Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

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.

rs1862942

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr3:120646163 (GRCh38.p12) 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=0.17416 (21869/125568, TOPMED)
A=0.2185 (17195/78696, PAGE_STUDY)
A=0.1643 (5152/31366, GnomAD) (+ 6 more)
A=0.169 (847/5008, 1000G)
A=0.073 (327/4480, Estonian)
A=0.105 (404/3854, ALSPAC)
A=0.107 (395/3708, TWINSUK)
A=0.10 (58/600, NorthernSweden)
A=0.04 (8/212, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HGD : 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.p12 chr 3 NC_000003.12:g.120646163G>A
GRCh37.p13 chr 3 NC_000003.11:g.120365010G>A
HGD RefSeqGene NG_011957.1:g.41319C>T
Gene: HGD, homogentisate 1,2-dioxygenase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HGD transcript NM_000187.4:c. N/A Intron Variant
HGD transcript variant X1 XM_005247412.2:c. N/A Intron Variant
HGD transcript variant X2 XM_005247413.2:c. N/A Intron Variant
HGD transcript variant X5 XM_005247414.5:c. N/A Intron Variant
HGD transcript variant X4 XM_011512746.2:c. N/A Intron Variant
HGD transcript variant X3 XM_017006277.2:c. 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

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 125568 G=0.82584 A=0.17416
The PAGE Study Global Study-wide 78696 G=0.7815 A=0.2185
The PAGE Study AfricanAmerican Sub 32516 G=0.6351 A=0.3649
The PAGE Study Mexican Sub 10808 G=0.9229 A=0.0771
The PAGE Study Asian Sub 8318 G=0.988 A=0.012
The PAGE Study PuertoRican Sub 7916 G=0.822 A=0.178
The PAGE Study NativeHawaiian Sub 4532 G=0.815 A=0.185
The PAGE Study Cuban Sub 4230 G=0.870 A=0.130
The PAGE Study Dominican Sub 3828 G=0.751 A=0.249
The PAGE Study CentralAmerican Sub 2450 G=0.898 A=0.102
The PAGE Study SouthAmerican Sub 1982 G=0.926 A=0.074
The PAGE Study NativeAmerican Sub 1260 G=0.875 A=0.125
The PAGE Study SouthAsian Sub 856 G=0.89 A=0.11
gnomAD - Genomes Global Study-wide 31366 G=0.8357 A=0.1643
gnomAD - Genomes European Sub 18894 G=0.9148 A=0.0852
gnomAD - Genomes African Sub 8690 G=0.620 A=0.380
gnomAD - Genomes East Asian Sub 1556 G=0.978 A=0.022
gnomAD - Genomes Other Sub 1088 G=0.898 A=0.102
gnomAD - Genomes American Sub 848 G=0.93 A=0.07
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.88 A=0.12
1000Genomes Global Study-wide 5008 G=0.831 A=0.169
1000Genomes African Sub 1322 G=0.573 A=0.427
1000Genomes East Asian Sub 1008 G=0.985 A=0.015
1000Genomes Europe Sub 1006 G=0.921 A=0.079
1000Genomes South Asian Sub 978 G=0.88 A=0.12
1000Genomes American Sub 694 G=0.90 A=0.10
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.927 A=0.073
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.895 A=0.105
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.893 A=0.107
Northern Sweden ACPOP Study-wide 600 G=0.90 A=0.10
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.96 A=0.04
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 Note
GRCh38.p12 chr 3 NC_000003.12:g.120646163= NC_000003.12:g.12064616...

NC_000003.12:g.120646163G>A

GRCh37.p13 chr 3 NC_000003.11:g.120365010= NC_000003.11:g.12036501...

NC_000003.11:g.120365010G>A

HGD RefSeqGene NG_011957.1:g.41319= NG_011957.1:g.41319C>T
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#.

57 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2737326 Jan 12, 2001 (92)
2 SC_JCM ss3859271 Sep 28, 2001 (100)
3 SC_JCM ss6117852 Feb 20, 2003 (111)
4 PERLEGEN ss23258734 Sep 20, 2004 (123)
5 ABI ss42108386 Mar 15, 2006 (126)
6 AFFY ss66352818 Nov 30, 2006 (127)
7 AFFY ss76065882 Dec 08, 2007 (130)
8 KRIBB_YJKIM ss81601898 Dec 15, 2007 (131)
9 BCMHGSC_JDW ss92257349 Mar 23, 2008 (130)
10 GMI ss156111229 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss164110642 Jul 04, 2010 (132)
12 AFFY ss172379556 Jul 04, 2010 (132)
13 BUSHMAN ss203091259 Jul 04, 2010 (132)
14 GMI ss277320339 May 04, 2012 (137)
15 PJP ss292898984 May 09, 2011 (134)
16 1000GENOMES ss331004709 May 09, 2011 (134)
17 TISHKOFF ss556900105 Apr 25, 2013 (138)
18 SSMP ss650612002 Apr 25, 2013 (138)
19 EVA-GONL ss979083744 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1070777233 Aug 21, 2014 (142)
21 1000GENOMES ss1305859489 Aug 21, 2014 (142)
22 DDI ss1429564036 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1580152469 Apr 01, 2015 (144)
24 EVA_DECODE ss1588565955 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1608059317 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1651053350 Apr 01, 2015 (144)
27 EVA_MGP ss1711029889 Apr 01, 2015 (144)
28 EVA_SVP ss1712606997 Apr 01, 2015 (144)
29 HAMMER_LAB ss1799930610 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1922310063 Feb 12, 2016 (147)
31 ILLUMINA ss1958598402 Feb 12, 2016 (147)
32 GENOMED ss1969505762 Jul 19, 2016 (147)
33 JJLAB ss2021722838 Sep 14, 2016 (149)
34 USC_VALOUEV ss2149814970 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2255253370 Dec 20, 2016 (150)
36 TOPMED ss2422577785 Dec 20, 2016 (150)
37 GNOMAD ss2798279998 Nov 08, 2017 (151)
38 AFFY ss2985267483 Nov 08, 2017 (151)
39 AFFY ss2985890763 Nov 08, 2017 (151)
40 SWEGEN ss2993074359 Nov 08, 2017 (151)
41 ILLUMINA ss3022278763 Nov 08, 2017 (151)
42 BIOINF_KMB_FNS_UNIBA ss3024628237 Nov 08, 2017 (151)
43 CSHL ss3345231369 Nov 08, 2017 (151)
44 TOPMED ss3403598581 Nov 08, 2017 (151)
45 OMUKHERJEE_ADBS ss3646291543 Oct 12, 2018 (152)
46 ILLUMINA ss3652757286 Oct 12, 2018 (152)
47 ILLUMINA ss3654036555 Oct 12, 2018 (152)
48 EGCUT_WGS ss3661001071 Jul 13, 2019 (153)
49 EVA_DECODE ss3710145402 Jul 13, 2019 (153)
50 ILLUMINA ss3726050082 Jul 13, 2019 (153)
51 ACPOP ss3730286687 Jul 13, 2019 (153)
52 EVA ss3760599307 Jul 13, 2019 (153)
53 PAGE_CC ss3771058422 Jul 13, 2019 (153)
54 PACBIO ss3784443275 Jul 13, 2019 (153)
55 PACBIO ss3789940729 Jul 13, 2019 (153)
56 PACBIO ss3794815164 Jul 13, 2019 (153)
57 KHV_HUMAN_GENOMES ss3803735586 Jul 13, 2019 (153)
58 1000Genomes NC_000003.11 - 120365010 Oct 12, 2018 (152)
59 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 120365010 Oct 12, 2018 (152)
60 Genetic variation in the Estonian population NC_000003.11 - 120365010 Oct 12, 2018 (152)
61 gnomAD - Genomes NC_000003.11 - 120365010 Jul 13, 2019 (153)
62 Northern Sweden NC_000003.11 - 120365010 Jul 13, 2019 (153)
63 The PAGE Study NC_000003.12 - 120646163 Jul 13, 2019 (153)
64 TopMed NC_000003.12 - 120646163 Oct 12, 2018 (152)
65 UK 10K study - Twins NC_000003.11 - 120365010 Oct 12, 2018 (152)
66 A Vietnamese Genetic Variation Database NC_000003.11 - 120365010 Jul 13, 2019 (153)
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)
rs56456627 May 25, 2008 (130)
rs58285162 Dec 02, 2009 (131)
rs61799352 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66352818, ss76065882, ss92257349, ss164110642, ss172379556, ss203091259, ss277320339, ss292898984, ss1588565955, ss1712606997 NC_000003.10:121847699:G:A NC_000003.12:120646162:G:A (self)
17112162, 9532205, 6739319, 46815519, 3571552, 9532205, 2077907, ss331004709, ss556900105, ss650612002, ss979083744, ss1070777233, ss1305859489, ss1429564036, ss1580152469, ss1608059317, ss1651053350, ss1711029889, ss1799930610, ss1922310063, ss1958598402, ss1969505762, ss2021722838, ss2149814970, ss2422577785, ss2798279998, ss2985267483, ss2985890763, ss2993074359, ss3022278763, ss3345231369, ss3646291543, ss3652757286, ss3654036555, ss3661001071, ss3730286687, ss3760599307, ss3784443275, ss3789940729, ss3794815164 NC_000003.11:120365009:G:A NC_000003.12:120646162:G:A (self)
279891, 261520635, ss2255253370, ss3024628237, ss3403598581, ss3710145402, ss3726050082, ss3771058422, ss3803735586 NC_000003.12:120646162:G:A NC_000003.12:120646162:G:A (self)
ss2737326, ss3859271, ss6117852, ss23258734, ss42108386, ss81601898, ss156111229 NT_005612.16:26860155:G:A NC_000003.12:120646162: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 rs1862942

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.post246+3cda961