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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.

rs239545

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:79967194 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.231988 (61405/264690, TOPMED)
G=0.231141 (32368/140036, GnomAD)
G=0.19821 (5601/28258, 14KJPN) (+ 16 more)
G=0.23675 (4208/17774, ALFA)
G=0.19475 (3264/16760, 8.3KJPN)
G=0.2726 (1746/6404, 1000G_30x)
G=0.2772 (1388/5008, 1000G)
G=0.2250 (867/3854, ALSPAC)
G=0.2344 (869/3708, TWINSUK)
G=0.2160 (633/2930, KOREAN)
G=0.2282 (418/1832, Korea1K)
G=0.209 (209/998, GoNL)
G=0.218 (131/600, NorthernSweden)
G=0.205 (106/518, SGDP_PRJ)
G=0.233 (76/326, HapMap)
G=0.315 (68/216, Qatari)
G=0.257 (54/210, Vietnamese)
G=0.26 (14/54, Siberian)
G=0.28 (11/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC124901351 : 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 17774 G=0.23675 A=0.00000, C=0.76325
European Sub 13652 G=0.23227 A=0.00000, C=0.76773
African Sub 2468 G=0.2597 A=0.0000, C=0.7403
African Others Sub 90 G=0.28 A=0.00, C=0.72
African American Sub 2378 G=0.2590 A=0.0000, C=0.7410
Asian Sub 112 G=0.170 A=0.000, C=0.830
East Asian Sub 86 G=0.16 A=0.00, C=0.84
Other Asian Sub 26 G=0.19 A=0.00, C=0.81
Latin American 1 Sub 146 G=0.281 A=0.000, C=0.719
Latin American 2 Sub 610 G=0.202 A=0.000, C=0.798
South Asian Sub 98 G=0.46 A=0.00, C=0.54
Other Sub 688 G=0.244 A=0.000, C=0.756


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 G=0.231988 C=0.768012
gnomAD - Genomes Global Study-wide 140036 G=0.231141 C=0.768859
gnomAD - Genomes European Sub 75862 G=0.22089 C=0.77911
gnomAD - Genomes African Sub 41944 G=0.26283 C=0.73717
gnomAD - Genomes American Sub 13636 G=0.19742 C=0.80258
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.2370 C=0.7630
gnomAD - Genomes East Asian Sub 3130 G=0.1997 C=0.8003
gnomAD - Genomes Other Sub 2144 G=0.2253 C=0.7747
14KJPN JAPANESE Study-wide 28258 G=0.19821 C=0.80179
Allele Frequency Aggregator Total Global 17774 G=0.23675 A=0.00000, C=0.76325
Allele Frequency Aggregator European Sub 13652 G=0.23227 A=0.00000, C=0.76773
Allele Frequency Aggregator African Sub 2468 G=0.2597 A=0.0000, C=0.7403
Allele Frequency Aggregator Other Sub 688 G=0.244 A=0.000, C=0.756
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.202 A=0.000, C=0.798
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.281 A=0.000, C=0.719
Allele Frequency Aggregator Asian Sub 112 G=0.170 A=0.000, C=0.830
Allele Frequency Aggregator South Asian Sub 98 G=0.46 A=0.00, C=0.54
8.3KJPN JAPANESE Study-wide 16760 G=0.19475 C=0.80525
1000Genomes_30x Global Study-wide 6404 G=0.2726 C=0.7274
1000Genomes_30x African Sub 1786 G=0.2436 C=0.7564
1000Genomes_30x Europe Sub 1266 G=0.2291 C=0.7709
1000Genomes_30x South Asian Sub 1202 G=0.4526 C=0.5474
1000Genomes_30x East Asian Sub 1170 G=0.2385 C=0.7615
1000Genomes_30x American Sub 980 G=0.202 C=0.798
1000Genomes Global Study-wide 5008 G=0.2772 C=0.7228
1000Genomes African Sub 1322 G=0.2474 C=0.7526
1000Genomes East Asian Sub 1008 G=0.2341 C=0.7659
1000Genomes Europe Sub 1006 G=0.2256 C=0.7744
1000Genomes South Asian Sub 978 G=0.464 C=0.536
1000Genomes American Sub 694 G=0.207 C=0.793
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.2250 C=0.7750
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.2344 C=0.7656
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2160 C=0.7840
Korean Genome Project KOREAN Study-wide 1832 G=0.2282 C=0.7718
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.209 C=0.791
Northern Sweden ACPOP Study-wide 600 G=0.218 C=0.782
SGDP_PRJ Global Study-wide 518 G=0.205 C=0.795
HapMap Global Study-wide 326 G=0.233 C=0.767
HapMap African Sub 120 G=0.250 C=0.750
HapMap American Sub 118 G=0.246 C=0.754
HapMap Asian Sub 88 G=0.19 C=0.81
Qatari Global Study-wide 216 G=0.315 C=0.685
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.257 C=0.743
Siberian Global Study-wide 54 G=0.26 C=0.74
The Danish reference pan genome Danish Study-wide 40 G=0.28 C=0.72
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.79967194G>A
GRCh38.p14 chr 6 NC_000006.12:g.79967194G>C
GRCh37.p13 chr 6 NC_000006.11:g.80676911G>A
GRCh37.p13 chr 6 NC_000006.11:g.80676911G>C
Gene: LOC124901351, uncharacterized LOC124901351 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC124901351 transcript XR_007059656.1:n. N/A Intron 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 G= A C
GRCh38.p14 chr 6 NC_000006.12:g.79967194= NC_000006.12:g.79967194G>A NC_000006.12:g.79967194G>C
GRCh37.p13 chr 6 NC_000006.11:g.80676911= NC_000006.11:g.80676911G>A NC_000006.11:g.80676911G>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#.

83 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss308536 Jul 12, 2000 (79)
2 KWOK ss437427 Jul 12, 2000 (85)
3 SC_JCM ss627972 Jul 16, 2000 (85)
4 KWOK ss1070475 Oct 13, 2000 (126)
5 KWOK ss1200507 Oct 13, 2000 (126)
6 KWOK ss1686858 Oct 18, 2000 (126)
7 KWOK ss1687502 Oct 18, 2000 (126)
8 KWOK ss1730893 Oct 18, 2000 (126)
9 KWOK ss1731388 Oct 18, 2000 (126)
10 SC_SNP ss12780056 Dec 05, 2003 (126)
11 PERLEGEN ss24415724 Sep 20, 2004 (126)
12 ABI ss42648283 Mar 10, 2006 (126)
13 HGSV ss78253600 Dec 07, 2007 (129)
14 BCMHGSC_JDW ss93501715 Mar 24, 2008 (129)
15 HUMANGENOME_JCVI ss98513032 Feb 05, 2009 (130)
16 BGI ss106014851 Feb 05, 2009 (130)
17 1000GENOMES ss110416800 Jan 24, 2009 (130)
18 1000GENOMES ss114630350 Jan 25, 2009 (130)
19 ILLUMINA-UK ss116567376 Dec 01, 2009 (131)
20 ENSEMBL ss143021494 Dec 01, 2009 (131)
21 ENSEMBL ss144090339 Dec 01, 2009 (131)
22 GMI ss157202393 Dec 01, 2009 (131)
23 COMPLETE_GENOMICS ss162545619 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss163812920 Jul 04, 2010 (132)
25 COMPLETE_GENOMICS ss166929412 Jul 04, 2010 (132)
26 BUSHMAN ss202076714 Jul 04, 2010 (132)
27 BCM-HGSC-SUB ss207338228 Jul 04, 2010 (132)
28 1000GENOMES ss222495913 Jul 14, 2010 (132)
29 1000GENOMES ss233553135 Jul 15, 2010 (132)
30 1000GENOMES ss240593393 Jul 15, 2010 (132)
31 BL ss254494654 May 09, 2011 (134)
32 GMI ss278887364 May 04, 2012 (137)
33 GMI ss285447769 Apr 25, 2013 (138)
34 PJP ss293646159 May 09, 2011 (134)
35 TISHKOFF ss559320050 Apr 25, 2013 (138)
36 SSMP ss653284363 Apr 25, 2013 (138)
37 EVA-GONL ss983143791 Aug 21, 2014 (142)
38 JMKIDD_LAB ss1073768629 Aug 21, 2014 (142)
39 1000GENOMES ss1320925045 Aug 21, 2014 (142)
40 DDI ss1430795169 Apr 01, 2015 (144)
41 EVA_GENOME_DK ss1581758488 Apr 01, 2015 (144)
42 EVA_DECODE ss1592690160 Apr 01, 2015 (144)
43 EVA_UK10K_ALSPAC ss1615978532 Apr 01, 2015 (144)
44 EVA_UK10K_TWINSUK ss1658972565 Apr 01, 2015 (144)
45 HAMMER_LAB ss1804523807 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1926402588 Feb 12, 2016 (147)
47 JJLAB ss2023843863 Sep 14, 2016 (149)
48 USC_VALOUEV ss2152036168 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2285517061 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2626416766 Nov 08, 2017 (151)
51 GRF ss2707649799 Nov 08, 2017 (151)
52 GNOMAD ss2841227364 Nov 08, 2017 (151)
53 SWEGEN ss2999406621 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3025715451 Nov 08, 2017 (151)
55 CSHL ss3347072313 Nov 08, 2017 (151)
56 URBANLAB ss3648397713 Oct 12, 2018 (152)
57 EVA_DECODE ss3717607857 Jul 13, 2019 (153)
58 ACPOP ss3733686269 Jul 13, 2019 (153)
59 EVA ss3765259728 Jul 13, 2019 (153)
60 PACBIO ss3785531130 Jul 13, 2019 (153)
61 PACBIO ss3790873767 Jul 13, 2019 (153)
62 PACBIO ss3795752865 Jul 13, 2019 (153)
63 KHV_HUMAN_GENOMES ss3808410249 Jul 13, 2019 (153)
64 EVA ss3830028664 Apr 26, 2020 (154)
65 EVA ss3838495499 Apr 26, 2020 (154)
66 EVA ss3843942934 Apr 26, 2020 (154)
67 SGDP_PRJ ss3865001106 Apr 26, 2020 (154)
68 KRGDB ss3911880184 Apr 26, 2020 (154)
69 KOGIC ss3959428075 Apr 26, 2020 (154)
70 TOPMED ss4709896069 Apr 26, 2021 (155)
71 TOMMO_GENOMICS ss5178400795 Apr 26, 2021 (155)
72 1000G_HIGH_COVERAGE ss5269156117 Oct 13, 2022 (156)
73 EVA ss5366866357 Oct 13, 2022 (156)
74 HUGCELL_USP ss5466722069 Oct 13, 2022 (156)
75 EVA ss5508580220 Oct 13, 2022 (156)
76 1000G_HIGH_COVERAGE ss5555456981 Oct 13, 2022 (156)
77 SANFORD_IMAGENETICS ss5640810150 Oct 13, 2022 (156)
78 TOMMO_GENOMICS ss5716842102 Oct 13, 2022 (156)
79 YY_MCH ss5807659140 Oct 13, 2022 (156)
80 EVA ss5842529905 Oct 13, 2022 (156)
81 EVA ss5855438146 Oct 13, 2022 (156)
82 EVA ss5884595699 Oct 13, 2022 (156)
83 EVA ss5969308881 Oct 13, 2022 (156)
84 1000Genomes NC_000006.11 - 80676911 Oct 12, 2018 (152)
85 1000Genomes_30x NC_000006.12 - 79967194 Oct 13, 2022 (156)
86 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 80676911 Oct 12, 2018 (152)
87 The Danish reference pan genome NC_000006.11 - 80676911 Apr 26, 2020 (154)
88 gnomAD - Genomes NC_000006.12 - 79967194 Apr 26, 2021 (155)
89 Genome of the Netherlands Release 5 NC_000006.11 - 80676911 Apr 26, 2020 (154)
90 HapMap NC_000006.12 - 79967194 Apr 26, 2020 (154)
91 KOREAN population from KRGDB NC_000006.11 - 80676911 Apr 26, 2020 (154)
92 Korean Genome Project NC_000006.12 - 79967194 Apr 26, 2020 (154)
93 Northern Sweden NC_000006.11 - 80676911 Jul 13, 2019 (153)
94 Qatari NC_000006.11 - 80676911 Apr 26, 2020 (154)
95 SGDP_PRJ NC_000006.11 - 80676911 Apr 26, 2020 (154)
96 Siberian NC_000006.11 - 80676911 Apr 26, 2020 (154)
97 8.3KJPN NC_000006.11 - 80676911 Apr 26, 2021 (155)
98 14KJPN NC_000006.12 - 79967194 Oct 13, 2022 (156)
99 TopMed NC_000006.12 - 79967194 Apr 26, 2021 (155)
100 UK 10K study - Twins NC_000006.11 - 80676911 Oct 12, 2018 (152)
101 A Vietnamese Genetic Variation Database NC_000006.11 - 80676911 Jul 13, 2019 (153)
102 ALFA NC_000006.12 - 79967194 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)
rs343666 Sep 19, 2000 (85)
rs1068839 Mar 10, 2006 (126)
rs1145855 Feb 20, 2003 (111)
rs1194134 Jan 18, 2001 (92)
rs1194247 Jan 18, 2001 (92)
rs17239346 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
5617645730 NC_000006.12:79967193:G:A NC_000006.12:79967193:G:A (self)
ss78253600 NC_000006.9:80733629:G:C NC_000006.12:79967193:G:C (self)
ss93501715, ss110416800, ss114630350, ss116567376, ss162545619, ss163812920, ss166929412, ss202076714, ss207338228, ss254494654, ss278887364, ss285447769, ss293646159, ss1592690160 NC_000006.10:80733629:G:C NC_000006.12:79967193:G:C (self)
32742543, 18238347, 7923427, 8127218, 19057578, 6971134, 8444518, 17018086, 4552522, 36370102, 18238347, 4053915, ss222495913, ss233553135, ss240593393, ss559320050, ss653284363, ss983143791, ss1073768629, ss1320925045, ss1430795169, ss1581758488, ss1615978532, ss1658972565, ss1804523807, ss1926402588, ss2023843863, ss2152036168, ss2626416766, ss2707649799, ss2841227364, ss2999406621, ss3347072313, ss3733686269, ss3765259728, ss3785531130, ss3790873767, ss3795752865, ss3830028664, ss3838495499, ss3865001106, ss3911880184, ss5178400795, ss5366866357, ss5508580220, ss5640810150, ss5842529905, ss5969308881 NC_000006.11:80676910:G:C NC_000006.12:79967193:G:C (self)
42982916, 231064107, 3174341, 15806076, 50679206, 547273627, 5617645730, ss2285517061, ss3025715451, ss3648397713, ss3717607857, ss3808410249, ss3843942934, ss3959428075, ss4709896069, ss5269156117, ss5466722069, ss5555456981, ss5716842102, ss5807659140, ss5855438146, ss5884595699 NC_000006.12:79967193:G:C NC_000006.12:79967193:G:C (self)
ss12780056 NT_007299.12:18497081:G:C NC_000006.12:79967193:G:C (self)
ss308536, ss437427, ss627972, ss1070475, ss1200507, ss1686858, ss1687502, ss1730893, ss1731388, ss24415724, ss42648283, ss98513032, ss106014851, ss143021494, ss144090339, ss157202393 NT_007299.13:18796744:G:C NC_000006.12:79967193:G: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 rs239545

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