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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.

rs12119601

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:149849089 (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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.280267 (74184/264690, TOPMED)
G=0.277673 (38897/140082, GnomAD)
G=0.30850 (24279/78700, PAGE_STUDY) (+ 3 more)
G=0.28147 (5317/18890, ALFA)
C=0.4285 (785/1832, Korea1K)
G=0.206 (67/326, HapMap)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
H2AC19 : 2KB Upstream 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.149849089C>G
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.6664502C>G
GRCh37.p13 chr 1 NC_000001.10:g.149820656G>C
Gene: H2AC19, H2A clustered histone 19 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
H2AC19 transcript NM_001040874.1:c. N/A 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

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 18890 C=0.71853 G=0.28147
European Sub 14286 C=0.70783 G=0.29217
African Sub 2946 C=0.8174 G=0.1826
African Others Sub 114 C=0.807 G=0.193
African American Sub 2832 C=0.8178 G=0.1822
Asian Sub 112 C=0.536 G=0.464
East Asian Sub 86 C=0.52 G=0.48
Other Asian Sub 26 C=0.58 G=0.42
Latin American 1 Sub 146 C=0.671 G=0.329
Latin American 2 Sub 610 C=0.539 G=0.461
South Asian Sub 98 C=0.59 G=0.41
Other Sub 692 C=0.734 G=0.266


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 C=0.719733 G=0.280267
gnomAD - Genomes Global Study-wide 140082 C=0.722327 G=0.277673
gnomAD - Genomes European Sub 75844 C=0.69668 G=0.30332
gnomAD - Genomes African Sub 42000 C=0.81412 G=0.18588
gnomAD - Genomes American Sub 13640 C=0.61078 G=0.38922
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.7632 G=0.2368
gnomAD - Genomes East Asian Sub 3124 C=0.5611 G=0.4389
gnomAD - Genomes Other Sub 2150 C=0.7126 G=0.2874
The PAGE Study Global Study-wide 78700 C=0.69150 G=0.30850
The PAGE Study AfricanAmerican Sub 32516 C=0.81028 G=0.18972
The PAGE Study Mexican Sub 10808 C=0.55598 G=0.44402
The PAGE Study Asian Sub 8318 C=0.4199 G=0.5801
The PAGE Study PuertoRican Sub 7918 C=0.6521 G=0.3479
The PAGE Study NativeHawaiian Sub 4534 C=0.7605 G=0.2395
The PAGE Study Cuban Sub 4230 C=0.7109 G=0.2891
The PAGE Study Dominican Sub 3828 C=0.7448 G=0.2552
The PAGE Study CentralAmerican Sub 2450 C=0.5939 G=0.4061
The PAGE Study SouthAmerican Sub 1982 C=0.5938 G=0.4062
The PAGE Study NativeAmerican Sub 1260 C=0.7095 G=0.2905
The PAGE Study SouthAsian Sub 856 C=0.674 G=0.326
Allele Frequency Aggregator Total Global 18890 C=0.71853 G=0.28147
Allele Frequency Aggregator European Sub 14286 C=0.70783 G=0.29217
Allele Frequency Aggregator African Sub 2946 C=0.8174 G=0.1826
Allele Frequency Aggregator Other Sub 692 C=0.734 G=0.266
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.539 G=0.461
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.671 G=0.329
Allele Frequency Aggregator Asian Sub 112 C=0.536 G=0.464
Allele Frequency Aggregator South Asian Sub 98 C=0.59 G=0.41
Korean Genome Project KOREAN Study-wide 1832 C=0.4285 G=0.5715
HapMap Global Study-wide 326 C=0.794 G=0.206
HapMap African Sub 120 C=0.975 G=0.025
HapMap American Sub 120 C=0.683 G=0.317
HapMap Asian Sub 86 C=0.70 G=0.30
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 C= G
GRCh38.p13 chr 1 NC_000001.11:g.149849089= NC_000001.11:g.149849089C>G
GRCh37.p13 chr 1 fix patch HG1287_PATCH NW_003871055.3:g.6664502= NW_003871055.3:g.6664502C>G
GRCh37.p13 chr 1 NC_000001.10:g.149820656G>C NC_000001.10:g.149820656=
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#.

95 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18248919 Feb 28, 2004 (120)
2 HGSV ss80927783 Dec 14, 2007 (130)
3 HUMANGENOME_JCVI ss99248490 Feb 03, 2009 (130)
4 BGI ss102783218 Dec 01, 2009 (131)
5 1000GENOMES ss108576779 Jan 23, 2009 (130)
6 1000GENOMES ss111111835 Jan 25, 2009 (130)
7 ILLUMINA-UK ss119016750 Feb 15, 2009 (130)
8 GMI ss155716770 Dec 01, 2009 (131)
9 ILLUMINA ss160035043 Dec 01, 2009 (131)
10 COMPLETE_GENOMICS ss164057399 Jul 04, 2010 (132)
11 COMPLETE_GENOMICS ss165177968 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss167097523 Jul 04, 2010 (132)
13 ILLUMINA ss171870506 Jul 04, 2010 (132)
14 BUSHMAN ss199048736 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss205044352 Jul 04, 2010 (132)
16 1000GENOMES ss218636481 Jul 14, 2010 (132)
17 1000GENOMES ss230722047 Jul 14, 2010 (132)
18 1000GENOMES ss238372086 Jul 15, 2010 (132)
19 BL ss253485933 May 09, 2011 (134)
20 GMI ss276040707 May 04, 2012 (137)
21 GMI ss284147324 Apr 25, 2013 (138)
22 PJP ss290631589 May 09, 2011 (134)
23 ILLUMINA ss479675941 May 04, 2012 (137)
24 ILLUMINA ss479681323 May 04, 2012 (137)
25 ILLUMINA ss480205904 Sep 11, 2015 (146)
26 ILLUMINA ss484636531 May 04, 2012 (137)
27 ILLUMINA ss536756315 Sep 11, 2015 (146)
28 TISHKOFF ss554662007 Apr 25, 2013 (138)
29 SSMP ss648394886 Apr 25, 2013 (138)
30 ILLUMINA ss778342335 Sep 11, 2015 (146)
31 ILLUMINA ss782765093 Sep 11, 2015 (146)
32 ILLUMINA ss783731397 Sep 11, 2015 (146)
33 ILLUMINA ss832017420 Sep 11, 2015 (146)
34 ILLUMINA ss833796946 Sep 11, 2015 (146)
35 EVA-GONL ss975652445 Apr 09, 2015 (144)
36 JMKIDD_LAB ss1068246978 Apr 09, 2015 (144)
37 1000GENOMES ss1292799622 Aug 28, 2014 (142)
38 DDI ss1425970480 Apr 09, 2015 (144)
39 EVA_GENOME_DK ss1574375497 Apr 09, 2015 (144)
40 EVA_DECODE ss1585033325 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1601149129 Apr 09, 2015 (144)
42 EVA_UK10K_TWINSUK ss1644143162 Apr 09, 2015 (144)
43 ILLUMINA ss1751869501 Sep 11, 2015 (146)
44 HAMMER_LAB ss1795050783 Sep 11, 2015 (146)
45 WEILL_CORNELL_DGM ss1918884087 Feb 17, 2016 (147)
46 ILLUMINA ss1958313187 Feb 17, 2016 (147)
47 GENOMED ss1966861785 Sep 28, 2016 (149)
48 JJLAB ss2019959008 Sep 28, 2016 (149)
49 USC_VALOUEV ss2147982484 Oct 11, 2018 (152)
50 HUMAN_LONGEVITY ss2166283109 Dec 20, 2016 (150)
51 TOPMED ss2328777502 Oct 11, 2018 (152)
52 SYSTEMSBIOZJU ss2624487357 Oct 11, 2018 (152)
53 ILLUMINA ss2632572398 Oct 11, 2018 (152)
54 GRF ss2697953697 Oct 11, 2018 (152)
55 ILLUMINA ss2710681942 Oct 11, 2018 (152)
56 GNOMAD ss2760939925 Oct 11, 2018 (152)
57 SWEGEN ss2987700851 Oct 11, 2018 (152)
58 ILLUMINA ss3021131773 Oct 11, 2018 (152)
59 BIOINF_KMB_FNS_UNIBA ss3023737051 Nov 08, 2017 (151)
60 TOPMED ss3091275354 Nov 08, 2017 (151)
61 CSHL ss3343697915 Oct 11, 2018 (152)
62 ILLUMINA ss3626200353 Oct 11, 2018 (152)
63 ILLUMINA ss3630605504 Oct 11, 2018 (152)
64 ILLUMINA ss3632908905 Oct 11, 2018 (152)
65 ILLUMINA ss3633604162 Oct 11, 2018 (152)
66 ILLUMINA ss3634347328 Oct 11, 2018 (152)
67 ILLUMINA ss3635297643 Oct 11, 2018 (152)
68 ILLUMINA ss3636026996 Oct 11, 2018 (152)
69 ILLUMINA ss3637048126 Oct 11, 2018 (152)
70 ILLUMINA ss3637785009 Oct 11, 2018 (152)
71 ILLUMINA ss3640054685 Oct 11, 2018 (152)
72 URBANLAB ss3646784896 Oct 11, 2018 (152)
73 ILLUMINA ss3651465284 Oct 11, 2018 (152)
74 EGCUT_WGS ss3655641989 Jul 12, 2019 (153)
75 EVA_DECODE ss3687718624 Jul 12, 2019 (153)
76 ILLUMINA ss3725061482 Jul 12, 2019 (153)
77 ACPOP ss3727461160 Jul 12, 2019 (153)
78 ILLUMINA ss3744648242 Jul 12, 2019 (153)
79 EVA ss3746770599 Jul 12, 2019 (153)
80 PAGE_CC ss3770837840 Jul 12, 2019 (153)
81 ILLUMINA ss3772149429 Jul 12, 2019 (153)
82 PACBIO ss3783557052 Jul 12, 2019 (153)
83 PACBIO ss3789190843 Jul 12, 2019 (153)
84 PACBIO ss3794062810 Jul 12, 2019 (153)
85 KHV_HUMAN_GENOMES ss3799773507 Jul 12, 2019 (153)
86 EVA ss3826409676 Apr 25, 2020 (154)
87 EVA ss3836598809 Apr 25, 2020 (154)
88 EVA ss3842007808 Apr 25, 2020 (154)
89 SGDP_PRJ ss3849941551 Apr 25, 2020 (154)
90 KRGDB ss3895133100 Apr 25, 2020 (154)
91 KOGIC ss3945583378 Apr 25, 2020 (154)
92 GNOMAD ss4003108752 Apr 27, 2021 (155)
93 EVA ss4016936199 Apr 27, 2021 (155)
94 TOPMED ss4467166203 Apr 27, 2021 (155)
95 TOMMO_GENOMICS ss5146327556 Apr 27, 2021 (155)
96 gnomAD - Genomes NC_000001.11 - 149849089 Apr 27, 2021 (155)
97 HapMap NC_000001.11 - 149849089 Apr 25, 2020 (154)
98 Korean Genome Project NC_000001.11 - 149849089 Apr 25, 2020 (154)
99 The PAGE Study NC_000001.11 - 149849089 Jul 12, 2019 (153)
100 TopMed NC_000001.11 - 149849089 Apr 27, 2021 (155)
101 ALFA NC_000001.11 - 149849089 Apr 27, 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)
rs56900878 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss80927783 NC_000001.8:146633728:G:G NC_000001.11:149849088:C:G (self)
ss108576779, ss111111835, ss119016750, ss164057399, ss165177968, ss167097523, ss199048736, ss205044352, ss253485933, ss276040707, ss284147324, ss290631589, ss479675941, ss1585033325 NC_000001.9:148087279:G:G NC_000001.11:149849088:C:G (self)
ss218636481, ss230722047, ss238372086, ss479681323, ss480205904, ss484636531, ss536756315, ss554662007, ss648394886, ss778342335, ss782765093, ss783731397, ss832017420, ss833796946, ss975652445, ss1068246978, ss1292799622, ss1425970480, ss1574375497, ss1601149129, ss1644143162, ss1751869501, ss1795050783, ss1918884087, ss1958313187, ss1966861785, ss2019959008, ss2147982484, ss2328777502, ss2624487357, ss2632572398, ss2697953697, ss2710681942, ss2760939925, ss2987700851, ss3021131773, ss3343697915, ss3626200353, ss3630605504, ss3632908905, ss3633604162, ss3634347328, ss3635297643, ss3636026996, ss3637048126, ss3637785009, ss3640054685, ss3651465284, ss3655641989, ss3727461160, ss3744648242, ss3746770599, ss3772149429, ss3783557052, ss3789190843, ss3794062810, ss3826409676, ss3836598809, ss3849941551, ss3895133100, ss4016936199, ss5146327556 NC_000001.10:149820655:G:G NC_000001.11:149849088:C:G (self)
26089503, 170882, 1961379, 59309, 19322676, 30772538, 589394696, ss2166283109, ss3023737051, ss3091275354, ss3646784896, ss3687718624, ss3725061482, ss3770837840, ss3799773507, ss3842007808, ss3945583378, ss4003108752, ss4467166203 NC_000001.11:149849088:C:G NC_000001.11:149849088:C:G (self)
ss99248490, ss102783218, ss155716770, ss160035043, ss171870506 NT_004487.19:1309297:G:G NC_000001.11:149849088:C:G (self)
ss18248919 NT_032962.5:311010:G:G NC_000001.11:149849088:C: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 rs12119601

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