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.

rs4823006

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr22:29055683 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.41024 (51513/125568, TOPMED)
G=0.3913 (12081/30874, GnomAD)
G=0.454 (2275/5008, 1000G) (+ 3 more)
G=0.361 (1619/4480, Estonian)
G=0.450 (1736/3854, ALSPAC)
G=0.445 (1651/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ZNRF3 : 3 Prime UTR Variant
Publications
11 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 22 NC_000022.11:g.29055683A>G
GRCh37.p13 chr 22 NC_000022.10:g.29451671A>G
Gene: ZNRF3, zinc and ring finger 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ZNRF3 transcript variant 2 NM_032173.3:c. N/A 3 Prime UTR Variant
ZNRF3 transcript variant 1 NM_001206998.1:c. N/A 3 Prime UTR Variant
ZNRF3 transcript variant X4 XM_011530437.1:c. N/A 3 Prime UTR Variant
ZNRF3 transcript variant X1 XM_017028990.1:c. N/A 3 Prime UTR Variant
ZNRF3 transcript variant X2 XM_011530435.2:c. N/A 3 Prime UTR Variant
ZNRF3 transcript variant X5 XM_011530438.2:c. N/A 3 Prime UTR Variant
ZNRF3 transcript variant X3 XM_011530436.3:c. N/A 3 Prime UTR Variant
ZNRF3 transcript variant X6 XM_024452286.1:c. N/A 3 Prime UTR 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 A=0.58976 G=0.41024
gnomAD - Genomes Global Study-wide 30874 A=0.6087 G=0.3913
gnomAD - Genomes European Sub 18446 A=0.5816 G=0.4184
gnomAD - Genomes African Sub 8700 A=0.713 G=0.287
gnomAD - Genomes East Asian Sub 1616 A=0.450 G=0.550
gnomAD - Genomes Other Sub 980 A=0.56 G=0.44
gnomAD - Genomes American Sub 832 A=0.54 G=0.46
gnomAD - Genomes Ashkenazi Jewish Sub 300 A=0.46 G=0.54
1000Genomes Global Study-wide 5008 A=0.546 G=0.454
1000Genomes African Sub 1322 A=0.721 G=0.279
1000Genomes East Asian Sub 1008 A=0.462 G=0.538
1000Genomes Europe Sub 1006 A=0.573 G=0.427
1000Genomes South Asian Sub 978 A=0.40 G=0.60
1000Genomes American Sub 694 A=0.51 G=0.49
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.639 G=0.361
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.550 G=0.450
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.555 G=0.445
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 Note
GRCh38.p12 chr 22 NC_000022.11:g.29055683A= NC_000022.11:g.29055683A>G
GRCh37.p13 chr 22 NC_000022.10:g.29451671A= NC_000022.10:g.29451671A>G
ZNRF3 transcript variant X3 XM_011530436.3:c.*2061A= XM_011530436.3:c.*2061A>G
ZNRF3 transcript variant 2 NM_032173.3:c.*2061A= NM_032173.3:c.*2061A>G
ZNRF3 transcript variant X5 XM_011530438.2:c.*2061A= XM_011530438.2:c.*2061A>G
ZNRF3 transcript variant X2 XM_011530435.2:c.*2061A= XM_011530435.2:c.*2061A>G
ZNRF3 transcript variant X4 XM_011530437.1:c.*2061A= XM_011530437.1:c.*2061A>G
ZNRF3 transcript variant X1 XM_017028990.1:c.*2061A= XM_017028990.1:c.*2061A>G
ZNRF3 transcript variant 1 NM_001206998.1:c.*2061A= NM_001206998.1:c.*2061A>G
ZNRF3 transcript variant X6 XM_024452286.1:c.*2061A= XM_024452286.1:c.*2061A>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#.

90 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6660782 Feb 20, 2003 (111)
2 BCM_SSAHASNP ss10998623 Jul 11, 2003 (116)
3 SC_SNP ss13368436 Dec 05, 2003 (119)
4 ABI ss44324293 Mar 13, 2006 (126)
5 SI_EXO ss52079411 Oct 14, 2006 (127)
6 ILLUMINA ss65743123 Oct 14, 2006 (127)
7 AFFY ss66451954 Nov 29, 2006 (127)
8 PERLEGEN ss69274753 May 17, 2007 (127)
9 ILLUMINA ss74859480 Dec 06, 2007 (129)
10 AFFY ss76242772 Dec 06, 2007 (129)
11 KRIBB_YJKIM ss82134942 Dec 16, 2007 (130)
12 HUMANGENOME_JCVI ss96120643 Feb 05, 2009 (130)
13 BGI ss106223374 Feb 05, 2009 (130)
14 1000GENOMES ss112600830 Jan 25, 2009 (130)
15 1000GENOMES ss114124689 Jan 25, 2009 (130)
16 ENSEMBL ss144085962 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss167823166 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss169075951 Jul 04, 2010 (132)
19 COMPLETE_GENOMICS ss171908606 Jul 04, 2010 (132)
20 ILLUMINA ss173830658 Jul 04, 2010 (132)
21 BUSHMAN ss204071532 Jul 04, 2010 (132)
22 1000GENOMES ss228652848 Jul 14, 2010 (132)
23 1000GENOMES ss238048312 Jul 15, 2010 (132)
24 1000GENOMES ss244172307 Jul 15, 2010 (132)
25 BL ss255875231 May 09, 2011 (134)
26 GMI ss283616203 May 04, 2012 (137)
27 GMI ss287560498 Apr 25, 2013 (138)
28 PJP ss292750106 May 09, 2011 (134)
29 ILLUMINA ss410936581 Sep 17, 2011 (135)
30 ILLUMINA ss479170223 May 04, 2012 (137)
31 ILLUMINA ss484300559 May 04, 2012 (137)
32 EXOME_CHIP ss491569919 May 04, 2012 (137)
33 ILLUMINA ss532764888 Sep 08, 2015 (146)
34 TISHKOFF ss566603734 Apr 25, 2013 (138)
35 SSMP ss662534859 Apr 25, 2013 (138)
36 ILLUMINA ss779473759 Sep 08, 2015 (146)
37 ILLUMINA ss780685388 Sep 08, 2015 (146)
38 ILLUMINA ss780914631 Sep 08, 2015 (146)
39 ILLUMINA ss783358875 Sep 08, 2015 (146)
40 ILLUMINA ss834943691 Sep 08, 2015 (146)
41 EVA-GONL ss995294982 Aug 21, 2014 (142)
42 JMKIDD_LAB ss1082618629 Aug 21, 2014 (142)
43 1000GENOMES ss1366956557 Aug 21, 2014 (142)
44 HAMMER_LAB ss1397784168 Sep 08, 2015 (146)
45 DDI ss1429241284 Apr 01, 2015 (144)
46 EVA_GENOME_DK ss1579730956 Apr 01, 2015 (144)
47 EVA_UK10K_ALSPAC ss1639883239 Apr 01, 2015 (144)
48 EVA_UK10K_TWINSUK ss1682877272 Apr 01, 2015 (144)
49 EVA_DECODE ss1699364060 Apr 01, 2015 (144)
50 EVA_SVP ss1713736880 Apr 01, 2015 (144)
51 ILLUMINA ss1752417693 Sep 08, 2015 (146)
52 HAMMER_LAB ss1809765134 Sep 08, 2015 (146)
53 ILLUMINA ss1917954539 Feb 12, 2016 (147)
54 WEILL_CORNELL_DGM ss1938861311 Feb 12, 2016 (147)
55 ILLUMINA ss1946584484 Feb 12, 2016 (147)
56 ILLUMINA ss1959973576 Feb 12, 2016 (147)
57 GENOMED ss1969261614 Jul 19, 2016 (147)
58 JJLAB ss2030202479 Sep 14, 2016 (149)
59 ILLUMINA ss2094811193 Dec 20, 2016 (150)
60 ILLUMINA ss2095121606 Dec 20, 2016 (150)
61 USC_VALOUEV ss2158818042 Dec 20, 2016 (150)
62 HUMAN_LONGEVITY ss2246908138 Dec 20, 2016 (150)
63 TOPMED ss2413844218 Dec 20, 2016 (150)
64 SYSTEMSBIOZJU ss2629599651 Nov 08, 2017 (151)
65 ILLUMINA ss2633871166 Nov 08, 2017 (151)
66 ILLUMINA ss2633871167 Nov 08, 2017 (151)
67 ILLUMINA ss2633871168 Nov 08, 2017 (151)
68 GRF ss2704568930 Nov 08, 2017 (151)
69 ILLUMINA ss2710955394 Nov 08, 2017 (151)
70 GNOMAD ss2973791318 Nov 08, 2017 (151)
71 AFFY ss2985236383 Nov 08, 2017 (151)
72 AFFY ss2985853003 Nov 08, 2017 (151)
73 SWEGEN ss3019216226 Nov 08, 2017 (151)
74 ILLUMINA ss3022180092 Nov 08, 2017 (151)
75 BIOINF_KMB_FNS_UNIBA ss3028938754 Nov 08, 2017 (151)
76 CSHL ss3352812171 Nov 08, 2017 (151)
77 TOPMED ss3375820159 Nov 08, 2017 (151)
78 ILLUMINA ss3628521252 Oct 12, 2018 (152)
79 ILLUMINA ss3628521253 Oct 12, 2018 (152)
80 ILLUMINA ss3631822874 Oct 12, 2018 (152)
81 ILLUMINA ss3634864709 Oct 12, 2018 (152)
82 ILLUMINA ss3638379221 Oct 12, 2018 (152)
83 ILLUMINA ss3640572012 Oct 12, 2018 (152)
84 ILLUMINA ss3643339232 Oct 12, 2018 (152)
85 ILLUMINA ss3644798459 Oct 12, 2018 (152)
86 OMUKHERJEE_ADBS ss3646565921 Oct 12, 2018 (152)
87 URBANLAB ss3651168480 Oct 12, 2018 (152)
88 ILLUMINA ss3652642159 Oct 12, 2018 (152)
89 ILLUMINA ss3652642160 Oct 12, 2018 (152)
90 ILLUMINA ss3654004273 Oct 12, 2018 (152)
91 1000Genomes NC_000022.10 - 29451671 Oct 12, 2018 (152)
92 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 29451671 Oct 12, 2018 (152)
93 Genetic variation in the Estonian population NC_000022.10 - 29451671 Oct 12, 2018 (152)
94 gnomAD - Genomes NC_000022.10 - 29451671 Oct 12, 2018 (152)
95 TopMed NC_000022.11 - 29055683 Oct 12, 2018 (152)
96 UK 10K study - Twins NC_000022.10 - 29451671 Oct 12, 2018 (152)
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)
rs61337029 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss112600830, ss114124689, ss167823166, ss169075951, ss171908606, ss204071532, ss255875231, ss283616203, ss287560498, ss292750106, ss484300559, ss1397784168, ss1699364060, ss1713736880, ss3643339232 NC_000022.9:27781670:A:G NC_000022.11:29055682:A:G (self)
80500757, 44525634, 31451562, 127145184, 44525634, ss228652848, ss238048312, ss244172307, ss479170223, ss491569919, ss532764888, ss566603734, ss662534859, ss779473759, ss780685388, ss780914631, ss783358875, ss834943691, ss995294982, ss1082618629, ss1366956557, ss1429241284, ss1579730956, ss1639883239, ss1682877272, ss1752417693, ss1809765134, ss1917954539, ss1938861311, ss1946584484, ss1959973576, ss1969261614, ss2030202479, ss2094811193, ss2095121606, ss2158818042, ss2413844218, ss2629599651, ss2633871166, ss2633871167, ss2633871168, ss2704568930, ss2710955394, ss2973791318, ss2985236383, ss2985853003, ss3019216226, ss3022180092, ss3352812171, ss3628521252, ss3628521253, ss3631822874, ss3634864709, ss3638379221, ss3640572012, ss3644798459, ss3646565921, ss3652642159, ss3652642160, ss3654004273 NC_000022.10:29451670:A:G NC_000022.11:29055682:A:G (self)
238896743, ss2246908138, ss3028938754, ss3375820159, ss3651168480 NC_000022.11:29055682:A:G NC_000022.11:29055682:A:G (self)
ss10998623, ss13368436 NT_011520.9:8842239:A:G NC_000022.11:29055682:A:G (self)
ss52079411 NT_011520.10:8842239:A:G NC_000022.11:29055682:A:G (self)
ss6660782, ss44324293, ss65743123, ss66451954, ss69274753, ss74859480, ss76242772, ss82134942, ss96120643, ss106223374, ss144085962, ss173830658, ss410936581 NT_011520.12:8842239:A:G NC_000022.11:29055682: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.

11 citations for rs4823006
PMID Title Author Year Journal
20935629 Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. Heid IM et al. 2010 Nature genetics
21466928 Genetics and epigenetics of obesity. Herrera BM et al. 2011 Maturitas
21525879 Pleiotropy of type 2 diabetes with obesity. Hasstedt SJ et al. 2011 Journal of human genetics
22044751 Heritability and genome-wide association analysis of renal sinus fat accumulation in the Framingham Heart Study. Foster MC et al. 2011 BMC medical genetics
22651247 Sex differences in human adipose tissues - the biology of pear shape. Karastergiou K et al. 2012 Biology of sex differences
23221025 Replication study of 15 recently published Loci for body fat distribution in the Japanese population. Hotta K et al. 2013 Journal of atherosclerosis and thrombosis
26848030 Effects of Obesity Related Genetic Variations on Visceral and Subcutaneous Fat Distribution in a Chinese Population. Wang T et al. 2016 Scientific reports
27104953 Effects of Genetic Loci Associated with Central Obesity on Adipocyte Lipolysis. Strawbridge RJ et al. 2016 PloS one
27195708 Investigation of Genetic Variation Underlying Central Obesity amongst South Asians. Scott WR et al. 2016 PloS one
27427429 Commentary: Two-sample Mendelian randomization: opportunities and challenges. Lawlor DA et al. 2016 International journal of epidemiology
27824919 Primary Angle Closure and Sequence Variants within MicroRNA Binding Sites of Genes Involved in Eye Development. Shi H et al. 2016 PloS one

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.post104+4a6ee9c