 978 T=0.591 C=0.409
1000Genomes American Sub 694 T=0.618 C=0.382
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.4188 C=0.5812
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.4121 C=0.5879
KOREAN population from KRGDB KOREAN Study-wide 2922 T=0.7960 C=0.2040
Korean Genome Project KOREAN Study-wide 1832 T=0.8013 C=0.1987
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.415 C=0.585
Northern Sweden ACPOP Study-wide 600 T=0.438 C=0.562
SGDP_PRJ Global Study-wide 316 T=0.358 C=0.642
Qatari Global Study-wide 216 T=0.505 C=0.495
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.887 C=0.113
The Danish reference pan genome Danish Study-wide 40 T=0.53 C=0.47
Siberian Global Study-wide 38 T=0.34 C=0.66
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.p14 chr 6 NC_000006.12:g.160701731T>C
GRCh37.p13 chr 6 NC_000006.11:g.161122763T>C
PLG RefSeqGene (LRG_571) NG_016200.1:g.4539T>C
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
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
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 T= C
GRCh38.p14 chr 6 NC_000006.12:g.160701731= NC_000006.12:g.160701731T>C
GRCh37.p13 chr 6 NC_000006.11:g.161122763= NC_000006.11:g.161122763T>C
PLG RefSeqGene (LRG_571) NG_016200.1:g.4539= NG_016200.1:g.4539T>C
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#.

66 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2739173 Jan 12, 2001 (92)
2 PGA-UW-FHCRC ss5607860 Feb 20, 2003 (111)
3 ABI ss44758922 Mar 14, 2006 (126)
4 HGSV ss85156891 Dec 15, 2007 (130)
5 BCMHGSC_JDW ss93594443 Mar 24, 2008 (129)
6 BGI ss104380334 Dec 01, 2009 (131)
7 1000GENOMES ss111223869 Jan 25, 2009 (130)
8 ENSEMBL ss142468944 Dec 01, 2009 (131)
9 BCM-HGSC-SUB ss207498784 Jul 04, 2010 (132)
10 1000GENOMES ss222796586 Jul 14, 2010 (132)
11 1000GENOMES ss233769044 Jul 15, 2010 (132)
12 1000GENOMES ss240766264 Jul 15, 2010 (132)
13 GMI ss279106114 May 04, 2012 (137)
14 GMI ss285540920 Apr 25, 2013 (138)
15 PJP ss293775934 May 09, 2011 (134)
16 TISHKOFF ss559670414 Apr 25, 2013 (138)
17 SSMP ss654013700 Apr 25, 2013 (138)
18 EVA-GONL ss983732536 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1074209568 Aug 21, 2014 (142)
20 1000GENOMES ss1323158442 Aug 21, 2014 (142)
21 DDI ss1430960396 Apr 01, 2015 (144)
22 EVA_GENOME_DK ss1581985456 Apr 01, 2015 (144)
23 EVA_DECODE ss1593309328 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1617175206 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1660169239 Apr 01, 2015 (144)
26 HAMMER_LAB ss1804772662 Sep 08, 2015 (146)
27 WEILL_CORNELL_DGM ss1926974852 Feb 12, 2016 (147)
28 GENOMED ss1970576608 Jul 19, 2016 (147)
29 JJLAB ss2024153618 Sep 14, 2016 (149)
30 USC_VALOUEV ss2152346836 Dec 20, 2016 (150)
31 SYSTEMSBIOZJU ss2626567001 Nov 08, 2017 (151)
32 GRF ss2707986109 Nov 08, 2017 (151)
33 GNOMAD ss2847619860 Nov 08, 2017 (151)
34 AFFY ss2985394384 Nov 08, 2017 (151)
35 AFFY ss2986021218 Nov 08, 2017 (151)
36 SWEGEN ss3000303755 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3025867851 Nov 08, 2017 (151)
38 CSHL ss3347330382 Nov 08, 2017 (151)
39 ILLUMINA ss3654154368 Oct 12, 2018 (152)
40 EVA_DECODE ss3718713394 Jul 13, 2019 (153)
41 ACPOP ss3734177970 Jul 13, 2019 (153)
42 EVA ss3765942917 Jul 13, 2019 (153)
43 PACBIO ss3785678628 Jul 13, 2019 (153)
44 PACBIO ss3790996587 Jul 13, 2019 (153)
45 PACBIO ss3795876044 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3809106029 Jul 13, 2019 (153)
47 EVA ss3830306142 Apr 26, 2020 (154)
48 EVA ss3838637274 Apr 26, 2020 (154)
49 EVA ss3844087416 Apr 26, 2020 (154)
50 SGDP_PRJ ss3866178133 Apr 26, 2020 (154)
51 KRGDB ss3913169404 Apr 26, 2020 (154)
52 KOGIC ss3960501285 Apr 26, 2020 (154)
53 TOPMED ss4729385563 Apr 26, 2021 (155)
54 TOMMO_GENOMICS ss5180921227 Apr 26, 2021 (155)
55 1000G_HIGH_COVERAGE ss5271128651 Oct 13, 2022 (156)
56 EVA ss5370426953 Oct 13, 2022 (156)
57 HUGCELL_USP ss5468502186 Oct 13, 2022 (156)
58 1000G_HIGH_COVERAGE ss5558454858 Oct 13, 2022 (156)
59 SANFORD_IMAGENETICS ss5641938371 Oct 13, 2022 (156)
60 TOMMO_GENOMICS ss5720090411 Oct 13, 2022 (156)
61 YY_MCH ss5808150449 Oct 13, 2022 (156)
62 EVA ss5843294335 Oct 13, 2022 (156)
63 EVA ss5855675386 Oct 13, 2022 (156)
64 EVA ss5886852501 Oct 13, 2022 (156)
65 EVA ss5971001537 Oct 13, 2022 (156)
66 EVA ss5971001538 Oct 13, 2022 (156)
67 1000Genomes NC_000006.11 - 161122763 Oct 12, 2018 (152)
68 1000Genomes_30x NC_000006.12 - 160701731 Oct 13, 2022 (156)
69 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 161122763 Oct 12, 2018 (152)
70 The Danish reference pan genome NC_000006.11 - 161122763 Apr 26, 2020 (154)
71 gnomAD - Genomes NC_000006.12 - 160701731 Apr 26, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000006.11 - 161122763 Apr 26, 2020 (154)
73 KOREAN population from KRGDB NC_000006.11 - 161122763 Apr 26, 2020 (154)
74 Korean Genome Project NC_000006.12 - 160701731 Apr 26, 2020 (154)
75 Northern Sweden NC_000006.11 - 161122763 Jul 13, 2019 (153)
76 Qatari NC_000006.11 - 161122763 Apr 26, 2020 (154)
77 SGDP_PRJ NC_000006.11 - 161122763 Apr 26, 2020 (154)
78 Siberian NC_000006.11 - 161122763 Apr 26, 2020 (154)
79 8.3KJPN NC_000006.11 - 161122763 Apr 26, 2021 (155)
80 14KJPN NC_000006.12 - 160701731 Oct 13, 2022 (156)
81 TopMed NC_000006.12 - 160701731 Apr 26, 2021 (155)
82 UK 10K study - Twins NC_000006.11 - 161122763 Oct 12, 2018 (152)
83 A Vietnamese Genetic Variation Database NC_000006.11 - 161122763 Jul 13, 2019 (153)
84 ALFA NC_000006.12 - 160701731 Apr 26, 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).

Associated ID History Updated (Build)
rs58776216 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss85156891 NC_000006.9:161093173:T:C NC_000006.12:160701730:T:C (self)
ss93594443, ss111223869, ss207498784, ss279106114, ss285540920, ss293775934, ss1593309328 NC_000006.10:161042752:T:C NC_000006.12:160701730:T:C (self)
35061088, 19554028, 8150395, 8701683, 20346798, 7462835, 9016782, 18195113, 4863190, 38890534, 19554028, 4351271, ss222796586, ss233769044, ss240766264, ss559670414, ss654013700, ss983732536, ss1074209568, ss1323158442, ss1430960396, ss1581985456, ss1617175206, ss1660169239, ss1804772662, ss1926974852, ss1970576608, ss2024153618, ss2152346836, ss2626567001, ss2707986109, ss2847619860, ss2985394384, ss2986021218, ss3000303755, ss3347330382, ss3654154368, ss3734177970, ss3765942917, ss3785678628, ss3790996587, ss3795876044, ss3830306142, ss3838637274, ss3866178133, ss3913169404, ss5180921227, ss5370426953, ss5641938371, ss5843294335, ss5971001537, ss5971001538 NC_000006.11:161122762:T:C NC_000006.12:160701730:T:C (self)
45980793, 247490418, 16879286, 53927515, 566763121, 352352816, ss3025867851, ss3718713394, ss3809106029, ss3844087416, ss3960501285, ss4729385563, ss5271128651, ss5468502186, ss5558454858, ss5720090411, ss5808150449, ss5855675386, ss5886852501 NC_000006.12:160701730:T:C NC_000006.12:160701730:T:C (self)
ss2739173, ss5607860, ss44758922, ss104380334, ss142468944 NT_025741.15:65292219:T:C NC_000006.12:160701730:T:C (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 rs1864449

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.post761+d5e8e07