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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.

rs10487981

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:83064584 (GRCh38.p13) 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 / T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.196766 (52082/264690, TOPMED)
C=0.211710 (29647/140036, GnomAD)
C=0.19437 (3583/18434, ALFA) (+ 15 more)
C=0.1585 (794/5008, 1000G)
C=0.2513 (1126/4480, Estonian)
C=0.1772 (683/3854, ALSPAC)
C=0.1764 (654/3708, TWINSUK)
C=0.0007 (2/2920, KOREAN)
C=0.148 (148/998, GoNL)
C=0.183 (110/600, NorthernSweden)
C=0.198 (65/328, HapMap)
C=0.125 (27/216, Qatari)
C=0.014 (3/212, Vietnamese)
T=0.429 (54/126, SGDP_PRJ)
C=0.09 (8/92, Ancient Sardinia)
C=0.17 (7/40, GENOME_DK)
T=0.50 (9/18, Siberian)
C=0.50 (9/18, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01362 : Intron Variant
LOC107985037 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 1 NC_000001.11:g.83064584T>C
GRCh38.p13 chr 1 NC_000001.11:g.83064584T>G
GRCh37.p13 chr 1 NC_000001.10:g.83530267T>C
GRCh37.p13 chr 1 NC_000001.10:g.83530267T>G
Gene: LINC01362, long intergenic non-protein coding RNA 1362 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01362 transcript NR_147074.1:n. N/A Intron Variant
Gene: LOC107985037, uncharacterized LOC107985037 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC107985037 transcript XR_001738121.1: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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 18434 T=0.80563 C=0.19437, G=0.00000
European Sub 14092 T=0.81145 C=0.18855, G=0.00000
African Sub 2684 T=0.7511 C=0.2489, G=0.0000
African Others Sub 104 T=0.721 C=0.279, G=0.000
African American Sub 2580 T=0.7523 C=0.2477, G=0.0000
Asian Sub 112 T=0.982 C=0.018, G=0.000
East Asian Sub 86 T=0.98 C=0.02, G=0.00
Other Asian Sub 26 T=1.00 C=0.00, G=0.00
Latin American 1 Sub 146 T=0.788 C=0.212, G=0.000
Latin American 2 Sub 610 T=0.851 C=0.149, G=0.000
South Asian Sub 98 T=0.89 C=0.11, G=0.00
Other Sub 692 T=0.822 C=0.178, G=0.000


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=0.803234 C=0.196766
gnomAD - Genomes Global Study-wide 140036 T=0.788290 C=0.211710
gnomAD - Genomes European Sub 75866 T=0.80709 C=0.19291
gnomAD - Genomes African Sub 41946 T=0.71344 C=0.28656
gnomAD - Genomes American Sub 13632 T=0.84999 C=0.15001
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.8492 C=0.1508
gnomAD - Genomes East Asian Sub 3122 T=0.9891 C=0.0109
gnomAD - Genomes Other Sub 2148 T=0.8082 C=0.1918
1000Genomes Global Study-wide 5008 T=0.8415 C=0.1585
1000Genomes African Sub 1322 T=0.7088 C=0.2912
1000Genomes East Asian Sub 1008 T=0.9891 C=0.0109
1000Genomes Europe Sub 1006 T=0.7932 C=0.2068
1000Genomes South Asian Sub 978 T=0.916 C=0.084
1000Genomes American Sub 694 T=0.844 C=0.156
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.7487 C=0.2513
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8228 C=0.1772
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8236 C=0.1764
KOREAN population from KRGDB KOREAN Study-wide 2920 T=0.9993 C=0.0007
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.852 C=0.148
Northern Sweden ACPOP Study-wide 600 T=0.817 C=0.183
HapMap Global Study-wide 328 T=0.802 C=0.198
HapMap African Sub 120 T=0.617 C=0.383
HapMap American Sub 120 T=0.842 C=0.158
HapMap Asian Sub 88 T=1.00 C=0.00
Qatari Global Study-wide 216 T=0.875 C=0.125
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.986 C=0.014
SGDP_PRJ Global Study-wide 126 T=0.429 C=0.571
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 92 T=0.91 C=0.09
The Danish reference pan genome Danish Study-wide 40 T=0.82 C=0.17
Siberian Global Study-wide 18 T=0.50 C=0.50
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 G
GRCh38.p13 chr 1 NC_000001.11:g.83064584= NC_000001.11:g.83064584T>C NC_000001.11:g.83064584T>G
GRCh37.p13 chr 1 NC_000001.10:g.83530267= NC_000001.10:g.83530267T>C NC_000001.10:g.83530267T>G
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#.

45 SubSNP, 17 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14874470 Dec 05, 2003 (119)
2 PERLEGEN ss23145050 Sep 20, 2004 (123)
3 AFFY ss65921364 Dec 02, 2006 (127)
4 PERLEGEN ss68772217 May 18, 2007 (127)
5 HGSV ss77711636 Dec 06, 2007 (129)
6 1000GENOMES ss108366650 Jan 23, 2009 (130)
7 ILLUMINA-UK ss118850587 Feb 14, 2009 (130)
8 COMPLETE_GENOMICS ss164666199 Jul 04, 2010 (132)
9 COMPLETE_GENOMICS ss166770415 Jul 04, 2010 (132)
10 BUSHMAN ss198701993 Jul 04, 2010 (132)
11 1000GENOMES ss210573061 Jul 14, 2010 (132)
12 1000GENOMES ss218491813 Jul 14, 2010 (132)
13 1000GENOMES ss230612788 Jul 14, 2010 (132)
14 BL ss253232633 May 09, 2011 (134)
15 GMI ss284085123 Apr 25, 2013 (138)
16 TISHKOFF ss554362122 Apr 25, 2013 (138)
17 SSMP ss648176161 Apr 25, 2013 (138)
18 EVA-GONL ss975365605 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1068043624 Aug 21, 2014 (142)
20 1000GENOMES ss1291669001 Aug 21, 2014 (142)
21 EVA_GENOME_DK ss1574191746 Apr 01, 2015 (144)
22 EVA_DECODE ss1584739543 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1600582874 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1643576907 Apr 01, 2015 (144)
25 WEILL_CORNELL_DGM ss1918568545 Feb 12, 2016 (147)
26 GENOMED ss1966794083 Jul 19, 2016 (147)
27 JJLAB ss2019804932 Sep 14, 2016 (149)
28 USC_VALOUEV ss2147822027 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2164129838 Dec 20, 2016 (150)
30 TOPMED ss2326422062 Dec 20, 2016 (150)
31 GNOMAD ss2757361930 Nov 08, 2017 (151)
32 SWEGEN ss2987125439 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3023665255 Nov 08, 2017 (151)
34 TOPMED ss3081730561 Nov 08, 2017 (151)
35 CSHL ss3343543767 Nov 08, 2017 (151)
36 EGCUT_WGS ss3655205992 Jul 12, 2019 (153)
37 EVA_DECODE ss3687150995 Jul 12, 2019 (153)
38 ACPOP ss3727217102 Jul 12, 2019 (153)
39 EVA ss3746440471 Jul 12, 2019 (153)
40 KHV_HUMAN_GENOMES ss3799446513 Jul 12, 2019 (153)
41 EVA ss3826271398 Apr 25, 2020 (154)
42 SGDP_PRJ ss3849250379 Apr 25, 2020 (154)
43 KRGDB ss3894301725 Apr 25, 2020 (154)
44 EVA ss3984808450 Apr 25, 2021 (155)
45 TOPMED ss4456689156 Apr 25, 2021 (155)
46 1000Genomes NC_000001.10 - 83530267 Oct 11, 2018 (152)
47 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 83530267 Oct 11, 2018 (152)
48 Genetic variation in the Estonian population NC_000001.10 - 83530267 Oct 11, 2018 (152)
49 The Danish reference pan genome NC_000001.10 - 83530267 Apr 25, 2020 (154)
50 gnomAD - Genomes NC_000001.11 - 83064584 Apr 25, 2021 (155)
51 Genome of the Netherlands Release 5 NC_000001.10 - 83530267 Apr 25, 2020 (154)
52 HapMap NC_000001.11 - 83064584 Apr 25, 2020 (154)
53 KOREAN population from KRGDB NC_000001.10 - 83530267 Apr 25, 2020 (154)
54 Northern Sweden NC_000001.10 - 83530267 Jul 12, 2019 (153)
55 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 83530267 Apr 25, 2021 (155)
56 Qatari NC_000001.10 - 83530267 Apr 25, 2020 (154)
57 SGDP_PRJ NC_000001.10 - 83530267 Apr 25, 2020 (154)
58 Siberian NC_000001.10 - 83530267 Apr 25, 2020 (154)
59 TopMed NC_000001.11 - 83064584 Apr 25, 2021 (155)
60 UK 10K study - Twins NC_000001.10 - 83530267 Oct 11, 2018 (152)
61 A Vietnamese Genetic Variation Database NC_000001.10 - 83530267 Jul 12, 2019 (153)
62 ALFA NC_000001.11 - 83064584 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
ss77711636 NC_000001.8:83242287:T:C NC_000001.11:83064583:T:C (self)
ss108366650, ss118850587, ss164666199, ss166770415, ss198701993, ss210573061, ss253232633, ss284085123, ss1584739543 NC_000001.9:83302854:T:C NC_000001.11:83064583:T:C (self)
2416196, 1326145, 944240, 1583128, 572605, 1479119, 501967, 34377, 610475, 1267359, 338381, 1326145, 284441, ss218491813, ss230612788, ss554362122, ss648176161, ss975365605, ss1068043624, ss1291669001, ss1574191746, ss1600582874, ss1643576907, ss1918568545, ss1966794083, ss2019804932, ss2147822027, ss2326422062, ss2757361930, ss2987125439, ss3343543767, ss3655205992, ss3727217102, ss3746440471, ss3826271398, ss3849250379, ss3894301725, ss3984808450 NC_000001.10:83530266:T:C NC_000001.11:83064583:T:C (self)
17051899, 112944, 12783638, 20295491, 8312522802, ss2164129838, ss3023665255, ss3081730561, ss3687150995, ss3799446513, ss4456689156 NC_000001.11:83064583:T:C NC_000001.11:83064583:T:C (self)
ss14874470, ss23145050, ss65921364, ss68772217 NT_032977.9:53502184:T:C NC_000001.11:83064583:T:C (self)
8312522802 NC_000001.11:83064583:T:G NC_000001.11:83064583:T:G
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 rs10487981

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.post596+ae089ad