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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs12119699

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:202003827 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.361502 (95686/264690, TOPMED)
A=0.361169 (50537/139926, GnomAD)
A=0.36371 (10277/28256, 14KJPN) (+ 19 more)
A=0.40049 (9583/23928, ALFA)
A=0.36712 (6153/16760, 8.3KJPN)
A=0.3100 (1985/6404, 1000G_30x)
A=0.3091 (1548/5008, 1000G)
A=0.4299 (1926/4480, Estonian)
A=0.4512 (1739/3854, ALSPAC)
A=0.4566 (1693/3708, TWINSUK)
A=0.4451 (1304/2930, KOREAN)
A=0.3122 (590/1890, HapMap)
A=0.4230 (775/1832, Korea1K)
A=0.441 (440/998, GoNL)
A=0.462 (289/626, Chileans)
A=0.398 (239/600, NorthernSweden)
G=0.377 (98/260, SGDP_PRJ)
A=0.333 (72/216, Qatari)
A=0.392 (83/212, Vietnamese)
A=0.44 (24/54, Ancient Sardinia)
A=0.42 (17/40, GENOME_DK)
G=0.45 (18/40, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ELF3-AS1 : Intron Variant
RNPEP : 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 23928 G=0.59951 A=0.40049
European Sub 15660 G=0.55294 A=0.44706
African Sub 3616 G=0.8175 A=0.1825
African Others Sub 126 G=0.857 A=0.143
African American Sub 3490 G=0.8160 A=0.1840
Asian Sub 160 G=0.644 A=0.356
East Asian Sub 102 G=0.578 A=0.422
Other Asian Sub 58 G=0.76 A=0.24
Latin American 1 Sub 292 G=0.575 A=0.425
Latin American 2 Sub 2748 G=0.5553 A=0.4447
South Asian Sub 110 G=0.736 A=0.264
Other Sub 1342 G=0.6349 A=0.3651


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=0.638498 A=0.361502
gnomAD - Genomes Global Study-wide 139926 G=0.638831 A=0.361169
gnomAD - Genomes European Sub 75808 G=0.56332 A=0.43668
gnomAD - Genomes African Sub 41926 G=0.82006 A=0.17994
gnomAD - Genomes American Sub 13610 G=0.54798 A=0.45202
gnomAD - Genomes Ashkenazi Jewish Sub 3316 G=0.5428 A=0.4572
gnomAD - Genomes East Asian Sub 3116 G=0.5587 A=0.4413
gnomAD - Genomes Other Sub 2150 G=0.6065 A=0.3935
14KJPN JAPANESE Study-wide 28256 G=0.63629 A=0.36371
Allele Frequency Aggregator Total Global 23928 G=0.59951 A=0.40049
Allele Frequency Aggregator European Sub 15660 G=0.55294 A=0.44706
Allele Frequency Aggregator African Sub 3616 G=0.8175 A=0.1825
Allele Frequency Aggregator Latin American 2 Sub 2748 G=0.5553 A=0.4447
Allele Frequency Aggregator Other Sub 1342 G=0.6349 A=0.3651
Allele Frequency Aggregator Latin American 1 Sub 292 G=0.575 A=0.425
Allele Frequency Aggregator Asian Sub 160 G=0.644 A=0.356
Allele Frequency Aggregator South Asian Sub 110 G=0.736 A=0.264
8.3KJPN JAPANESE Study-wide 16760 G=0.63288 A=0.36712
1000Genomes_30x Global Study-wide 6404 G=0.6900 A=0.3100
1000Genomes_30x African Sub 1786 G=0.8415 A=0.1585
1000Genomes_30x Europe Sub 1266 G=0.5632 A=0.4368
1000Genomes_30x South Asian Sub 1202 G=0.7920 A=0.2080
1000Genomes_30x East Asian Sub 1170 G=0.5880 A=0.4120
1000Genomes_30x American Sub 980 G=0.574 A=0.426
1000Genomes Global Study-wide 5008 G=0.6909 A=0.3091
1000Genomes African Sub 1322 G=0.8427 A=0.1573
1000Genomes East Asian Sub 1008 G=0.6022 A=0.3978
1000Genomes Europe Sub 1006 G=0.5706 A=0.4294
1000Genomes South Asian Sub 978 G=0.792 A=0.208
1000Genomes American Sub 694 G=0.562 A=0.438
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.5701 A=0.4299
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5488 A=0.4512
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5434 A=0.4566
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5549 A=0.4451
HapMap Global Study-wide 1890 G=0.6878 A=0.3122
HapMap American Sub 770 G=0.630 A=0.370
HapMap African Sub 692 G=0.814 A=0.186
HapMap Asian Sub 252 G=0.607 A=0.393
HapMap Europe Sub 176 G=0.562 A=0.438
Korean Genome Project KOREAN Study-wide 1832 G=0.5770 A=0.4230
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.559 A=0.441
Chileans Chilean Study-wide 626 G=0.538 A=0.462
Northern Sweden ACPOP Study-wide 600 G=0.602 A=0.398
SGDP_PRJ Global Study-wide 260 G=0.377 A=0.623
Qatari Global Study-wide 216 G=0.667 A=0.333
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.608 A=0.392
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 54 G=0.56 A=0.44
The Danish reference pan genome Danish Study-wide 40 G=0.57 A=0.42
Siberian Global Study-wide 40 G=0.45 A=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.202003827G>A
GRCh37.p13 chr 1 NC_000001.10:g.201972955G>A
Gene: RNPEP, arginyl aminopeptidase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RNPEP transcript variant 2 NM_001319182.2:c.1258+366…

NM_001319182.2:c.1258+366G>A

 		N/A Intron Variant
RNPEP transcript variant 3 NM_001319183.2:c.781+366G…

NM_001319183.2:c.781+366G>A

 		N/A Intron Variant
RNPEP transcript variant 4 NM_001319184.2:c.781+366G…

NM_001319184.2:c.781+366G>A

 		N/A Intron Variant
RNPEP transcript variant 1 NM_020216.4:c.1651+366G>A N/A Intron Variant
Gene: ELF3-AS1, ELF3 antisense RNA 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ELF3-AS1 transcript NR_146472.1: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
GRCh38.p14 chr 1 NC_000001.11:g.202003827= NC_000001.11:g.202003827G>A
GRCh37.p13 chr 1 NC_000001.10:g.201972955= NC_000001.10:g.201972955G>A
RNPEP transcript variant 2 NM_001319182.2:c.1258+366= NM_001319182.2:c.1258+366G>A
RNPEP transcript variant 3 NM_001319183.2:c.781+366= NM_001319183.2:c.781+366G>A
RNPEP transcript variant 4 NM_001319184.2:c.781+366= NM_001319184.2:c.781+366G>A
RNPEP transcript variant 1 NM_020216.3:c.1651+366= NM_020216.3:c.1651+366G>A
RNPEP transcript variant 1 NM_020216.4:c.1651+366= NM_020216.4:c.1651+366G>A
RNPEP transcript variant X1 XM_005245418.1:c.1258+366= XM_005245418.1:c.1258+366G>A
RNPEP transcript variant X2 XM_005245419.1:c.1039+366= XM_005245419.1:c.1039+366G>A
RNPEP transcript variant X3 XM_005245420.1:c.781+366= XM_005245420.1:c.781+366G>A
RNPEP transcript variant X1 XM_005245421.1:c.781+366= XM_005245421.1:c.781+366G>A
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#.

71 SubSNP, 22 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18249101 Feb 28, 2004 (120)
2 PERLEGEN ss23847414 Sep 20, 2004 (123)
3 AFFY ss66041051 Dec 01, 2006 (127)
4 AFFY ss75934425 Dec 06, 2007 (129)
5 HGSV ss77476545 Dec 06, 2007 (129)
6 HGSV ss78341992 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss82954208 Dec 14, 2007 (130)
8 HGSV ss83213436 Dec 15, 2007 (130)
9 BCMHGSC_JDW ss87936688 Mar 23, 2008 (129)
10 BGI ss106624761 Feb 05, 2009 (130)
11 1000GENOMES ss108868934 Jan 23, 2009 (130)
12 1000GENOMES ss111636179 Jan 25, 2009 (130)
13 ENSEMBL ss138137188 Dec 01, 2009 (131)
14 GMI ss156164841 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss164920203 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss165687433 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss167434716 Jul 04, 2010 (132)
18 1000GENOMES ss218828561 Jul 14, 2010 (132)
19 1000GENOMES ss230861630 Jul 14, 2010 (132)
20 1000GENOMES ss238481455 Jul 15, 2010 (132)
21 BL ss253752874 May 09, 2011 (134)
22 GMI ss276177700 May 04, 2012 (137)
23 PJP ss290713559 May 09, 2011 (134)
24 TISHKOFF ss555050729 Apr 25, 2013 (138)
25 SSMP ss648630252 Apr 25, 2013 (138)
26 EVA-GONL ss976035740 Aug 21, 2014 (142)
27 JMKIDD_LAB ss1068522950 Aug 21, 2014 (142)
28 1000GENOMES ss1294242852 Aug 21, 2014 (142)
29 DDI ss1426081028 Apr 01, 2015 (144)
30 EVA_GENOME_DK ss1574609860 Apr 01, 2015 (144)
31 EVA_DECODE ss1585430216 Apr 01, 2015 (144)
32 EVA_UK10K_ALSPAC ss1601920024 Apr 01, 2015 (144)
33 EVA_UK10K_TWINSUK ss1644914057 Apr 01, 2015 (144)
34 EVA_SVP ss1712396469 Apr 01, 2015 (144)
35 WEILL_CORNELL_DGM ss1919263806 Feb 12, 2016 (147)
36 GENOMED ss1966947887 Jul 19, 2016 (147)
37 JJLAB ss2020151977 Sep 14, 2016 (149)
38 USC_VALOUEV ss2148179547 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2169266476 Dec 20, 2016 (150)
40 SYSTEMSBIOZJU ss2624583645 Nov 08, 2017 (151)
41 GRF ss2698169307 Nov 08, 2017 (151)
42 GNOMAD ss2765067669 Nov 08, 2017 (151)
43 SWEGEN ss2988281810 Nov 08, 2017 (151)
44 BIOINF_KMB_FNS_UNIBA ss3023835924 Nov 08, 2017 (151)
45 CSHL ss3343864384 Nov 08, 2017 (151)
46 EGCUT_WGS ss3656243175 Jul 12, 2019 (153)
47 EVA_DECODE ss3688426494 Jul 12, 2019 (153)
48 ACPOP ss3727772346 Jul 12, 2019 (153)
49 EVA ss3747208137 Jul 12, 2019 (153)
50 KHV_HUMAN_GENOMES ss3800216442 Jul 12, 2019 (153)
51 EVA ss3826592070 Apr 25, 2020 (154)
52 EVA ss3836695664 Apr 25, 2020 (154)
53 EVA ss3842106794 Apr 25, 2020 (154)
54 SGDP_PRJ ss3850687442 Apr 25, 2020 (154)
55 KRGDB ss3895975256 Apr 25, 2020 (154)
56 KOGIC ss3946282747 Apr 25, 2020 (154)
57 EVA ss3984845001 Apr 25, 2021 (155)
58 TOPMED ss4480007641 Apr 25, 2021 (155)
59 TOMMO_GENOMICS ss5147967966 Apr 25, 2021 (155)
60 1000G_HIGH_COVERAGE ss5245439848 Oct 12, 2022 (156)
61 EVA ss5324137820 Oct 12, 2022 (156)
62 HUGCELL_USP ss5445913292 Oct 12, 2022 (156)
63 EVA ss5506154900 Oct 12, 2022 (156)
64 1000G_HIGH_COVERAGE ss5519360451 Oct 12, 2022 (156)
65 SANFORD_IMAGENETICS ss5627247323 Oct 12, 2022 (156)
66 TOMMO_GENOMICS ss5675591892 Oct 12, 2022 (156)
67 YY_MCH ss5801548238 Oct 12, 2022 (156)
68 EVA ss5833119567 Oct 12, 2022 (156)
69 EVA ss5849241132 Oct 12, 2022 (156)
70 EVA ss5911563578 Oct 12, 2022 (156)
71 EVA ss5939075707 Oct 12, 2022 (156)
72 1000Genomes NC_000001.10 - 201972955 Oct 11, 2018 (152)
73 1000Genomes_30x NC_000001.11 - 202003827 Oct 12, 2022 (156)
74 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 201972955 Oct 11, 2018 (152)
75 Chileans NC_000001.10 - 201972955 Apr 25, 2020 (154)
76 Genetic variation in the Estonian population NC_000001.10 - 201972955 Oct 11, 2018 (152)
77 The Danish reference pan genome NC_000001.10 - 201972955 Apr 25, 2020 (154)
78 gnomAD - Genomes NC_000001.11 - 202003827 Apr 25, 2021 (155)
79 Genome of the Netherlands Release 5 NC_000001.10 - 201972955 Apr 25, 2020 (154)
80 HapMap NC_000001.11 - 202003827 Apr 25, 2020 (154)
81 KOREAN population from KRGDB NC_000001.10 - 201972955 Apr 25, 2020 (154)
82 Korean Genome Project NC_000001.11 - 202003827 Apr 25, 2020 (154)
83 Northern Sweden NC_000001.10 - 201972955 Jul 12, 2019 (153)
84 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 201972955 Apr 25, 2021 (155)
85 Qatari NC_000001.10 - 201972955 Apr 25, 2020 (154)
86 SGDP_PRJ NC_000001.10 - 201972955 Apr 25, 2020 (154)
87 Siberian NC_000001.10 - 201972955 Apr 25, 2020 (154)
88 8.3KJPN NC_000001.10 - 201972955 Apr 25, 2021 (155)
89 14KJPN NC_000001.11 - 202003827 Oct 12, 2022 (156)
90 TopMed NC_000001.11 - 202003827 Apr 25, 2021 (155)
91 UK 10K study - Twins NC_000001.10 - 201972955 Oct 11, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000001.10 - 201972955 Jul 12, 2019 (153)
93 ALFA NC_000001.11 - 202003827 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).

Associated ID History Updated (Build)
rs56825844 Feb 26, 2009 (130)
rs59064973 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77476545, ss78341992, ss83213436 NC_000001.8:198704611:G:A NC_000001.11:202003826:G:A (self)
ss87936688, ss108868934, ss111636179, ss164920203, ss165687433, ss167434716, ss253752874, ss276177700, ss290713559, ss1585430216, ss1712396469 NC_000001.9:200239577:G:A NC_000001.11:202003826:G:A (self)
5083010, 2797052, 29805, 1981423, 1843289, 1221858, 3152650, 1057211, 70928, 1305736, 2704422, 695901, 5937273, 2797052, 604449, ss218828561, ss230861630, ss238481455, ss555050729, ss648630252, ss976035740, ss1068522950, ss1294242852, ss1426081028, ss1574609860, ss1601920024, ss1644914057, ss1919263806, ss1966947887, ss2020151977, ss2148179547, ss2624583645, ss2698169307, ss2765067669, ss2988281810, ss3343864384, ss3656243175, ss3727772346, ss3747208137, ss3826592070, ss3836695664, ss3850687442, ss3895975256, ss3984845001, ss5147967966, ss5324137820, ss5506154900, ss5627247323, ss5833119567, ss5939075707 NC_000001.10:201972954:G:A NC_000001.11:202003826:G:A (self)
6886386, 36640202, 245541, 2660748, 9428996, 43613976, 11234018795, ss2169266476, ss3023835924, ss3688426494, ss3800216442, ss3842106794, ss3946282747, ss4480007641, ss5245439848, ss5445913292, ss5519360451, ss5675591892, ss5801548238, ss5849241132, ss5911563578 NC_000001.11:202003826:G:A NC_000001.11:202003826:G:A (self)
ss23847414, ss66041051, ss75934425, ss82954208, ss106624761, ss138137188, ss156164841 NT_004487.19:53461596:G:A NC_000001.11:202003826:G:A (self)
ss18249101 NT_004671.15:13327938:G:A NC_000001.11:202003826:G:A (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 rs12119699

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