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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs600718

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr3:101851531 (GRCh38.p7) 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 / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.18267 (22938/125568, TOPMED)
A=0.2145 (6636/30938, GnomAD)
A=0.199 (998/5008, 1000G) (+ 2 more)
A=0.228 (880/3854, ALSPAC)
A=0.211 (784/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NFKBIZ : Intron Variant
Publications
1 citation
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.p7 chr 3 NC_000003.12:g.101851531A>G
GRCh38.p7 chr 3 NC_000003.12:g.101851531A>T
GRCh37.p13 chr 3 NC_000003.11:g.101570375A>G
GRCh37.p13 chr 3 NC_000003.11:g.101570375A>T
Gene: NFKBIZ, NFKB inhibitor zeta (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NFKBIZ transcript variant 2 NM_001005474.2:c. N/A Intron Variant
NFKBIZ transcript variant 1 NM_031419.3: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
Trans-Omics for Precision Medicine Global Study-wide 125568 A=0.18267 T=0.81733
The Genome Aggregation Database Global Study-wide 30938 A=0.2145 T=0.7855
The Genome Aggregation Database European Sub 18478 A=0.2687 T=0.7313
The Genome Aggregation Database African Sub 8724 A=0.066 T=0.934
The Genome Aggregation Database East Asian Sub 1616 A=0.380 T=0.620
The Genome Aggregation Database Other Sub 982 A=0.29 T=0.71
The Genome Aggregation Database American Sub 836 A=0.16 T=0.84
The Genome Aggregation Database Ashkenazi Jewish Sub 302 A=0.21 T=0.79
1000Genomes Global Study-wide 5008 A=0.199 T=0.801
1000Genomes African Sub 1322 A=0.047 T=0.953
1000Genomes East Asian Sub 1008 A=0.401 T=0.599
1000Genomes Europe Sub 1006 A=0.222 T=0.778
1000Genomes South Asian Sub 978 A=0.17 T=0.83
1000Genomes American Sub 694 A=0.21 T=0.79
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.228 T=0.772
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.211 T=0.789
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 T Note
GRCh38.p7 chr 3 NC_000003.12:g.10...

NC_000003.12:g.101851531A=

NC_000003.12:g.10...

NC_000003.12:g.101851531A>G

NC_000003.12:g.10...

NC_000003.12:g.101851531A>T

GRCh37.p13 chr 3 NC_000003.11:g.10...

NC_000003.11:g.101570375A=

NC_000003.11:g.10...

NC_000003.11:g.101570375A>G

NC_000003.11:g.10...

NC_000003.11:g.101570375A>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#.

5 Frequency, 58 SubSNP submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss772681 Aug 11, 2000 (83)
2 KWOK ss878332 Oct 04, 2000 (86)
3 TSC-CSHL ss5522428 Oct 08, 2002 (108)
4 SC_JCM ss6087942 Feb 20, 2003 (111)
5 WI_SSAHASNP ss11583060 Jul 11, 2003 (116)
6 BCM_SSAHASNP ss14172242 Dec 05, 2003 (119)
7 CSHL-HAPMAP ss20150877 Feb 27, 2004 (120)
8 PERLEGEN ss24152681 Sep 20, 2004 (123)
9 ABI ss44366288 Mar 15, 2006 (126)
10 AFFY ss74851517 Aug 16, 2007 (128)
11 HGSV ss80428204 Dec 15, 2007 (130)
12 HGSV ss85937413 Dec 15, 2007 (130)
13 BCMHGSC_JDW ss92208613 Mar 24, 2008 (129)
14 BGI ss106283735 Feb 06, 2009 (130)
15 1000GENOMES ss110625032 Jan 25, 2009 (130)
16 1000GENOMES ss112239515 Jan 25, 2009 (130)
17 ILLUMINA-UK ss117202732 Feb 14, 2009 (130)
18 ENSEMBL ss139057700 Dec 01, 2009 (131)
19 GMI ss155945350 Dec 01, 2009 (131)
20 ENSEMBL ss161370864 Dec 01, 2009 (131)
21 COMPLETE_GENOMICS ss162427475 Jul 04, 2010 (132)
22 COMPLETE_GENOMICS ss163842076 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss166946945 Jul 04, 2010 (132)
24 BUSHMAN ss202937789 Jul 04, 2010 (132)
25 BCM-HGSC-SUB ss206007350 Jul 04, 2010 (132)
26 1000GENOMES ss220314949 Jul 14, 2010 (132)
27 1000GENOMES ss231949419 Jul 14, 2010 (132)
28 1000GENOMES ss239338361 Jul 15, 2010 (132)
29 BL ss253342969 May 09, 2011 (134)
30 GMI ss277266941 May 04, 2012 (137)
31 GMI ss284709337 Apr 25, 2013 (138)
32 PJP ss292871969 May 09, 2011 (134)
33 TISHKOFF ss556815148 Apr 25, 2013 (138)
34 SSMP ss650521408 Apr 25, 2013 (138)
35 EVA-GONL ss978945201 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1070670268 Aug 21, 2014 (142)
37 1000GENOMES ss1305340894 Aug 21, 2014 (142)
38 DDI ss1429519807 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1580094451 Apr 01, 2015 (144)
40 EVA_DECODE ss1588420174 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1607774886 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1650768919 Apr 01, 2015 (144)
43 HAMMER_LAB ss1799753863 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1922174989 Feb 12, 2016 (147)
45 GENOMED ss1969470877 Jul 19, 2016 (147)
46 JJLAB ss2021647333 Sep 14, 2016 (149)
47 USC_VALOUEV ss2149739804 Dec 20, 2016 (150)
48 HUMAN_LONGEVITY ss2254157235 Dec 20, 2016 (150)
49 TOPMED ss2421483218 Dec 20, 2016 (150)
50 SYSTEMSBIOZJU ss2625326782 Nov 08, 2017 (151)
51 GRF ss2705138989 Nov 08, 2017 (151)
52 GNOMAD ss2796802084 Nov 08, 2017 (151)
53 AFFY ss2985264310 Nov 08, 2017 (151)
54 SWEGEN ss2992864124 Nov 08, 2017 (151)
55 BIOINF_KMB_FNS_UNIBA ss3024589261 Nov 08, 2017 (151)
56 CSHL ss3345168429 Nov 08, 2017 (151)
57 TOPMED ss3400197531 Nov 08, 2017 (151)
58 TOPMED ss3400197532 Nov 08, 2017 (151)
59 1000Genomes NC_000003.11 - 101570375 Jul 20, 2018 (151)
60 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 101570375 Jul 20, 2018 (151)
61 The Genome Aggregation Database NC_000003.11 - 101570375 Jul 20, 2018 (151)
62 Trans-Omics for Precision Medicine NC_000003.12 - 101851531 Jul 20, 2018 (151)
63 UK 10K study - Twins NC_000003.11 - 101570375 Jul 20, 2018 (151)
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)
rs52834599 Sep 21, 2007 (128)
rs60191346 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss80428204, ss85937413 NC_000003.9:103053064:A= NC_000003.12:101851530:A= (self)
ss92208613, ss110625032, ss112239515, ss117202732, ss162427475, ss163842076, ss166946945, ss202937789, ss206007350, ss253342969, ss277266941, ss284709337, ss292871969, ss1588420174 NC_000003.10:103053064:A= NC_000003.12:101851530:A= (self)
16574080, 9219648, 137429838, 9219648, ss220314949, ss231949419, ss239338361, ss556815148, ss650521408, ss978945201, ss1070670268, ss1305340894, ss1429519807, ss1580094451, ss1607774886, ss1650768919, ss1799753863, ss1922174989, ss1969470877, ss2021647333, ss2149739804, ss2421483218, ss2625326782, ss2705138989, ss2796802084, ss2985264310, ss2992864124, ss3345168429 NC_000003.11:101570374:A= NC_000003.12:101851530:A= (self)
258654188, ss2254157235, ss3024589261, ss3400197531, ss3400197532 NC_000003.12:101851530:A= NC_000003.12:101851530:A= (self)
ss11583060 NT_005612.13:7969528:A= NC_000003.12:101851530:A= (self)
ss14172242, ss20150877 NT_005612.14:8065520:A= NC_000003.12:101851530:A= (self)
ss772681, ss878332, ss5522428, ss6087942, ss24152681, ss44366288, ss74851517, ss106283735, ss139057700, ss155945350, ss161370864 NT_005612.16:8065520:A= NC_000003.12:101851530:A= (self)
ss3400197531 NC_000003.12:101851530:A>G NC_000003.12:101851530:A>G (self)
ss80428204, ss85937413 NC_000003.9:103053064:A>T NC_000003.12:101851530:A>T (self)
ss92208613, ss110625032, ss112239515, ss117202732, ss162427475, ss163842076, ss166946945, ss202937789, ss206007350, ss253342969, ss277266941, ss284709337, ss292871969, ss1588420174 NC_000003.10:103053064:A>T NC_000003.12:101851530:A>T (self)
16574080, 9219648, 137429838, 9219648, ss220314949, ss231949419, ss239338361, ss556815148, ss650521408, ss978945201, ss1070670268, ss1305340894, ss1429519807, ss1580094451, ss1607774886, ss1650768919, ss1799753863, ss1922174989, ss1969470877, ss2021647333, ss2149739804, ss2421483218, ss2625326782, ss2705138989, ss2796802084, ss2985264310, ss2992864124, ss3345168429 NC_000003.11:101570374:A>T NC_000003.12:101851530:A>T (self)
258654188, ss2254157235, ss3024589261, ss3400197532 NC_000003.12:101851530:A>T NC_000003.12:101851530:A>T (self)
ss11583060 NT_005612.13:7969528:A>T NC_000003.12:101851530:A>T (self)
ss14172242, ss20150877 NT_005612.14:8065520:A>T NC_000003.12:101851530:A>T (self)
ss772681, ss878332, ss5522428, ss6087942, ss24152681, ss44366288, ss74851517, ss106283735, ss139057700, ss155945350, ss161370864 NT_005612.16:8065520:A>T NC_000003.12:101851530:A>T (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 rs600718
PMID Title Author Year Journal
19798075 NFKBIZ polymorphisms and susceptibility to pneumococcal disease in European and African populations. Chapman SJ et al. 2010 Genes and immunity

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: 0.1.4.post833+d3ba21e