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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.

rs2562796

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:190248283 (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
T>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.315240 (83441/264690, TOPMED)
G=0.298446 (41789/140022, GnomAD)
G=0.47466 (13412/28256, 14KJPN) (+ 18 more)
G=0.26090 (6704/25696, ALFA)
G=0.48174 (8074/16760, 8.3KJPN)
G=0.3413 (2186/6404, 1000G_30x)
G=0.3411 (1708/5008, 1000G)
G=0.1875 (840/4480, Estonian)
G=0.2369 (913/3854, ALSPAC)
G=0.2470 (916/3708, TWINSUK)
G=0.4993 (1463/2930, KOREAN)
T=0.4962 (909/1832, Korea1K)
G=0.3998 (714/1786, HapMap)
G=0.268 (267/998, GoNL)
G=0.280 (175/626, Chileans)
G=0.192 (115/600, NorthernSweden)
T=0.370 (117/316, SGDP_PRJ)
G=0.380 (82/216, Qatari)
G=0.453 (96/212, Vietnamese)
G=0.28 (11/40, GENOME_DK)
T=0.39 (11/28, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HIBCH : Intron Variant
Publications
1 citation
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 25696 T=0.73910 G=0.26090
European Sub 17396 T=0.76908 G=0.23092
African Sub 3624 T=0.5833 G=0.4167
African Others Sub 126 T=0.563 G=0.437
African American Sub 3498 T=0.5840 G=0.4160
Asian Sub 160 T=0.581 G=0.419
East Asian Sub 102 T=0.539 G=0.461
Other Asian Sub 58 T=0.66 G=0.34
Latin American 1 Sub 292 T=0.712 G=0.288
Latin American 2 Sub 2768 T=0.7760 G=0.2240
South Asian Sub 110 T=0.764 G=0.236
Other Sub 1346 T=0.7177 G=0.2823


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=0.684760 G=0.315240
gnomAD - Genomes Global Study-wide 140022 T=0.701554 G=0.298446
gnomAD - Genomes European Sub 75888 T=0.76903 G=0.23097
gnomAD - Genomes African Sub 41888 T=0.57861 G=0.42139
gnomAD - Genomes American Sub 13650 T=0.72322 G=0.27678
gnomAD - Genomes Ashkenazi Jewish Sub 3318 T=0.7815 G=0.2185
gnomAD - Genomes East Asian Sub 3128 T=0.5448 G=0.4552
gnomAD - Genomes Other Sub 2150 T=0.6823 G=0.3177
14KJPN JAPANESE Study-wide 28256 T=0.52534 G=0.47466
Allele Frequency Aggregator Total Global 25696 T=0.73910 G=0.26090
Allele Frequency Aggregator European Sub 17396 T=0.76908 G=0.23092
Allele Frequency Aggregator African Sub 3624 T=0.5833 G=0.4167
Allele Frequency Aggregator Latin American 2 Sub 2768 T=0.7760 G=0.2240
Allele Frequency Aggregator Other Sub 1346 T=0.7177 G=0.2823
Allele Frequency Aggregator Latin American 1 Sub 292 T=0.712 G=0.288
Allele Frequency Aggregator Asian Sub 160 T=0.581 G=0.419
Allele Frequency Aggregator South Asian Sub 110 T=0.764 G=0.236
8.3KJPN JAPANESE Study-wide 16760 T=0.51826 G=0.48174
1000Genomes_30x Global Study-wide 6404 T=0.6587 G=0.3413
1000Genomes_30x African Sub 1786 T=0.5476 G=0.4524
1000Genomes_30x Europe Sub 1266 T=0.7583 G=0.2417
1000Genomes_30x South Asian Sub 1202 T=0.7446 G=0.2554
1000Genomes_30x East Asian Sub 1170 T=0.5641 G=0.4359
1000Genomes_30x American Sub 980 T=0.740 G=0.260
1000Genomes Global Study-wide 5008 T=0.6589 G=0.3411
1000Genomes African Sub 1322 T=0.5416 G=0.4584
1000Genomes East Asian Sub 1008 T=0.5704 G=0.4296
1000Genomes Europe Sub 1006 T=0.7565 G=0.2435
1000Genomes South Asian Sub 978 T=0.755 G=0.245
1000Genomes American Sub 694 T=0.735 G=0.265
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.8125 G=0.1875
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.7631 G=0.2369
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.7530 G=0.2470
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.5007 G=0.4993
Korean Genome Project KOREAN Study-wide 1832 T=0.4962 G=0.5038
HapMap Global Study-wide 1786 T=0.6002 G=0.3998
HapMap American Sub 770 T=0.695 G=0.305
HapMap African Sub 586 T=0.483 G=0.517
HapMap Asian Sub 254 T=0.520 G=0.480
HapMap Europe Sub 176 T=0.693 G=0.307
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.732 G=0.268
Chileans Chilean Study-wide 626 T=0.720 G=0.280
Northern Sweden ACPOP Study-wide 600 T=0.808 G=0.192
SGDP_PRJ Global Study-wide 316 T=0.370 G=0.630
Qatari Global Study-wide 216 T=0.620 G=0.380
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.547 G=0.453
The Danish reference pan genome Danish Study-wide 40 T=0.72 G=0.28
Siberian Global Study-wide 28 T=0.39 G=0.61
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 2 NC_000002.12:g.190248283T>G
GRCh37.p13 chr 2 NC_000002.11:g.191113009T>G
HIBCH RefSeqGene NG_017062.1:g.76763A>C
Gene: HIBCH, 3-hydroxyisobutyryl-CoA hydrolase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HIBCH transcript variant 1 NM_014362.4:c.750+1357A>C N/A Intron Variant
HIBCH transcript variant 2 NM_198047.3:c.750+1357A>C N/A Intron Variant
HIBCH transcript variant X1 XM_011510953.3:c.750+1357…

XM_011510953.3:c.750+1357A>C

N/A Intron Variant
HIBCH transcript variant X4 XM_011510954.2:c.252+1357…

XM_011510954.2:c.252+1357A>C

N/A Intron Variant
HIBCH transcript variant X2 XM_047443905.1:c.750+1357…

XM_047443905.1:c.750+1357A>C

N/A Intron Variant
HIBCH transcript variant X3 XR_922903.3: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 T= G
GRCh38.p14 chr 2 NC_000002.12:g.190248283= NC_000002.12:g.190248283T>G
GRCh37.p13 chr 2 NC_000002.11:g.191113009= NC_000002.11:g.191113009T>G
HIBCH RefSeqGene NG_017062.1:g.76763= NG_017062.1:g.76763A>C
HIBCH transcript variant 1 NM_014362.3:c.750+1357= NM_014362.3:c.750+1357A>C
HIBCH transcript variant 1 NM_014362.4:c.750+1357= NM_014362.4:c.750+1357A>C
HIBCH transcript variant 2 NM_198047.2:c.750+1357= NM_198047.2:c.750+1357A>C
HIBCH transcript variant 2 NM_198047.3:c.750+1357= NM_198047.3:c.750+1357A>C
HIBCH transcript variant X1 XM_005246461.1:c.750+1357= XM_005246461.1:c.750+1357A>C
HIBCH transcript variant X1 XM_011510953.3:c.750+1357= XM_011510953.3:c.750+1357A>C
HIBCH transcript variant X4 XM_011510954.2:c.252+1357= XM_011510954.2:c.252+1357A>C
HIBCH transcript variant X2 XM_047443905.1:c.750+1357= XM_047443905.1:c.750+1357A>C
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#.

74 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss3597735 Sep 28, 2001 (100)
2 CSHL-HAPMAP ss17637517 Feb 27, 2004 (120)
3 PERLEGEN ss23886891 Sep 20, 2004 (123)
4 ABI ss44208079 Mar 13, 2006 (126)
5 AFFY ss66005674 Dec 02, 2006 (127)
6 AFFY ss66233085 Dec 02, 2006 (127)
7 AFFY ss76379006 Dec 07, 2007 (129)
8 HGSV ss77689190 Dec 07, 2007 (129)
9 HGSV ss80405044 Dec 15, 2007 (130)
10 KRIBB_YJKIM ss81818983 Dec 15, 2007 (130)
11 HGSV ss84666207 Dec 15, 2007 (130)
12 BGI ss106149600 Feb 05, 2009 (130)
13 1000GENOMES ss111431548 Jan 25, 2009 (130)
14 ILLUMINA-UK ss118017502 Feb 14, 2009 (130)
15 GMI ss158113918 Dec 01, 2009 (131)
16 ENSEMBL ss161218493 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss165130864 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss165759962 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss167497728 Jul 04, 2010 (132)
20 AFFY ss173424714 Jul 04, 2010 (132)
21 BUSHMAN ss201526939 Jul 04, 2010 (132)
22 1000GENOMES ss219720728 Jul 14, 2010 (132)
23 1000GENOMES ss231520710 Jul 14, 2010 (132)
24 1000GENOMES ss238997147 Jul 15, 2010 (132)
25 BL ss253769064 May 09, 2011 (134)
26 GMI ss276836552 May 04, 2012 (137)
27 GMI ss284509175 Apr 25, 2013 (138)
28 PJP ss292448499 May 09, 2011 (134)
29 TISHKOFF ss556113498 Apr 25, 2013 (138)
30 SSMP ss649776142 Apr 25, 2013 (138)
31 EVA-GONL ss977778574 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1069805210 Aug 21, 2014 (142)
33 1000GENOMES ss1300934953 Aug 21, 2014 (142)
34 DDI ss1428859094 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1579252986 Apr 01, 2015 (144)
36 EVA_DECODE ss1587224708 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1605418710 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1648412743 Apr 01, 2015 (144)
39 EVA_SVP ss1712518426 Apr 01, 2015 (144)
40 HAMMER_LAB ss1798096415 Sep 08, 2015 (146)
41 WEILL_CORNELL_DGM ss1921026884 Feb 12, 2016 (147)
42 GENOMED ss1968983074 Jul 19, 2016 (147)
43 JJLAB ss2021054638 Sep 14, 2016 (149)
44 USC_VALOUEV ss2149119523 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2237645742 Dec 20, 2016 (150)
46 SYSTEMSBIOZJU ss2625030309 Nov 08, 2017 (151)
47 GRF ss2703762212 Nov 08, 2017 (151)
48 GNOMAD ss2784274379 Nov 08, 2017 (151)
49 SWEGEN ss2991072284 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3024287987 Nov 08, 2017 (151)
51 CSHL ss3344665158 Nov 08, 2017 (151)
52 EGCUT_WGS ss3658954688 Jul 13, 2019 (153)
53 EVA_DECODE ss3705674317 Jul 13, 2019 (153)
54 ACPOP ss3729220829 Jul 13, 2019 (153)
55 EVA ss3757875019 Jul 13, 2019 (153)
56 KHV_HUMAN_GENOMES ss3802233354 Jul 13, 2019 (153)
57 EVA ss3827418173 Apr 25, 2020 (154)
58 SGDP_PRJ ss3854234452 Apr 25, 2020 (154)
59 KRGDB ss3899901362 Apr 25, 2020 (154)
60 KOGIC ss3949739440 Apr 25, 2020 (154)
61 TOPMED ss4538268023 Apr 26, 2021 (155)
62 TOMMO_GENOMICS ss5155689085 Apr 26, 2021 (155)
63 1000G_HIGH_COVERAGE ss5251409816 Oct 12, 2022 (156)
64 EVA ss5334900035 Oct 12, 2022 (156)
65 HUGCELL_USP ss5451087591 Oct 12, 2022 (156)
66 EVA ss5506737399 Oct 12, 2022 (156)
67 1000G_HIGH_COVERAGE ss5528432075 Oct 12, 2022 (156)
68 SANFORD_IMAGENETICS ss5630604258 Oct 12, 2022 (156)
69 TOMMO_GENOMICS ss5686334990 Oct 12, 2022 (156)
70 YY_MCH ss5803076071 Oct 12, 2022 (156)
71 EVA ss5821352495 Oct 12, 2022 (156)
72 EVA ss5852884471 Oct 12, 2022 (156)
73 EVA ss5933991686 Oct 12, 2022 (156)
74 EVA ss5956845523 Oct 12, 2022 (156)
75 1000Genomes NC_000002.11 - 191113009 Oct 11, 2018 (152)
76 1000Genomes_30x NC_000002.12 - 190248283 Oct 12, 2022 (156)
77 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 191113009 Oct 11, 2018 (152)
78 Chileans NC_000002.11 - 191113009 Apr 25, 2020 (154)
79 Genetic variation in the Estonian population NC_000002.11 - 191113009 Oct 11, 2018 (152)
80 The Danish reference pan genome NC_000002.11 - 191113009 Apr 25, 2020 (154)
81 gnomAD - Genomes NC_000002.12 - 190248283 Apr 26, 2021 (155)
82 Genome of the Netherlands Release 5 NC_000002.11 - 191113009 Apr 25, 2020 (154)
83 HapMap NC_000002.12 - 190248283 Apr 25, 2020 (154)
84 KOREAN population from KRGDB NC_000002.11 - 191113009 Apr 25, 2020 (154)
85 Korean Genome Project NC_000002.12 - 190248283 Apr 25, 2020 (154)
86 Northern Sweden NC_000002.11 - 191113009 Jul 13, 2019 (153)
87 Qatari NC_000002.11 - 191113009 Apr 25, 2020 (154)
88 SGDP_PRJ NC_000002.11 - 191113009 Apr 25, 2020 (154)
89 Siberian NC_000002.11 - 191113009 Apr 25, 2020 (154)
90 8.3KJPN NC_000002.11 - 191113009 Apr 26, 2021 (155)
91 14KJPN NC_000002.12 - 190248283 Oct 12, 2022 (156)
92 TopMed NC_000002.12 - 190248283 Apr 26, 2021 (155)
93 UK 10K study - Twins NC_000002.11 - 191113009 Oct 11, 2018 (152)
94 A Vietnamese Genetic Variation Database NC_000002.11 - 191113009 Jul 13, 2019 (153)
95 ALFA NC_000002.12 - 190248283 Apr 26, 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)
rs59481247 May 25, 2008 (130)
rs60194984 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77689190, ss80405044, ss84666207 NC_000002.9:190938514:T:G NC_000002.12:190248282:T:G (self)
ss66233085, ss76379006, ss111431548, ss118017502, ss165130864, ss165759962, ss167497728, ss173424714, ss201526939, ss253769064, ss276836552, ss284509175, ss292448499, ss1587224708, ss1712518426 NC_000002.10:190821253:T:G NC_000002.12:190248282:T:G (self)
12012560, 6637584, 238821, 4692936, 5417925, 2915639, 7078756, 2505694, 3068814, 6251432, 1635877, 13658392, 6637584, 1447329, ss219720728, ss231520710, ss238997147, ss556113498, ss649776142, ss977778574, ss1069805210, ss1300934953, ss1428859094, ss1579252986, ss1605418710, ss1648412743, ss1798096415, ss1921026884, ss1968983074, ss2021054638, ss2149119523, ss2625030309, ss2703762212, ss2784274379, ss2991072284, ss3344665158, ss3658954688, ss3729220829, ss3757875019, ss3827418173, ss3854234452, ss3899901362, ss5155689085, ss5334900035, ss5506737399, ss5630604258, ss5821352495, ss5956845523 NC_000002.11:191113008:T:G NC_000002.12:190248282:T:G (self)
15958010, 85615236, 1976016, 6117441, 20172094, 342090902, 5415731747, ss2237645742, ss3024287987, ss3705674317, ss3802233354, ss3949739440, ss4538268023, ss5251409816, ss5451087591, ss5528432075, ss5686334990, ss5803076071, ss5852884471, ss5933991686 NC_000002.12:190248282:T:G NC_000002.12:190248282:T:G (self)
ss17637517 NT_005403.14:41322424:T:G NC_000002.12:190248282:T:G (self)
ss3597735, ss23886891, ss44208079, ss66005674, ss81818983, ss106149600, ss158113918, ss161218493 NT_005403.17:41322426:T:G NC_000002.12:190248282:T:G (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs2562796
PMID Title Author Year Journal
24325914 A genome-wide gene-gene interaction analysis identifies an epistatic gene pair for lung cancer susceptibility in Han Chinese. Chu M et al. 2014 Carcinogenesis
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