Skip to main page content
Accesskeys

dbSNP Short Genetic Variations

Reference SNP (rs) Report

Alpha

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.

rs2282151

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr6:44258458 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.18327 (23013/125568, TOPMED)
C=0.1765 (5452/30888, GnomAD)
C=0.228 (1142/5008, 1000G) (+ 2 more)
C=0.230 (888/3854, ALSPAC)
C=0.224 (830/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NFKBIE : 3 Prime UTR Variant
SLC35B2 : 2KB Upstream Variant
Publications
2 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.p7 chr 6 NC_000006.12:g.44258458T>C
GRCh37.p13 chr 6 NC_000006.11:g.44226195T>C
Gene: NFKBIE, NFKB inhibitor epsilon (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NFKBIE transcript NM_004556.2:c. N/A 3 Prime UTR Variant
Gene: SLC35B2, solute carrier family 35 member B2 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SLC35B2 transcript variant 2 NM_001286509.1:c. N/A Upstream Transcript Variant
SLC35B2 transcript variant 3 NM_001286510.1:c. N/A Upstream Transcript Variant
SLC35B2 transcript variant 4 NM_001286511.1:c. N/A Upstream Transcript Variant
SLC35B2 transcript variant 5 NM_001286512.1:c. N/A Upstream Transcript Variant
SLC35B2 transcript variant 6 NM_001286513.1:c. N/A Upstream Transcript Variant
SLC35B2 transcript variant 7 NM_001286517.1:c. N/A Upstream Transcript Variant
SLC35B2 transcript variant 8 NM_001286519.1:c. N/A Upstream Transcript Variant
SLC35B2 transcript variant 9 NM_001286520.1:c. N/A Upstream Transcript Variant
SLC35B2 transcript variant 1 NM_178148.3: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
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 T=0.81673 C=0.18327
The Genome Aggregation Database Global Study-wide 30888 T=0.8235 C=0.1765
The Genome Aggregation Database European Sub 18446 T=0.7926 C=0.2074
The Genome Aggregation Database African Sub 8710 T=0.936 C=0.064
The Genome Aggregation Database East Asian Sub 1618 T=0.648 C=0.352
The Genome Aggregation Database Other Sub 978 T=0.80 C=0.20
The Genome Aggregation Database American Sub 834 T=0.68 C=0.32
The Genome Aggregation Database Ashkenazi Jewish Sub 302 T=0.89 C=0.11
1000Genomes Global Study-wide 5008 T=0.772 C=0.228
1000Genomes African Sub 1322 T=0.961 C=0.039
1000Genomes East Asian Sub 1008 T=0.594 C=0.406
1000Genomes Europe Sub 1006 T=0.781 C=0.219
1000Genomes South Asian Sub 978 T=0.71 C=0.29
1000Genomes American Sub 694 T=0.74 C=0.26
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.770 C=0.230
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.776 C=0.224
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= C Note
GRCh38.p7 chr 6 NC_000006.12:g.44258458T= NC_000006.12:g.44258458T>C
GRCh37.p13 chr 6 NC_000006.11:g.44226195T= NC_000006.11:g.44226195T>C
NFKBIE transcript NM_004556.2:c.*761A= NM_004556.2:c.*761A>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#.

66 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3220951 Sep 28, 2001 (100)
2 CSHL-HAPMAP ss17149447 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss19695676 Feb 27, 2004 (120)
4 PGA-UW-FHCRC ss35073548 May 24, 2005 (125)
5 ABI ss44698840 Mar 13, 2006 (126)
6 SNP500CANCER ss48295981 Mar 13, 2006 (126)
7 PGA-UW-FHCRC ss52088156 Oct 15, 2006 (127)
8 PERLEGEN ss68975564 May 17, 2007 (127)
9 SI_EXO ss76894881 Dec 07, 2007 (129)
10 HGSV ss78817634 Dec 07, 2007 (129)
11 BCMHGSC_JDW ss93451320 Mar 24, 2008 (129)
12 BGI ss104307916 Dec 01, 2009 (131)
13 1000GENOMES ss110036434 Jan 24, 2009 (130)
14 ENSEMBL ss143874524 Dec 01, 2009 (131)
15 GMI ss156870182 Dec 01, 2009 (131)
16 ILLUMINA ss160528169 Dec 01, 2009 (131)
17 ILLUMINA ss173247189 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss207732156 Jul 04, 2010 (132)
19 1000GENOMES ss233452309 Jul 14, 2010 (132)
20 1000GENOMES ss240513700 Jul 15, 2010 (132)
21 GMI ss278776583 May 04, 2012 (137)
22 PJP ss293848552 May 09, 2011 (134)
23 ILLUMINA ss480505476 May 04, 2012 (137)
24 ILLUMINA ss480519805 May 04, 2012 (137)
25 ILLUMINA ss481327076 Sep 08, 2015 (146)
26 ILLUMINA ss485050194 May 04, 2012 (137)
27 ILLUMINA ss535710438 Sep 08, 2015 (146)
28 SSMP ss653115267 Apr 25, 2013 (138)
29 ILLUMINA ss778489755 Sep 08, 2015 (146)
30 ILLUMINA ss782971315 Sep 08, 2015 (146)
31 ILLUMINA ss783932830 Sep 08, 2015 (146)
32 ILLUMINA ss832227650 Sep 08, 2015 (146)
33 ILLUMINA ss833945743 Sep 08, 2015 (146)
34 EVA-GONL ss982879882 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1073577395 Aug 21, 2014 (142)
36 1000GENOMES ss1319932239 Aug 21, 2014 (142)
37 DDI ss1430706579 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1581652690 Apr 01, 2015 (144)
39 EVA_DECODE ss1592416035 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1615476746 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1658470779 Apr 01, 2015 (144)
42 ILLUMINA ss1752638419 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1926136173 Feb 12, 2016 (147)
44 GENOMED ss1970385347 Jul 19, 2016 (147)
45 JJLAB ss2023707691 Sep 14, 2016 (149)
46 USC_VALOUEV ss2151886465 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2283675856 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2626341267 Nov 08, 2017 (151)
49 ILLUMINA ss2634447863 Nov 08, 2017 (151)
50 ILLUMINA ss2635157031 Nov 08, 2017 (151)
51 GRF ss2707485433 Nov 08, 2017 (151)
52 GNOMAD ss2838441862 Nov 08, 2017 (151)
53 SWEGEN ss2998985799 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3025645020 Nov 08, 2017 (151)
55 CSHL ss3346940072 Nov 08, 2017 (151)
56 TOPMED ss3496145514 Nov 08, 2017 (151)
57 ILLUMINA ss3629538859 Jul 20, 2018 (151)
58 ILLUMINA ss3632364755 Jul 20, 2018 (151)
59 ILLUMINA ss3633420720 Jul 20, 2018 (151)
60 ILLUMINA ss3634143601 Jul 20, 2018 (151)
61 ILLUMINA ss3635066305 Jul 20, 2018 (151)
62 ILLUMINA ss3635824451 Jul 20, 2018 (151)
63 ILLUMINA ss3636789013 Jul 20, 2018 (151)
64 ILLUMINA ss3637577266 Jul 20, 2018 (151)
65 ILLUMINA ss3638628394 Jul 20, 2018 (151)
66 ILLUMINA ss3640773604 Jul 20, 2018 (151)
67 1000Genomes NC_000006.11 - 44226195 Jul 20, 2018 (151)
68 The Avon Longitudinal Study of Parents and Children NC_000006.11 - 44226195 Jul 20, 2018 (151)
69 The Genome Aggregation Database NC_000006.11 - 44226195 Jul 20, 2018 (151)
70 Trans-Omics for Precision Medicine NC_000006.12 - 44258458 Jul 20, 2018 (151)
71 UK 10K study - Twins NC_000006.11 - 44226195 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss78817634 NC_000006.9:44334172:T= NC_000006.12:44258457:T= (self)
ss93451320, ss110036434, ss207732156, ss278776583, ss293848552, ss480505476, ss1592416035, ss2635157031 NC_000006.10:44334172:T= NC_000006.12:44258457:T= (self)
31713950, 17687595, 179069619, 17687595, ss233452309, ss240513700, ss480519805, ss481327076, ss485050194, ss535710438, ss653115267, ss778489755, ss782971315, ss783932830, ss832227650, ss833945743, ss982879882, ss1073577395, ss1319932239, ss1430706579, ss1581652690, ss1615476746, ss1658470779, ss1752638419, ss1926136173, ss1970385347, ss2023707691, ss2151886465, ss2626341267, ss2634447863, ss2707485433, ss2838441862, ss2998985799, ss3346940072, ss3629538859, ss3632364755, ss3633420720, ss3634143601, ss3635066305, ss3635824451, ss3636789013, ss3637577266, ss3638628394, ss3640773604 NC_000006.11:44226194:T= NC_000006.12:44258457:T= (self)
336853320, ss2283675856, ss3025645020, ss3496145514 NC_000006.12:44258457:T= NC_000006.12:44258457:T= (self)
ss17149447, ss19695676 NT_007592.13:35023321:T= NC_000006.12:44258457:T= (self)
ss76894881 NT_007592.14:35084444:T= NC_000006.12:44258457:T= (self)
ss3220951, ss35073548, ss44698840, ss48295981, ss52088156, ss68975564, ss104307916, ss143874524, ss156870182, ss160528169, ss173247189 NT_007592.15:44166194:T= NC_000006.12:44258457:T= (self)
ss78817634 NC_000006.9:44334172:T>C NC_000006.12:44258457:T>C (self)
ss93451320, ss110036434, ss207732156, ss278776583, ss293848552, ss480505476, ss1592416035, ss2635157031 NC_000006.10:44334172:T>C NC_000006.12:44258457:T>C (self)
31713950, 17687595, 179069619, 17687595, ss233452309, ss240513700, ss480519805, ss481327076, ss485050194, ss535710438, ss653115267, ss778489755, ss782971315, ss783932830, ss832227650, ss833945743, ss982879882, ss1073577395, ss1319932239, ss1430706579, ss1581652690, ss1615476746, ss1658470779, ss1752638419, ss1926136173, ss1970385347, ss2023707691, ss2151886465, ss2626341267, ss2634447863, ss2707485433, ss2838441862, ss2998985799, ss3346940072, ss3629538859, ss3632364755, ss3633420720, ss3634143601, ss3635066305, ss3635824451, ss3636789013, ss3637577266, ss3638628394, ss3640773604 NC_000006.11:44226194:T>C NC_000006.12:44258457:T>C (self)
336853320, ss2283675856, ss3025645020, ss3496145514 NC_000006.12:44258457:T>C NC_000006.12:44258457:T>C (self)
ss17149447, ss19695676 NT_007592.13:35023321:T>C NC_000006.12:44258457:T>C (self)
ss76894881 NT_007592.14:35084444:T>C NC_000006.12:44258457:T>C (self)
ss3220951, ss35073548, ss44698840, ss48295981, ss52088156, ss68975564, ss104307916, ss143874524, ss156870182, ss160528169, ss173247189 NT_007592.15:44166194:T>C NC_000006.12:44258457:T>C (self)
Help

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

2 citations for rs2282151
PMID Title Author Year Journal
27756247 A novel variant on chromosome 6p21.1 is associated with the risk of developing colorectal cancer: a two-stage case-control study in Han Chinese. Xu C et al. 2016 BMC cancer
29407193 Genetic susceptibility to invasive pneumococcal disease. Sangil A et al. 2018 Infection, genetics and evolution

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