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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.

rs12124819

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:841166 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.161521 (42753/264690, TOPMED)
G=0.175734 (24634/140178, GnomAD)
G=0.246315 (27542/111816, ALFA) (+ 15 more)
G=0.00024 (4/16760, 8.3KJPN)
G=0.0757 (379/5008, 1000G)
G=0.2686 (1035/3854, ALSPAC)
G=0.2613 (969/3708, TWINSUK)
G=0.0003 (1/2922, KOREAN)
G=0.0016 (3/1832, Korea1K)
G=0.0752 (114/1516, HapMap)
G=0.285 (284/998, GoNL)
G=0.363 (218/600, NorthernSweden)
G=0.139 (30/216, Qatari)
G=0.005 (1/216, Vietnamese)
A=0.482 (53/110, SGDP_PRJ)
G=0.23 (14/60, Ancient Sardinia)
G=0.20 (8/40, GENOME_DK)
A=0.43 (6/14, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01128 : 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.841166A>G
GRCh37.p13 chr 1 NC_000001.10:g.776546A>G
Gene: LINC01128, long intergenic non-protein coding RNA 1128 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01128 transcript variant 1 NR_047519.1:n. N/A Intron Variant
LINC01128 transcript variant 3 NR_047521.1:n. N/A Intron Variant
LINC01128 transcript variant 5 NR_047523.1:n. N/A Intron Variant
LINC01128 transcript variant 7 NR_047524.1:n. N/A Intron Variant
LINC01128 transcript variant 8 NR_047525.1:n. N/A Intron Variant
LINC01128 transcript variant 9 NR_047526.1: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 111816 A=0.753685 G=0.246315
European Sub 97238 A=0.73428 G=0.26572
African Sub 6254 A=0.9517 G=0.0483
African Others Sub 234 A=1.000 G=0.000
African American Sub 6020 A=0.9498 G=0.0502
Asian Sub 338 A=1.000 G=0.000
East Asian Sub 244 A=1.000 G=0.000
Other Asian Sub 94 A=1.00 G=0.00
Latin American 1 Sub 646 A=0.810 G=0.190
Latin American 2 Sub 2078 A=0.8638 G=0.1362
South Asian Sub 166 A=0.928 G=0.072
Other Sub 5096 A=0.8069 G=0.1931


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 A=0.838479 G=0.161521
gnomAD - Genomes Global Study-wide 140178 A=0.824266 G=0.175734
gnomAD - Genomes European Sub 75888 A=0.73585 G=0.26415
gnomAD - Genomes African Sub 42028 A=0.95282 G=0.04718
gnomAD - Genomes American Sub 13654 A=0.86795 G=0.13205
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.8655 G=0.1345
gnomAD - Genomes East Asian Sub 3134 A=0.9990 G=0.0010
gnomAD - Genomes Other Sub 2150 A=0.8363 G=0.1637
8.3KJPN JAPANESE Study-wide 16760 A=0.99976 G=0.00024
1000Genomes Global Study-wide 5008 A=0.9243 G=0.0757
1000Genomes African Sub 1322 A=0.9864 G=0.0136
1000Genomes East Asian Sub 1008 A=0.9980 G=0.0020
1000Genomes Europe Sub 1006 A=0.7714 G=0.2286
1000Genomes South Asian Sub 978 A=0.944 G=0.056
1000Genomes American Sub 694 A=0.893 G=0.107
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.7314 G=0.2686
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.7387 G=0.2613
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9997 G=0.0003
Korean Genome Project KOREAN Study-wide 1832 A=0.9984 G=0.0016
HapMap Global Study-wide 1516 A=0.9248 G=0.0752
HapMap American Sub 590 A=0.871 G=0.129
HapMap African Sub 586 A=0.990 G=0.010
HapMap Asian Sub 170 A=1.000 G=0.000
HapMap Europe Sub 170 A=0.812 G=0.188
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.715 G=0.285
Northern Sweden ACPOP Study-wide 600 A=0.637 G=0.363
Qatari Global Study-wide 216 A=0.861 G=0.139
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.995 G=0.005
SGDP_PRJ Global Study-wide 110 A=0.482 G=0.518
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 60 A=0.77 G=0.23
The Danish reference pan genome Danish Study-wide 40 A=0.80 G=0.20
Siberian Global Study-wide 14 A=0.43 G=0.57
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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.841166= NC_000001.11:g.841166A>G
GRCh37.p13 chr 1 NC_000001.10:g.776546= NC_000001.10:g.776546A>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#.

77 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18258615 Feb 28, 2004 (120)
2 ILLUMINA ss75285022 Dec 07, 2007 (129)
3 HUMANGENOME_JCVI ss99179619 Feb 04, 2009 (130)
4 1000GENOMES ss107938279 Jan 22, 2009 (130)
5 KRIBB_YJKIM ss119753357 Dec 01, 2009 (131)
6 ILLUMINA ss123327333 Dec 01, 2009 (131)
7 ILLUMINA ss153136124 Dec 01, 2009 (131)
8 ILLUMINA ss160035469 Dec 01, 2009 (131)
9 ILLUMINA ss170049362 Jul 04, 2010 (132)
10 ILLUMINA ss171875411 Jul 04, 2010 (132)
11 1000GENOMES ss230395475 Jul 14, 2010 (132)
12 GMI ss283987399 Apr 25, 2013 (138)
13 PJP ss290493805 May 09, 2011 (134)
14 ILLUMINA ss479677171 May 04, 2012 (137)
15 ILLUMINA ss479682583 May 04, 2012 (137)
16 ILLUMINA ss480207576 Sep 08, 2015 (146)
17 ILLUMINA ss484637140 May 04, 2012 (137)
18 ILLUMINA ss536756860 Sep 08, 2015 (146)
19 SSMP ss647516268 Apr 25, 2013 (138)
20 ILLUMINA ss778774839 Sep 08, 2015 (146)
21 ILLUMINA ss782765402 Sep 08, 2015 (146)
22 ILLUMINA ss783731702 Sep 08, 2015 (146)
23 ILLUMINA ss825664578 Jul 19, 2016 (147)
24 ILLUMINA ss832017736 Sep 08, 2015 (146)
25 ILLUMINA ss834234721 Sep 08, 2015 (146)
26 EVA-GONL ss974769433 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1067612357 Aug 21, 2014 (142)
28 1000GENOMES ss1289339536 Aug 21, 2014 (142)
29 EVA_GENOME_DK ss1573851172 Apr 01, 2015 (144)
30 EVA_DECODE ss1584129514 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1599378414 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1642372447 Apr 01, 2015 (144)
33 EVA_SVP ss1712305461 Apr 01, 2015 (144)
34 ILLUMINA ss1751933372 Sep 08, 2015 (146)
35 WEILL_CORNELL_DGM ss1917960482 Feb 12, 2016 (147)
36 GENOMED ss1966667333 Jul 19, 2016 (147)
37 JJLAB ss2019498429 Sep 14, 2016 (149)
38 USC_VALOUEV ss2147484418 Dec 20, 2016 (150)
39 TOPMED ss2321503861 Dec 20, 2016 (150)
40 ILLUMINA ss2632465453 Nov 08, 2017 (151)
41 GNOMAD ss2750639370 Nov 08, 2017 (151)
42 SWEGEN ss2986149152 Nov 08, 2017 (151)
43 BIOINF_KMB_FNS_UNIBA ss3023513712 Nov 08, 2017 (151)
44 TOPMED ss3066401257 Nov 08, 2017 (151)
45 CSHL ss3343272609 Nov 08, 2017 (151)
46 ILLUMINA ss3626006507 Oct 11, 2018 (152)
47 ILLUMINA ss3630505578 Oct 11, 2018 (152)
48 ILLUMINA ss3632878029 Oct 11, 2018 (152)
49 ILLUMINA ss3633571435 Oct 11, 2018 (152)
50 ILLUMINA ss3634301815 Oct 11, 2018 (152)
51 ILLUMINA ss3635265640 Oct 11, 2018 (152)
52 ILLUMINA ss3635978607 Oct 11, 2018 (152)
53 ILLUMINA ss3637015979 Oct 11, 2018 (152)
54 ILLUMINA ss3637732364 Oct 11, 2018 (152)
55 ILLUMINA ss3640009181 Oct 11, 2018 (152)
56 ILLUMINA ss3640973131 Oct 11, 2018 (152)
57 ILLUMINA ss3641266947 Oct 11, 2018 (152)
58 ILLUMINA ss3642746667 Oct 11, 2018 (152)
59 EVA_DECODE ss3685992205 Jul 12, 2019 (153)
60 ACPOP ss3726716406 Jul 12, 2019 (153)
61 ILLUMINA ss3744602747 Jul 12, 2019 (153)
62 EVA ss3745721034 Jul 12, 2019 (153)
63 ILLUMINA ss3772104512 Jul 12, 2019 (153)
64 PACBIO ss3783302159 Jul 12, 2019 (153)
65 PACBIO ss3788980024 Jul 12, 2019 (153)
66 PACBIO ss3793852560 Jul 12, 2019 (153)
67 KHV_HUMAN_GENOMES ss3798743666 Jul 12, 2019 (153)
68 EVA ss3825981473 Apr 25, 2020 (154)
69 EVA ss3836378426 Apr 25, 2020 (154)
70 EVA ss3841782426 Apr 25, 2020 (154)
71 SGDP_PRJ ss3847995628 Apr 25, 2020 (154)
72 KRGDB ss3892835931 Apr 25, 2020 (154)
73 KOGIC ss3943629713 Apr 25, 2020 (154)
74 EVA ss3984774075 Apr 25, 2021 (155)
75 EVA ss4016889038 Apr 25, 2021 (155)
76 TOPMED ss4436434486 Apr 25, 2021 (155)
77 TOMMO_GENOMICS ss5142052394 Apr 25, 2021 (155)
78 1000Genomes NC_000001.10 - 776546 Oct 11, 2018 (152)
79 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 776546 Oct 11, 2018 (152)
80 The Danish reference pan genome NC_000001.10 - 776546 Apr 25, 2020 (154)
81 gnomAD - Genomes NC_000001.11 - 841166 Apr 25, 2021 (155)
82 Genome of the Netherlands Release 5 NC_000001.10 - 776546 Apr 25, 2020 (154)
83 HapMap NC_000001.11 - 841166 Apr 25, 2020 (154)
84 KOREAN population from KRGDB NC_000001.10 - 776546 Apr 25, 2020 (154)
85 Korean Genome Project NC_000001.11 - 841166 Apr 25, 2020 (154)
86 Northern Sweden NC_000001.10 - 776546 Jul 12, 2019 (153)
87 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 776546 Apr 25, 2021 (155)
88 Qatari NC_000001.10 - 776546 Apr 25, 2020 (154)
89 SGDP_PRJ NC_000001.10 - 776546 Apr 25, 2020 (154)
90 Siberian NC_000001.10 - 776546 Apr 25, 2020 (154)
91 8.3KJPN NC_000001.10 - 776546 Apr 25, 2021 (155)
92 TopMed NC_000001.11 - 841166 Apr 25, 2021 (155)
93 UK 10K study - Twins NC_000001.10 - 776546 Oct 11, 2018 (152)
94 A Vietnamese Genetic Variation Database NC_000001.10 - 776546 Jul 12, 2019 (153)
95 ALFA NC_000001.11 - 841166 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
ss107938279, ss283987399, ss290493805, ss479677171, ss825664578, ss1584129514, ss1712305461, ss3642746667 NC_000001.9:766408:A:G NC_000001.11:841165:A:G (self)
4274, 340, 1358406, 473, 13325, 1271, 2, 2412, 12608, 772, 21701, 340, 69, ss230395475, ss479682583, ss480207576, ss484637140, ss536756860, ss647516268, ss778774839, ss782765402, ss783731702, ss832017736, ss834234721, ss974769433, ss1067612357, ss1289339536, ss1573851172, ss1599378414, ss1642372447, ss1751933372, ss1917960482, ss1966667333, ss2019498429, ss2147484418, ss2321503861, ss2632465453, ss2750639370, ss2986149152, ss3343272609, ss3626006507, ss3630505578, ss3632878029, ss3633571435, ss3634301815, ss3635265640, ss3635978607, ss3637015979, ss3637732364, ss3640009181, ss3640973131, ss3641266947, ss3726716406, ss3744602747, ss3745721034, ss3772104512, ss3783302159, ss3788980024, ss3793852560, ss3825981473, ss3836378426, ss3847995628, ss3892835931, ss3984774075, ss4016889038, ss5142052394 NC_000001.10:776545:A:G NC_000001.11:841165:A:G (self)
66560, 65, 7714, 17838, 40821, 5851909141, ss3023513712, ss3066401257, ss3685992205, ss3798743666, ss3841782426, ss3943629713, ss4436434486 NC_000001.11:841165:A:G NC_000001.11:841165:A:G (self)
ss75285022, ss99179619, ss119753357, ss123327333, ss153136124, ss160035469, ss170049362, ss171875411 NT_004350.19:255177:A:G NC_000001.11:841165:A:G (self)
ss18258615 NT_034471.3:255177:A:G NC_000001.11:841165:A:G (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 rs12124819

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