Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs12076360

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:80545144 (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=0.177959 (47104/264690, TOPMED)
C=0.174776 (24475/140036, GnomAD)
C=0.22351 (6316/28258, 14KJPN) (+ 17 more)
C=0.15056 (3394/22542, ALFA)
C=0.22190 (3719/16760, 8.3KJPN)
C=0.2417 (1548/6404, 1000G_30x)
C=0.2406 (1205/5008, 1000G)
C=0.0998 (447/4480, Estonian)
C=0.1079 (416/3854, ALSPAC)
C=0.0922 (342/3708, TWINSUK)
C=0.2433 (713/2930, KOREAN)
C=0.2445 (448/1832, Korea1K)
C=0.110 (110/998, GoNL)
C=0.128 (77/600, NorthernSweden)
C=0.223 (73/328, HapMap)
T=0.421 (101/240, SGDP_PRJ)
C=0.218 (47/216, Qatari)
C=0.308 (66/214, Vietnamese)
C=0.17 (7/40, GENOME_DK)
T=0.45 (9/20, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01781 : 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 22542 T=0.84944 C=0.15056
European Sub 16454 T=0.89206 C=0.10794
African Sub 4084 T=0.6819 C=0.3181
African Others Sub 144 T=0.632 C=0.368
African American Sub 3940 T=0.6838 C=0.3162
Asian Sub 116 T=0.672 C=0.328
East Asian Sub 88 T=0.68 C=0.32
Other Asian Sub 28 T=0.64 C=0.36
Latin American 1 Sub 154 T=0.760 C=0.240
Latin American 2 Sub 616 T=0.922 C=0.078
South Asian Sub 98 T=0.74 C=0.26
Other Sub 1020 T=0.8324 C=0.1676


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=0.822041 C=0.177959
gnomAD - Genomes Global Study-wide 140036 T=0.825224 C=0.174776
gnomAD - Genomes European Sub 75892 T=0.89254 C=0.10746
gnomAD - Genomes African Sub 41908 T=0.68739 C=0.31261
gnomAD - Genomes American Sub 13640 T=0.89113 C=0.10887
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=0.8469 C=0.1531
gnomAD - Genomes East Asian Sub 3122 T=0.7255 C=0.2745
gnomAD - Genomes Other Sub 2150 T=0.8288 C=0.1712
14KJPN JAPANESE Study-wide 28258 T=0.77649 C=0.22351
Allele Frequency Aggregator Total Global 22542 T=0.84944 C=0.15056
Allele Frequency Aggregator European Sub 16454 T=0.89206 C=0.10794
Allele Frequency Aggregator African Sub 4084 T=0.6819 C=0.3181
Allele Frequency Aggregator Other Sub 1020 T=0.8324 C=0.1676
Allele Frequency Aggregator Latin American 2 Sub 616 T=0.922 C=0.078
Allele Frequency Aggregator Latin American 1 Sub 154 T=0.760 C=0.240
Allele Frequency Aggregator Asian Sub 116 T=0.672 C=0.328
Allele Frequency Aggregator South Asian Sub 98 T=0.74 C=0.26
8.3KJPN JAPANESE Study-wide 16760 T=0.77810 C=0.22190
1000Genomes_30x Global Study-wide 6404 T=0.7583 C=0.2417
1000Genomes_30x African Sub 1786 T=0.6153 C=0.3847
1000Genomes_30x Europe Sub 1266 T=0.8752 C=0.1248
1000Genomes_30x South Asian Sub 1202 T=0.7621 C=0.2379
1000Genomes_30x East Asian Sub 1170 T=0.7154 C=0.2846
1000Genomes_30x American Sub 980 T=0.914 C=0.086
1000Genomes Global Study-wide 5008 T=0.7594 C=0.2406
1000Genomes African Sub 1322 T=0.6172 C=0.3828
1000Genomes East Asian Sub 1008 T=0.7282 C=0.2718
1000Genomes Europe Sub 1006 T=0.8797 C=0.1203
1000Genomes South Asian Sub 978 T=0.754 C=0.246
1000Genomes American Sub 694 T=0.909 C=0.091
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9002 C=0.0998
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8921 C=0.1079
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9078 C=0.0922
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.7567 C=0.2433
Korean Genome Project KOREAN Study-wide 1832 T=0.7555 C=0.2445
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.890 C=0.110
Northern Sweden ACPOP Study-wide 600 T=0.872 C=0.128
HapMap Global Study-wide 328 T=0.777 C=0.223
HapMap African Sub 120 T=0.658 C=0.342
HapMap American Sub 120 T=0.883 C=0.117
HapMap Asian Sub 88 T=0.80 C=0.20
SGDP_PRJ Global Study-wide 240 T=0.421 C=0.579
Qatari Global Study-wide 216 T=0.782 C=0.218
A Vietnamese Genetic Variation Database Global Study-wide 214 T=0.692 C=0.308
The Danish reference pan genome Danish Study-wide 40 T=0.82 C=0.17
Siberian Global Study-wide 20 T=0.45 C=0.55
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 1 NC_000001.11:g.80545144T>C
GRCh37.p13 chr 1 NC_000001.10:g.81010829T>C
Gene: LINC01781, long intergenic non-protein coding RNA 1781 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01781 transcript variant 1 NR_125940.1:n. N/A Intron Variant
LINC01781 transcript variant 2 NR_125941.1:n. N/A Intron Variant
LINC01781 transcript variant 3 NR_125942.1:n. N/A Genic 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 1 NC_000001.11:g.80545144= NC_000001.11:g.80545144T>C
GRCh37.p13 chr 1 NC_000001.10:g.81010829= NC_000001.10:g.81010829T>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#.

63 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18172119 Feb 28, 2004 (120)
2 PERLEGEN ss23156016 Sep 20, 2004 (123)
3 BCMHGSC_JDW ss87571682 Mar 23, 2008 (129)
4 ILLUMINA-UK ss118838455 Dec 01, 2009 (131)
5 ENSEMBL ss138018605 Dec 01, 2009 (131)
6 GMI ss155243609 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss166748165 Jul 04, 2010 (132)
8 ILLUMINA ss171837811 Jul 04, 2010 (132)
9 BUSHMAN ss198679532 Jul 04, 2010 (132)
10 1000GENOMES ss210569019 Jul 14, 2010 (132)
11 1000GENOMES ss218481426 Jul 14, 2010 (132)
12 1000GENOMES ss230604808 Jul 14, 2010 (132)
13 1000GENOMES ss238284398 Jul 15, 2010 (132)
14 GMI ss275895418 May 04, 2012 (137)
15 ILLUMINA ss536752524 Sep 08, 2015 (146)
16 TISHKOFF ss554307039 Apr 25, 2013 (138)
17 SSMP ss648162327 Apr 25, 2013 (138)
18 EVA-GONL ss975344720 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1068027789 Aug 21, 2014 (142)
20 1000GENOMES ss1291594911 Aug 21, 2014 (142)
21 EVA_GENOME_DK ss1574180239 Apr 01, 2015 (144)
22 EVA_DECODE ss1584718415 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1600543543 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1643537576 Apr 01, 2015 (144)
25 HAMMER_LAB ss1794624246 Sep 08, 2015 (146)
26 WEILL_CORNELL_DGM ss1918548821 Feb 12, 2016 (147)
27 JJLAB ss2019794900 Sep 14, 2016 (149)
28 USC_VALOUEV ss2147811469 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2163976621 Dec 20, 2016 (150)
30 SYSTEMSBIOZJU ss2624408588 Nov 08, 2017 (151)
31 GRF ss2697732363 Nov 08, 2017 (151)
32 GNOMAD ss2757157209 Nov 08, 2017 (151)
33 SWEGEN ss2987095188 Nov 08, 2017 (151)
34 BIOINF_KMB_FNS_UNIBA ss3023659540 Nov 08, 2017 (151)
35 CSHL ss3343534774 Nov 08, 2017 (151)
36 ILLUMINA ss3626136224 Oct 11, 2018 (152)
37 ILLUMINA ss3637767294 Oct 11, 2018 (152)
38 EGCUT_WGS ss3655174590 Jul 12, 2019 (153)
39 EVA_DECODE ss3687114963 Jul 12, 2019 (153)
40 ACPOP ss3727200426 Jul 12, 2019 (153)
41 EVA ss3746417062 Jul 12, 2019 (153)
42 PACBIO ss3783458298 Jul 12, 2019 (153)
43 PACBIO ss3789109198 Jul 12, 2019 (153)
44 PACBIO ss3793981962 Jul 12, 2019 (153)
45 KHV_HUMAN_GENOMES ss3799423030 Jul 12, 2019 (153)
46 SGDP_PRJ ss3849211096 Apr 25, 2020 (154)
47 KRGDB ss3894259835 Apr 25, 2020 (154)
48 KOGIC ss3944847054 Apr 25, 2020 (154)
49 EVA ss4016920131 Apr 25, 2021 (155)
50 TOPMED ss4456044377 Apr 25, 2021 (155)
51 TOMMO_GENOMICS ss5144730883 Apr 25, 2021 (155)
52 1000G_HIGH_COVERAGE ss5242876055 Oct 12, 2022 (156)
53 EVA ss5319854047 Oct 12, 2022 (156)
54 HUGCELL_USP ss5443879114 Oct 12, 2022 (156)
55 EVA ss5505917081 Oct 12, 2022 (156)
56 1000G_HIGH_COVERAGE ss5515480383 Oct 12, 2022 (156)
57 SANFORD_IMAGENETICS ss5625878527 Oct 12, 2022 (156)
58 TOMMO_GENOMICS ss5669725403 Oct 12, 2022 (156)
59 YY_MCH ss5800748017 Oct 12, 2022 (156)
60 EVA ss5832193488 Oct 12, 2022 (156)
61 EVA ss5848980277 Oct 12, 2022 (156)
62 EVA ss5908963177 Oct 12, 2022 (156)
63 EVA ss5937725282 Oct 12, 2022 (156)
64 1000Genomes NC_000001.10 - 81010829 Oct 11, 2018 (152)
65 1000Genomes_30x NC_000001.11 - 80545144 Oct 12, 2022 (156)
66 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 81010829 Oct 11, 2018 (152)
67 Genetic variation in the Estonian population NC_000001.10 - 81010829 Oct 11, 2018 (152)
68 The Danish reference pan genome NC_000001.10 - 81010829 Apr 25, 2020 (154)
69 gnomAD - Genomes NC_000001.11 - 80545144 Apr 25, 2021 (155)
70 Genome of the Netherlands Release 5 NC_000001.10 - 81010829 Apr 25, 2020 (154)
71 HapMap NC_000001.11 - 80545144 Apr 25, 2020 (154)
72 KOREAN population from KRGDB NC_000001.10 - 81010829 Apr 25, 2020 (154)
73 Korean Genome Project NC_000001.11 - 80545144 Apr 25, 2020 (154)
74 Northern Sweden NC_000001.10 - 81010829 Jul 12, 2019 (153)
75 Qatari NC_000001.10 - 81010829 Apr 25, 2020 (154)
76 SGDP_PRJ NC_000001.10 - 81010829 Apr 25, 2020 (154)
77 Siberian NC_000001.10 - 81010829 Apr 25, 2020 (154)
78 8.3KJPN NC_000001.10 - 81010829 Apr 25, 2021 (155)
79 14KJPN NC_000001.11 - 80545144 Oct 12, 2022 (156)
80 TopMed NC_000001.11 - 80545144 Apr 25, 2021 (155)
81 UK 10K study - Twins NC_000001.10 - 81010829 Oct 11, 2018 (152)
82 A Vietnamese Genetic Variation Database NC_000001.10 - 81010829 Jul 12, 2019 (153)
83 ALFA NC_000001.11 - 80545144 Apr 25, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss87571682, ss118838455, ss166748165, ss198679532, ss210569019, ss275895418, ss1584718415 NC_000001.9:80783416:T:C NC_000001.11:80545143:T:C (self)
2339153, 1282847, 912838, 1574941, 552011, 1437229, 485291, 590751, 1228076, 327823, 2700190, 1282847, 273343, ss218481426, ss230604808, ss238284398, ss536752524, ss554307039, ss648162327, ss975344720, ss1068027789, ss1291594911, ss1574180239, ss1600543543, ss1643537576, ss1794624246, ss1918548821, ss2019794900, ss2147811469, ss2624408588, ss2697732363, ss2757157209, ss2987095188, ss3343534774, ss3626136224, ss3637767294, ss3655174590, ss3727200426, ss3746417062, ss3783458298, ss3789109198, ss3793981962, ss3849211096, ss3894259835, ss4016920131, ss5144730883, ss5319854047, ss5505917081, ss5625878527, ss5832193488, ss5937725282 NC_000001.10:81010828:T:C NC_000001.11:80545143:T:C (self)
3006318, 16525962, 108306, 1225055, 3562507, 19650712, 11819196174, ss2163976621, ss3023659540, ss3687114963, ss3799423030, ss3944847054, ss4456044377, ss5242876055, ss5443879114, ss5515480383, ss5669725403, ss5800748017, ss5848980277, ss5908963177 NC_000001.11:80545143:T:C NC_000001.11:80545143:T:C (self)
ss18172119 NT_026943.13:5831002:T:C NC_000001.11:80545143:T:C (self)
ss23156016, ss138018605, ss155243609, ss171837811 NT_032977.9:50982746:T:C NC_000001.11:80545143: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 rs12076360

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