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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.

rs2066847

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr16:50729868-50729870 (GRCh38.p13) 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
delC / dupC
Variation Type
Indel Insertion and Deletion
Frequency
dupC=0.013457 (3562/264690, TOPMED)
dupC=0.015002 (3771/251370, GnomAD_exome)
dupC=0.015546 (2180/140232, GnomAD) (+ 9 more)
dupC=0.013057 (1584/121312, ExAC)
dupC=0.08544 (8493/99406, ALFA)
dupC=0.01622 (203/12518, GO-ESP)
dupC=0.0060 (30/5008, 1000G)
dupC=0.0377 (169/4480, Estonian)
dupC=0.0241 (93/3854, ALSPAC)
dupC=0.0232 (86/3708, TWINSUK)
dupC=0.028 (28/998, GoNL)
dupC=0.017 (10/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
NOD2 : Frameshift Variant
Publications
92 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.p13 chr 16 NC_000016.10:g.50729870del
GRCh38.p13 chr 16 NC_000016.10:g.50729870dup
GRCh37.p13 chr 16 NC_000016.9:g.50763781del
GRCh37.p13 chr 16 NC_000016.9:g.50763781dup
NOD2 RefSeqGene (LRG_177) NG_007508.1:g.37732del
NOD2 RefSeqGene (LRG_177) NG_007508.1:g.37732dup
Gene: NOD2, nucleotide binding oligomerization domain containing 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NOD2 transcript variant 1 NM_022162.3:c.3019del L [CTT] > L [TT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 1 NP_071445.1:p.Glu1008fs L (Leu) > L (Leu) Frameshift Variant
NOD2 transcript variant 1 NM_022162.3:c.3019dup L [CTT] > P [CCTT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 1 NP_071445.1:p.Leu1007fs L (Leu) > P (Pro) Frameshift Variant
NOD2 transcript variant 2 NM_001293557.2:c.2938del L [CTT] > L [TT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001280486.1:p.Glu981fs L (Leu) > L (Leu) Frameshift Variant
NOD2 transcript variant 2 NM_001293557.2:c.2938dup L [CTT] > P [CCTT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001280486.1:p.Leu980fs L (Leu) > P (Pro) Frameshift Variant
NOD2 transcript variant 3 NM_001370466.1:c.2938del L [CTT] > L [TT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001357395.1:p.Glu981fs L (Leu) > L (Leu) Frameshift Variant
NOD2 transcript variant 3 NM_001370466.1:c.2938dup L [CTT] > P [CCTT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001357395.1:p.Leu980fs L (Leu) > P (Pro) Frameshift Variant
NOD2 transcript variant 4 NR_163434.1:n.3150del N/A Non Coding Transcript Variant
NOD2 transcript variant 4 NR_163434.1:n.3150dup N/A Non Coding Transcript Variant
NOD2 transcript variant X9 XM_006721243.4:c. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X10 XM_011523260.3:c. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X12 XM_011523261.2:c. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X3 XM_017023535.1:c.2446del L [CTT] > L [TT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X3 XP_016879024.1:p.Glu817fs L (Leu) > L (Leu) Frameshift Variant
NOD2 transcript variant X3 XM_017023535.1:c.2446dup L [CTT] > P [CCTT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X3 XP_016879024.1:p.Leu816fs L (Leu) > P (Pro) Frameshift Variant
NOD2 transcript variant X4 XM_017023536.1:c.2353del L [CTT] > L [TT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879025.1:p.Glu786fs L (Leu) > L (Leu) Frameshift Variant
NOD2 transcript variant X4 XM_017023536.1:c.2353dup L [CTT] > P [CCTT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879025.1:p.Leu785fs L (Leu) > P (Pro) Frameshift Variant
NOD2 transcript variant X5 XM_011523259.2:c.2353del L [CTT] > L [TT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_011521561.1:p.Glu786fs L (Leu) > L (Leu) Frameshift Variant
NOD2 transcript variant X5 XM_011523259.2:c.2353dup L [CTT] > P [CCTT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_011521561.1:p.Leu785fs L (Leu) > P (Pro) Frameshift Variant
NOD2 transcript variant X6 XM_017023537.1:c.2353del L [CTT] > L [TT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879026.1:p.Glu786fs L (Leu) > L (Leu) Frameshift Variant
NOD2 transcript variant X6 XM_017023537.1:c.2353dup L [CTT] > P [CCTT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879026.1:p.Leu785fs L (Leu) > P (Pro) Frameshift Variant
NOD2 transcript variant X13 XM_017023538.1:c.2353del L [CTT] > L [TT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879027.1:p.Glu786fs L (Leu) > L (Leu) Frameshift Variant
NOD2 transcript variant X13 XM_017023538.1:c.2353dup L [CTT] > P [CCTT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879027.1:p.Leu785fs L (Leu) > P (Pro) Frameshift Variant
NOD2 transcript variant X2 XM_006721242.4:c.2854del L [CTT] > L [TT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X2 XP_006721305.1:p.Glu953fs L (Leu) > L (Leu) Frameshift Variant
NOD2 transcript variant X2 XM_006721242.4:c.2854dup L [CTT] > P [CCTT] Coding Sequence Variant
nucleotide-binding oligomerization domain-containing protein 2 isoform X2 XP_006721305.1:p.Leu952fs L (Leu) > P (Pro) Frameshift Variant
NOD2 transcript variant X8 XR_429725.3:n. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X11 XR_429726.3:n. N/A Genic Downstream Transcript Variant
NOD2 transcript variant X7 XR_933387.2:n. N/A Genic Downstream 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.

Allele: dupC (allele ID: 19730 )
ClinVar Accession Disease Names Clinical Significance
RCV000004955.5 Inflammatory bowel disease 1 Risk-Factor
RCV000334899.1 Crohn disease Likely-Benign
RCV000389442.2 Blau syndrome Conflicting-Interpretations-Of-Pathogenicity
RCV000416485.1 Yao syndrome Risk-Factor
RCV000525152.6 Blau syndrome,Inflammatory bowel disease 1 Association
RCV001002511.2 none provided Likely-Benign

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 99406 CCC=0.91456 CCCC=0.08544
European Sub 86108 CCC=0.90571 CCCC=0.09429
African Sub 4306 CCC=0.9947 CCCC=0.0053
African Others Sub 174 CCC=1.000 CCCC=0.000
African American Sub 4132 CCC=0.9944 CCCC=0.0056
Asian Sub 3330 CCC=1.0000 CCCC=0.0000
East Asian Sub 2674 CCC=1.0000 CCCC=0.0000
Other Asian Sub 656 CCC=1.000 CCCC=0.000
Latin American 1 Sub 436 CCC=1.000 CCCC=0.000
Latin American 2 Sub 928 CCC=0.994 CCCC=0.006
South Asian Sub 274 CCC=0.996 CCCC=0.004
Other Sub 4024 CCC=0.9145 CCCC=0.0855


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 -

No frequency provided

dupC=0.013457
gnomAD - Exomes Global Study-wide 251370 -

No frequency provided

dupC=0.015002
gnomAD - Exomes European Sub 135328 -

No frequency provided

dupC=0.021762
gnomAD - Exomes Asian Sub 49004 -

No frequency provided

dupC=0.00096
gnomAD - Exomes American Sub 34572 -

No frequency provided

dupC=0.00845
gnomAD - Exomes African Sub 16254 -

No frequency provided

dupC=0.00289
gnomAD - Exomes Ashkenazi Jewish Sub 10074 -

No frequency provided

dupC=0.03445
gnomAD - Exomes Other Sub 6138 -

No frequency provided

dupC=0.0152
gnomAD - Genomes Global Study-wide 140232 -

No frequency provided

dupC=0.015546
gnomAD - Genomes European Sub 75932 -

No frequency provided

dupC=0.02255
gnomAD - Genomes African Sub 42034 -

No frequency provided

dupC=0.00357
gnomAD - Genomes American Sub 13660 -

No frequency provided

dupC=0.01310
gnomAD - Genomes Ashkenazi Jewish Sub 3324 -

No frequency provided

dupC=0.0283
gnomAD - Genomes East Asian Sub 3132 -

No frequency provided

dupC=0.0000
gnomAD - Genomes Other Sub 2150 -

No frequency provided

dupC=0.0209
ExAC Global Study-wide 121312 -

No frequency provided

dupC=0.013057
ExAC Europe Sub 73310 -

No frequency provided

dupC=0.01968
ExAC Asian Sub 25160 -

No frequency provided

dupC=0.00115
ExAC American Sub 11536 -

No frequency provided

dupC=0.00685
ExAC African Sub 10398 -

No frequency provided

dupC=0.00269
ExAC Other Sub 908 -

No frequency provided

dupC=0.006
GO Exome Sequencing Project Global Study-wide 12518 -

No frequency provided

dupC=0.01622
GO Exome Sequencing Project European American Sub 8254 -

No frequency provided

dupC=0.0222
GO Exome Sequencing Project African American Sub 4264 -

No frequency provided

dupC=0.0047
1000Genomes Global Study-wide 5008 -

No frequency provided

dupC=0.0060
1000Genomes African Sub 1322 -

No frequency provided

dupC=0.0038
1000Genomes East Asian Sub 1008 -

No frequency provided

dupC=0.0000
1000Genomes Europe Sub 1006 -

No frequency provided

dupC=0.0139
1000Genomes South Asian Sub 978 -

No frequency provided

dupC=0.000
1000Genomes American Sub 694 -

No frequency provided

dupC=0.016
Genetic variation in the Estonian population Estonian Study-wide 4480 -

No frequency provided

dupC=0.0377
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 -

No frequency provided

dupC=0.0241
UK 10K study - Twins TWIN COHORT Study-wide 3708 -

No frequency provided

dupC=0.0232
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 -

No frequency provided

dupC=0.028
Northern Sweden ACPOP Study-wide 600 -

No frequency provided

dupC=0.017
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 CCC= delC dupC
GRCh38.p13 chr 16 NC_000016.10:g.50729868_50729870= NC_000016.10:g.50729870del NC_000016.10:g.50729870dup
GRCh37.p13 chr 16 NC_000016.9:g.50763779_50763781= NC_000016.9:g.50763781del NC_000016.9:g.50763781dup
NOD2 RefSeqGene (LRG_177) NG_007508.1:g.37730_37732= NG_007508.1:g.37732del NG_007508.1:g.37732dup
NOD2 transcript variant 1 NM_022162.3:c.3017_3019= NM_022162.3:c.3019del NM_022162.3:c.3019dup
NOD2 transcript variant 1 NM_022162.2:c.3017_3019= NM_022162.2:c.3019del NM_022162.2:c.3019dup
NOD2 transcript NM_022162.1:c.3017_3019= NM_022162.1:c.3019del NM_022162.1:c.3019dup
NOD2 transcript variant 2 NM_001293557.2:c.2936_2938= NM_001293557.2:c.2938del NM_001293557.2:c.2938dup
NOD2 transcript variant 2 NM_001293557.1:c.2936_2938= NM_001293557.1:c.2938del NM_001293557.1:c.2938dup
NOD2 transcript variant 4 NR_163434.1:n.3148_3150= NR_163434.1:n.3150del NR_163434.1:n.3150dup
NOD2 transcript variant 3 NM_001370466.1:c.2936_2938= NM_001370466.1:c.2938del NM_001370466.1:c.2938dup
NOD2 transcript variant X2 XM_006721242.4:c.2852_2854= XM_006721242.4:c.2854del XM_006721242.4:c.2854dup
NOD2 transcript variant X5 XM_011523259.2:c.2351_2353= XM_011523259.2:c.2353del XM_011523259.2:c.2353dup
NOD2 transcript variant X3 XM_017023535.1:c.2444_2446= XM_017023535.1:c.2446del XM_017023535.1:c.2446dup
NOD2 transcript variant X4 XM_017023536.1:c.2351_2353= XM_017023536.1:c.2353del XM_017023536.1:c.2353dup
NOD2 transcript variant X13 XM_017023538.1:c.2351_2353= XM_017023538.1:c.2353del XM_017023538.1:c.2353dup
NOD2 transcript variant X6 XM_017023537.1:c.2351_2353= XM_017023537.1:c.2353del XM_017023537.1:c.2353dup
nucleotide-binding oligomerization domain-containing protein 2 isoform 1 NP_071445.1:p.Ala1006_Leu1007= NP_071445.1:p.Glu1008fs NP_071445.1:p.Leu1007fs
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001280486.1:p.Ala979_Leu980= NP_001280486.1:p.Glu981fs NP_001280486.1:p.Leu980fs
nucleotide-binding oligomerization domain-containing protein 2 isoform 2 NP_001357395.1:p.Ala979_Leu980= NP_001357395.1:p.Glu981fs NP_001357395.1:p.Leu980fs
nucleotide-binding oligomerization domain-containing protein 2 isoform X2 XP_006721305.1:p.Ala951_Leu952= XP_006721305.1:p.Glu953fs XP_006721305.1:p.Leu952fs
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_011521561.1:p.Ala784_Leu785= XP_011521561.1:p.Glu786fs XP_011521561.1:p.Leu785fs
nucleotide-binding oligomerization domain-containing protein 2 isoform X3 XP_016879024.1:p.Ala815_Leu816= XP_016879024.1:p.Glu817fs XP_016879024.1:p.Leu816fs
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879025.1:p.Ala784_Leu785= XP_016879025.1:p.Glu786fs XP_016879025.1:p.Leu785fs
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879027.1:p.Ala784_Leu785= XP_016879027.1:p.Glu786fs XP_016879027.1:p.Leu785fs
nucleotide-binding oligomerization domain-containing protein 2 isoform X4 XP_016879026.1:p.Ala784_Leu785= XP_016879026.1:p.Glu786fs XP_016879026.1:p.Leu785fs
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#.

69 SubSNP, 12 Frequency, 6 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CEPH ss2978539 Apr 12, 2001 (94)
2 GKT-CGM ss2992224 Jun 15, 2001 (96)
3 IIPGA-WEISS-MARTINEZ ss7987119 Apr 21, 2003 (136)
4 SNP500CANCER ss8819692 Jul 02, 2003 (116)
5 JDRF_WT_DIL ss28514842 Sep 24, 2004 (136)
6 1000GENOMES ss327852094 May 09, 2011 (135)
7 1000GENOMES ss499091602 May 04, 2012 (137)
8 LUNTER ss552473692 Apr 25, 2013 (138)
9 ILLUMINA ss780680140 Aug 21, 2014 (136)
10 ILLUMINA ss783353405 Aug 21, 2014 (136)
11 ILLUMINA ss783356203 Aug 21, 2014 (142)
12 EVA-GONL ss992477782 Aug 21, 2014 (142)
13 1000GENOMES ss1375814782 Aug 21, 2014 (142)
14 OMIM-CURATED-RECORDS ss1505811023 Dec 08, 2014 (136)
15 EVA_DECODE ss1696511023 Apr 01, 2015 (144)
16 EVA_UK10K_TWINSUK ss1708539277 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1708539278 Apr 01, 2015 (144)
18 EVA_EXAC ss1712110799 Apr 01, 2015 (144)
19 ILLUMINA ss1752193410 Oct 12, 2018 (152)
20 ILLUMINA ss1752193411 Sep 08, 2015 (146)
21 ILLUMINA ss1946414632 Oct 12, 2018 (152)
22 ILLUMINA ss1946414633 Feb 12, 2016 (147)
23 ILLUMINA ss1959677490 Oct 12, 2018 (152)
24 ILLUMINA ss1959677491 Oct 12, 2018 (152)
25 JJLAB ss2031303129 Sep 14, 2016 (149)
26 ILLUMINA ss2094799737 Dec 20, 2016 (136)
27 ILLUMINA ss2095066640 Dec 20, 2016 (150)
28 ILLUMINA ss2095066641 Dec 20, 2016 (136)
29 ILLUMINA ss2133041214 Dec 20, 2016 (150)
30 ILLUMINA ss2136247254 Dec 20, 2016 (150)
31 TOPMED ss2376991854 Dec 20, 2016 (150)
32 ILLUMINA ss2633316060 Nov 08, 2017 (151)
33 GNOMAD ss2741976343 Nov 08, 2017 (151)
34 GNOMAD ss2749540298 Nov 08, 2017 (151)
35 GNOMAD ss2942902049 Nov 08, 2017 (151)
36 AFFY ss2985068325 Nov 08, 2017 (151)
37 AFFY ss2985703987 Nov 08, 2017 (151)
38 AFFY ss2985703988 Nov 08, 2017 (151)
39 SWEGEN ss3014498408 Nov 08, 2017 (151)
40 ILLUMINA ss3021704792 Nov 08, 2017 (151)
41 ILLUMINA ss3021704793 Nov 08, 2017 (151)
42 TOPMED ss3246277349 Nov 08, 2017 (151)
43 ILLUMINA ss3627520014 Oct 12, 2018 (152)
44 ILLUMINA ss3627520015 Oct 12, 2018 (152)
45 ILLUMINA ss3634641418 Oct 12, 2018 (152)
46 ILLUMINA ss3634641419 Oct 12, 2018 (152)
47 ILLUMINA ss3640348737 Oct 12, 2018 (152)
48 ILLUMINA ss3640348738 Oct 12, 2018 (152)
49 ILLUMINA ss3644667706 Oct 12, 2018 (152)
50 ILLUMINA ss3644667707 Oct 12, 2018 (152)
51 ILLUMINA ss3652113314 Oct 12, 2018 (152)
52 ILLUMINA ss3652113315 Oct 12, 2018 (152)
53 ILLUMINA ss3652113316 Oct 12, 2018 (152)
54 ILLUMINA ss3652113317 Oct 12, 2018 (152)
55 ILLUMINA ss3653840099 Oct 12, 2018 (152)
56 EGCUT_WGS ss3681472445 Jul 13, 2019 (153)
57 EVA_DECODE ss3699242745 Jul 13, 2019 (153)
58 ILLUMINA ss3725560666 Jul 13, 2019 (153)
59 ACPOP ss3741502045 Jul 13, 2019 (153)
60 ILLUMINA ss3744432070 Jul 13, 2019 (153)
61 ILLUMINA ss3744432071 Jul 13, 2019 (153)
62 ILLUMINA ss3744941840 Jul 13, 2019 (153)
63 ILLUMINA ss3744941841 Jul 13, 2019 (153)
64 ILLUMINA ss3772440129 Jul 13, 2019 (153)
65 ILLUMINA ss3772440130 Jul 13, 2019 (153)
66 EVA ss3825014716 Apr 27, 2020 (154)
67 EVA ss3834564513 Apr 27, 2020 (154)
68 EVA ss3986686735 Apr 26, 2021 (155)
69 TOPMED ss5015027775 Apr 26, 2021 (155)
70 1000Genomes NC_000016.9 - 50763779 Oct 12, 2018 (152)
71 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 50763779 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000016.9 - 50763779 Oct 12, 2018 (152)
73 ExAC NC_000016.9 - 50763779 Oct 12, 2018 (152)
74 gnomAD - Genomes NC_000016.10 - 50729868 Apr 26, 2021 (155)
75 gnomAD - Exomes NC_000016.9 - 50763779 Jul 13, 2019 (153)
76 GO Exome Sequencing Project NC_000016.9 - 50763779 Oct 12, 2018 (152)
77 Genome of the Netherlands Release 5 NC_000016.9 - 50763779 Apr 27, 2020 (154)
78 Northern Sweden NC_000016.9 - 50763779 Jul 13, 2019 (153)
79 TopMed NC_000016.10 - 50729868 Apr 26, 2021 (155)
80 UK 10K study - Twins NC_000016.9 - 50763779 Oct 12, 2018 (152)
81 ALFA NC_000016.10 - 50729868 Apr 26, 2021 (155)
82 ClinVar RCV000004955.5 Oct 12, 2018 (152)
83 ClinVar RCV000334899.1 Oct 12, 2018 (152)
84 ClinVar RCV000389442.2 Apr 27, 2020 (154)
85 ClinVar RCV000416485.1 Oct 12, 2018 (152)
86 ClinVar RCV000525152.6 Apr 26, 2021 (155)
87 ClinVar RCV001002511.2 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)
rs5743293 May 11, 2017 (136)
rs17860493 Mar 11, 2006 (126)
rs138539019 Sep 17, 2011 (135)
rs540973741 May 11, 2017 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss2985703987 NC_000016.9:50763778:C: NC_000016.10:50729867:CCC:CC (self)
ss327852094, ss552473692, ss1696511023 NC_000016.8:49321279::C NC_000016.10:50729867:CCC:CCCC (self)
69363916, 38472142, 27210693, 2703713, 11255500, 1471889, 17158099, 14786910, 38472142, ss499091602, ss780680140, ss783353405, ss783356203, ss992477782, ss1375814782, ss1708539277, ss1708539278, ss1712110799, ss1752193410, ss1752193411, ss1946414632, ss1946414633, ss1959677490, ss1959677491, ss2031303129, ss2095066640, ss2133041214, ss2136247254, ss2376991854, ss2633316060, ss2741976343, ss2749540298, ss2942902049, ss2985068325, ss2985703988, ss3014498408, ss3021704792, ss3021704793, ss3627520014, ss3627520015, ss3634641418, ss3634641419, ss3640348737, ss3640348738, ss3644667706, ss3644667707, ss3652113314, ss3652113315, ss3652113316, ss3653840099, ss3681472445, ss3741502045, ss3744432070, ss3744432071, ss3744941840, ss3744941841, ss3772440129, ss3772440130, ss3825014716, ss3834564513, ss3986686735 NC_000016.9:50763778::C NC_000016.10:50729867:CCC:CCCC (self)
ss2094799737, ss2095066641, ss3652113317 NC_000016.9:50763781::C NC_000016.10:50729867:CCC:CCCC (self)
489290030, 143973686, 230573436, ss3246277349, ss3699242745, ss3725560666, ss5015027775 NC_000016.10:50729867::C NC_000016.10:50729867:CCC:CCCC (self)
RCV000004955.5, RCV000334899.1, RCV000389442.2, RCV000416485.1, RCV000525152.6, RCV001002511.2, 6332943962 NC_000016.10:50729867:CCC:CCCC NC_000016.10:50729867:CCC:CCCC (self)
ss1505811023 NC_000016.10:50729868::C NC_000016.10:50729867:CCC:CCCC (self)
ss2978539, ss2992224, ss8819692 NT_010498.15:4377977::C NC_000016.10:50729867:CCC:CCCC (self)
ss7987119, ss28514842 NT_010498.15:4377980::C NC_000016.10:50729867:CCC:CCCC (self)
Help

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

92 citations for rs2066847
PMID Title Author Year Journal
16380915 Replication of putative candidate-gene associations with rheumatoid arthritis in >4,000 samples from North America and Sweden: association of susceptibility with PTPN22, CTLA4, and PADI4. Plenge RM et al. 2005 American journal of human genetics
16859562 Do host genetic traits in the bacterial sensing system play a role in the development of Chlamydia trachomatis-associated tubal pathology in subfertile women? den Hartog JE et al. 2006 BMC infectious diseases
17327408 Prognostic significance of host immune gene polymorphisms in follicular lymphoma survival. Cerhan JR et al. 2007 Blood
17684544 Systematic association mapping identifies NELL1 as a novel IBD disease gene. Franke A et al. 2007 PloS one
17786191 rs1004819 is the main disease-associated IL23R variant in German Crohn's disease patients: combined analysis of IL23R, CARD15, and OCTN1/2 variants. Glas J et al. 2007 PloS one
18070336 CD209 in inflammatory bowel disease: a case-control study in the Spanish population. Núñez C et al. 2007 BMC medical genetics
18382655 Maternal TLR4 and NOD2 gene variants, pro-inflammatory phenotype and susceptibility to early-onset preeclampsia and HELLP syndrome. van Rijn BB et al. 2008 PloS one
18587394 Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Barrett JC et al. 2008 Nature genetics
18633131 Host immune gene polymorphisms in combination with clinical and demographic factors predict late survival in diffuse large B-cell lymphoma patients in the pre-rituximab era. Habermann TM et al. 2008 Blood
18698678 Replication of interleukin 23 receptor and autophagy-related 16-like 1 association in adult- and pediatric-onset inflammatory bowel disease in Italy. Latiano A et al. 2008 World journal of gastroenterology
19147066 Genomic and proteomic analysis of allogeneic hematopoietic cell transplant outcome. Seeking greater understanding the pathogenesis of GVHD and mortality. Hansen JA et al. 2009 Biology of blood and marrow transplantation
19185283 Searching for genotype-phenotype structure: using hierarchical log-linear models in Crohn disease. Chapman JM et al. 2009 American journal of human genetics
19843337 Investigation of innate immunity genes CARD4, CARD8 and CARD15 as germline susceptibility factors for colorectal cancer. Möckelmann N et al. 2009 BMC gastroenterology
20047977 Tumor necrosis factor (TNF) and lymphotoxin-alpha (LTA) polymorphisms and risk of non-Hodgkin lymphoma in the InterLymph Consortium. Skibola CF et al. 2010 American journal of epidemiology
20066736 Interaction of the major inflammatory bowel disease susceptibility alleles in Crohn's disease patients. Csöngei V et al. 2010 World journal of gastroenterology
20082483 NOD2, IL23R and ATG16L1 polymorphisms in Lithuanian patients with inflammatory bowel disease. Sventoraityte J et al. 2010 World journal of gastroenterology
20155851 NOD2 status and human ileal gene expression. Hamm CM et al. 2010 Inflammatory bowel diseases
20177049 Insufficient evidence for association of NOD2/CARD15 or other inflammatory bowel disease-associated markers on GVHD incidence or other adverse outcomes in T-replete, unrelated donor transplantation. Nguyen Y et al. 2010 Blood
20228799 Genome-wide association identifies multiple ulcerative colitis susceptibility loci. McGovern DP et al. 2010 Nature genetics
20434130 Interpretation of association signals and identification of causal variants from genome-wide association studies. Wang K et al. 2010 American journal of human genetics
20485703 Replication and meta-analysis of 13,000 cases defines the risk for interleukin-23 receptor and autophagy-related 16-like 1 variants in Crohn's disease. Cotterill L et al. 2010 Canadian journal of gastroenterology = Journal canadien de gastroenterologie
20570966 Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease. McGovern DP et al. 2010 Human molecular genetics
20805105 Synthetic associations in the context of genome-wide association scan signals. Orozco G et al. 2010 Human molecular genetics
20827186 Defining genetic risk for graft-versus-host disease and mortality following allogeneic hematopoietic stem cell transplantation. Hansen JA et al. 2010 Current opinion in hematology
20839241 Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Frank DN et al. 2011 Inflammatory bowel diseases
20876667 Genome-wide significant associations for variants with minor allele frequency of 5% or less--an overview: A HuGE review. Panagiotou OA et al. 2010 American journal of epidemiology
20886065 Molecular reclassification of Crohn's disease by cluster analysis of genetic variants. Cleynen I et al. 2010 PloS one
20940596 NOD2/CARD15 mutations correlate with severe pouchitis after ileal pouch-anal anastomosis. Sehgal R et al. 2010 Diseases of the colon and rectum
20959815 NOD2 gene polymorphism rs2066844 associates with need for combined liver-intestine transplantation in children with short-gut syndrome. Ningappa M et al. 2011 The American journal of gastroenterology
21209938 The NOD2 single nucleotide polymorphisms rs2066843 and rs2076756 are novel and common Crohn's disease susceptibility gene variants. Glas J et al. 2010 PloS one
21253534 IL23R and IL12B SNPs and Haplotypes Strongly Associate with Crohn's Disease Risk in a New Zealand Population. Ferguson LR et al. 2010 Gastroenterology research and practice
21304977 An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians. Juyal G et al. 2011 PloS one
21333900 The role of genetics in IBS. Saito YA et al. 2011 Gastroenterology clinics of North America
21548950 Evaluation of 22 genetic variants with Crohn's disease risk in the Ashkenazi Jewish population: a case-control study. Peter I et al. 2011 BMC medical genetics
21559399 CEACAM6 gene variants in inflammatory bowel disease. Glas J et al. 2011 PloS one
21636646 Association of TNFSF15 polymorphism with irritable bowel syndrome. Zucchelli M et al. 2011 Gut
21658613 Host genetics in follicular lymphoma. Cerhan JR et al. 2011 Best practice & research. Clinical haematology
21730793 Influence of Crohn's disease risk alleles and smoking on disease location. Chen H et al. 2011 Diseases of the colon and rectum
21734790 NOD2 and ATG16L1 polymorphisms affect monocyte responses in Crohn's disease. Glubb DM et al. 2011 World journal of gastroenterology
21818367 Investigation of multiple susceptibility loci for inflammatory bowel disease in an Italian cohort of patients. Latiano A et al. 2011 PloS one
21830272 Distinct and overlapping genetic loci in Crohn's disease and ulcerative colitis: correlations with pathogenesis. Waterman M et al. 2011 Inflammatory bowel diseases
21858135 Efficient replication of over 180 genetic associations with self-reported medical data. Tung JY et al. 2011 PloS one
22113576 Polymorphisms in immune function genes and non-Hodgkin lymphoma survival. Aschebrook-Kilfoy B et al. 2012 Journal of cancer survivorship
22275320 Pattern recognition receptor and autophagy gene variants are associated with development of antimicrobial antibodies in Crohn's disease. Murdoch TB et al. 2012 Inflammatory bowel diseases
22319155 Crohn's disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation. Nakagome S et al. 2012 Molecular biology and evolution
22457781 PTPN2 gene variants are associated with susceptibility to both Crohn's disease and ulcerative colitis supporting a common genetic disease background. Glas J et al. 2012 PloS one
22654485 Role of cytokines in systemic lupus erythematosus: recent progress from GWAS and sequencing. Connolly JJ et al. 2012 Journal of biomedicine & biotechnology
22719818 Inflammatory bowel diseases phenotype, C. difficile and NOD2 genotype are associated with shifts in human ileum associated microbial composition. Li E et al. 2012 PloS one
22879519 The NOD2insC polymorphism is associated with worse outcome following ileal pouch-anal anastomosis for ulcerative colitis. Tyler AD et al. 2013 Gut
23300620 Genotype/phenotype analyses for 53 Crohn's disease associated genetic polymorphisms. Jung C et al. 2012 PloS one
23300802 PTGER4 expression-modulating polymorphisms in the 5p13.1 region predispose to Crohn's disease and affect NF-κB and XBP1 binding sites. Glas J et al. 2012 PloS one
23365659 IRGM variants and susceptibility to inflammatory bowel disease in the German population. Glas J et al. 2013 PloS one
23651603 P268S in NOD2 associates with susceptibility to Parkinson's disease in Chinese population. Ma Q et al. 2013 Behavioral and brain functions
23725363 Predicting complicated Crohn's disease and surgery: phenotypes, genetics, serology and psychological characteristics of a population-based cohort. Ryan JD et al. 2013 Alimentary pharmacology & therapeutics
23946381 Genetic variants associated with colorectal cancer risk: comprehensive research synopsis, meta-analysis, and epidemiological evidence. Ma X et al. 2014 Gut
24223725 Intestinal DMBT1 expression is modulated by Crohn's disease-associated IL23R variants and by a DMBT1 variant which influences binding of the transcription factors CREB1 and ATF-2. Diegelmann J et al. 2013 PloS one
24627602 ATG16L1 and NOD2 polymorphisms enhance phagocytosis in monocytes of Crohn's disease patients. Wolfkamp SC et al. 2014 World journal of gastroenterology
25117299 Cumulative effects of genetic markers and the detection of advanced colorectal neoplasias by population screening. Kurlapska A et al. 2015 Clinical genetics
25365249 The NOD2 p.Leu1007fsX1008 mutation (rs2066847) is a stronger predictor of the clinical course of Crohn's disease than the FOXO3A intron variant rs12212067. Schnitzler F et al. 2014 PloS one
25962811 Non-Hodgkin Lymphoma, Body Mass Index, and Cytokine Polymorphisms: A Pooled Analysis from the InterLymph Consortium. Kane E et al. 2015 Cancer epidemiology, biomarkers & prevention
26147989 The NOD2 Single Nucleotide Polymorphism rs72796353 (IVS4+10 A>C) Is a Predictor for Perianal Fistulas in Patients with Crohn's Disease in the Absence of Other NOD2 Mutations. Schnitzler F et al. 2015 PloS one
26238283 The role of NOD1/CARD4 and NOD2/CARD15 genetic variations in lung cancer risk. Ozbayer C et al. 2015 Inflammation research
26490195 Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study. Cleynen I et al. 2016 Lancet (London, England)
26732016 Collecting Biospecimens From an Internet-Based Prospective Cohort Study of Inflammatory Bowel Disease (CCFA Partners): A Feasibility Study. Randell RL et al. 2016 JMIR research protocols
26827181 Single Nucleotide Polymorphisms in MORC4, CD14, and TLR4 Are Related to Outcome of Allogeneic Stem Cell Transplantation. Norén E et al. 2016 Annals of transplantation
26839472 Clinical and Genetic Features of Korean Patients with Recurrent Fever and Multi-System Inflammation without Infectious or Autoimmune Evidence. Yang JA et al. 2016 Journal of Korean medical science
27152134 NOD2 mutations and colorectal cancer - Where do we stand? Branquinho D et al. 2016 World journal of gastrointestinal surgery
27156530 Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility. Ye BD et al. 2016 Expert review of clinical immunology
27303667 Genetic Influences on the Development of Fibrosis in Crohn's Disease. Verstockt B et al. 2016 Frontiers in medicine
27306066 Genetic Association Analysis Reveals Differences in the Contribution of NOD2 Variants to the Clinical Phenotypes of Orofacial Granulomatosis. Mentzer A et al. 2016 Inflammatory bowel diseases
27404661 Polymorphisms in the Mannose-Binding Lectin Gene are Associated with Defective Mannose-Binding Lectin Functional Activity in Crohn's Disease Patients. Choteau L et al. 2016 Scientific reports
27670835 Systematic meta-analyses and field synopsis of genetic and epigenetic studies in paediatric inflammatory bowel disease. Li X et al. 2016 Scientific reports
27802154 Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Imhann F et al. 2018 Gut
27885704 Effects of genetic variations in the genes encoding NOD1 and NOD2 on type 2 diabetes mellitus and insulin resistance. Ozbayer C et al. 2017 Journal of clinical pharmacy and therapeutics
28067910 Exploring the genetic architecture of inflammatory bowel disease by whole-genome sequencing identifies association at ADCY7. Luo Y et al. 2017 Nature genetics
28506689 Genetic Factors Interact With Tobacco Smoke to Modify Risk for Inflammatory Bowel Disease in Humans and Mice. Yadav P et al. 2017 Gastroenterology
28687809 Genetic variants of TRAF6 modulate peritoneal immunity and the risk of spontaneous bacterial peritonitis in cirrhosis: A combined prospective-retrospective study. Mai M et al. 2017 Scientific reports
28827732 Genetic predisposition to lung cancer: comprehensive literature integration, meta-analysis, and multiple evidence assessment of candidate-gene association studies. Wang J et al. 2017 Scientific reports
29228965 Genetic polymorphism in ATG16L1 gene is associated with adalimumab use in inflammatory bowel disease. Nuij VJAA et al. 2017 Journal of translational medicine
29434451 Impaired granulocyte-macrophage colony-stimulating factor bioactivity accelerates surgical recurrence in ileal Crohn's disease. Gathungu G et al. 2018 World journal of gastroenterology
29446656 Crohn's Disease Candidate Gene Alleles Predict Time to Progression from Inflammatory B1 to Stricturing B2, or Penetrating B3 Phenotype. Pernat Drobež C et al. 2018 Genetic testing and molecular biomarkers
29701818 Determinants of IBD Heritability: Genes, Bugs, and More. Turpin W et al. 2018 Inflammatory bowel diseases
30061834 Influence of <i>NOD2</i> Variants on <i>Trichuris suis</i> ova Treatment Outcome in Crohn's Disease. Jaeger SU et al. 2018 Frontiers in pharmacology
30167848 Rare coding variant analysis in a large cohort of Ashkenazi Jewish families with inflammatory bowel disease. Schiff ER et al. 2018 Human genetics
31052430 Genetic Studies of Inflammatory Bowel Disease-Focusing on Asian Patients. Park SC et al. 2019 Cells
31403980 Genetic Variations at rs3129891 and rs77005575 are Associated With Reduced Expression of Enteric α-defensins in IBD Patients. Deng Q et al. 2020 Journal of clinical gastroenterology
31818908 Systematic meta-analyses, field synopsis and global assessment of the evidence of genetic association studies in colorectal cancer. Montazeri Z et al. 2020 Gut
32476786 Genetic association analysis of <i>CLEC5A</i> and <i>CLEC7A</i> gene single-nucleotide polymorphisms and Crohn's disease. Elleisy N et al. 2020 World journal of gastroenterology
32476890 NOD2/CARD15 gene polymorphisms and sarcoidosis susceptibility: review and meta-analysis. Chen X et al. 2018 Sarcoidosis, vasculitis, and diffuse lung diseases
32578848 Genetic variation in NOD1/CARD4 and NOD2/CARD15 immune sensors and risk of osteoporosis. Soyocak A et al. 2020 Bioscience reports
32716958 Development of a uniform, very aggressive disease phenotype in all homozygous carriers of the NOD2 mutation p.Leu1007fsX1008 with Crohn's disease and active smoking status resulting in ileal stenosis requiring surgery. Schnitzler F et al. 2020 PloS one
33059653 Associations of NOD2 polymorphisms with Erysipelotrichaceae in stool of in healthy first degree relatives of Crohn's disease subjects. Turpin W et al. 2020 BMC medical genetics
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The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

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Select flank length:

Genomic regions, transcripts, and products
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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.
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Software version is: 2.0.1.post596+ae089ad