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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.

rs11929668

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr3:119816948 (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
C>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.140013 (37060/264690, TOPMED)
G=0.137677 (19286/140082, GnomAD)
G=0.13855 (3112/22462, ALFA) (+ 17 more)
G=0.00006 (1/16760, 8.3KJPN)
G=0.1050 (526/5008, 1000G)
G=0.0906 (406/4480, Estonian)
G=0.1598 (616/3854, ALSPAC)
G=0.1491 (553/3708, TWINSUK)
G=0.0003 (1/2922, KOREAN)
G=0.0005 (1/1832, Korea1K)
G=0.1435 (223/1554, HapMap)
G=0.145 (145/998, GoNL)
G=0.183 (110/600, NorthernSweden)
G=0.002 (1/534, MGP)
G=0.153 (33/216, Qatari)
G=0.082 (16/194, PharmGKB)
C=0.47 (44/94, SGDP_PRJ)
G=0.12 (5/40, GENOME_DK)
C=0.5 (2/4, Siberian)
G=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NR1I2 : Intron 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.p13 chr 3 NC_000003.12:g.119816948C>G
GRCh37.p13 chr 3 NC_000003.11:g.119535795C>G
NR1I2 RefSeqGene NG_011856.1:g.41465C>G
Gene: NR1I2, nuclear receptor subfamily 1 group I member 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NR1I2 transcript variant 1 NM_003889.4:c.1161-120C>G N/A Intron Variant
NR1I2 transcript variant 2 NM_022002.3:c.1278-120C>G N/A Intron Variant
NR1I2 transcript variant 3 NM_033013.3:c.1050-120C>G 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 22462 C=0.86145 G=0.13855
European Sub 17722 C=0.86232 G=0.13768
African Sub 2976 C=0.8424 G=0.1576
African Others Sub 114 C=0.833 G=0.167
African American Sub 2862 C=0.8428 G=0.1572
Asian Sub 114 C=1.000 G=0.000
East Asian Sub 88 C=1.00 G=0.00
Other Asian Sub 26 C=1.00 G=0.00
Latin American 1 Sub 150 C=0.847 G=0.153
Latin American 2 Sub 626 C=0.890 G=0.110
South Asian Sub 98 C=0.93 G=0.07
Other Sub 776 C=0.866 G=0.134


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 C=0.859987 G=0.140013
gnomAD - Genomes Global Study-wide 140082 C=0.862323 G=0.137677
gnomAD - Genomes European Sub 75870 C=0.86183 G=0.13817
gnomAD - Genomes African Sub 41968 C=0.85613 G=0.14387
gnomAD - Genomes American Sub 13648 C=0.85881 G=0.14119
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.8473 G=0.1527
gnomAD - Genomes East Asian Sub 3134 C=0.9990 G=0.0010
gnomAD - Genomes Other Sub 2142 C=0.8469 G=0.1531
Allele Frequency Aggregator Total Global 22462 C=0.86145 G=0.13855
Allele Frequency Aggregator European Sub 17722 C=0.86232 G=0.13768
Allele Frequency Aggregator African Sub 2976 C=0.8424 G=0.1576
Allele Frequency Aggregator Other Sub 776 C=0.866 G=0.134
Allele Frequency Aggregator Latin American 2 Sub 626 C=0.890 G=0.110
Allele Frequency Aggregator Latin American 1 Sub 150 C=0.847 G=0.153
Allele Frequency Aggregator Asian Sub 114 C=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 C=0.93 G=0.07
8.3KJPN JAPANESE Study-wide 16760 C=0.99994 G=0.00006
1000Genomes Global Study-wide 5008 C=0.8950 G=0.1050
1000Genomes African Sub 1322 C=0.8442 G=0.1558
1000Genomes East Asian Sub 1008 C=0.9980 G=0.0020
1000Genomes Europe Sub 1006 C=0.8310 G=0.1690
1000Genomes South Asian Sub 978 C=0.949 G=0.051
1000Genomes American Sub 694 C=0.859 G=0.141
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9094 G=0.0906
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8402 G=0.1598
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8509 G=0.1491
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9997 G=0.0003
Korean Genome Project KOREAN Study-wide 1832 C=0.9995 G=0.0005
HapMap Global Study-wide 1554 C=0.8565 G=0.1435
HapMap African Sub 692 C=0.867 G=0.133
HapMap American Sub 598 C=0.848 G=0.152
HapMap Europe Sub 174 C=0.770 G=0.230
HapMap Asian Sub 90 C=1.00 G=0.00
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.855 G=0.145
Northern Sweden ACPOP Study-wide 600 C=0.817 G=0.183
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.998 G=0.002
Qatari Global Study-wide 216 C=0.847 G=0.153
PharmGKB Aggregated Global Study-wide 194 C=0.918 G=0.082
PharmGKB Aggregated PA130609632 Sub 194 C=0.918 G=0.082
SGDP_PRJ Global Study-wide 94 C=0.47 G=0.53
The Danish reference pan genome Danish Study-wide 40 C=0.88 G=0.12
Siberian Global Study-wide 4 C=0.5 G=0.5
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 C= G
GRCh38.p13 chr 3 NC_000003.12:g.119816948= NC_000003.12:g.119816948C>G
GRCh37.p13 chr 3 NC_000003.11:g.119535795= NC_000003.11:g.119535795C>G
NR1I2 RefSeqGene NG_011856.1:g.41465= NG_011856.1:g.41465C>G
NR1I2 transcript variant 1 NM_003889.3:c.1161-120= NM_003889.3:c.1161-120C>G
NR1I2 transcript variant 1 NM_003889.4:c.1161-120= NM_003889.4:c.1161-120C>G
NR1I2 transcript variant 2 NM_022002.2:c.1278-120= NM_022002.2:c.1278-120C>G
NR1I2 transcript variant 2 NM_022002.3:c.1278-120= NM_022002.3:c.1278-120C>G
NR1I2 transcript variant 3 NM_033013.2:c.1050-120= NM_033013.2:c.1050-120C>G
NR1I2 transcript variant 3 NM_033013.3:c.1050-120= NM_033013.3:c.1050-120C>G
NR1I2 transcript variant X1 XM_005247866.1:c.995+1117= XM_005247866.1:c.995+1117C>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#.

80 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 CSHL-HAPMAP ss17773077 Feb 28, 2004 (120)
2 ABI ss44410098 Mar 13, 2006 (126)
3 PHARMGKB_PAAR-UCHI ss68756193 May 17, 2007 (127)
4 ILLUMINA ss75268331 Dec 07, 2007 (129)
5 AFFY ss76536786 Dec 07, 2007 (129)
6 HGSV ss84912405 Dec 15, 2007 (130)
7 1000GENOMES ss110817315 Jan 25, 2009 (130)
8 1000GENOMES ss112406778 Jan 25, 2009 (130)
9 ILLUMINA-UK ss117247453 Feb 14, 2009 (130)
10 KRIBB_YJKIM ss119732083 Dec 01, 2009 (131)
11 ILLUMINA ss160018369 Dec 01, 2009 (131)
12 ENSEMBL ss161383121 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss164100152 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss167107640 Jul 04, 2010 (132)
15 ILLUMINA ss171724730 Jul 04, 2010 (132)
16 BUSHMAN ss203084642 Jul 04, 2010 (132)
17 1000GENOMES ss220386638 Jul 14, 2010 (132)
18 1000GENOMES ss232002165 Jul 14, 2010 (132)
19 ILLUMINA ss244274658 Jul 04, 2010 (132)
20 ILLUMINA ss479630935 May 04, 2012 (137)
21 ILLUMINA ss479636085 May 04, 2012 (137)
22 ILLUMINA ss480139294 Sep 08, 2015 (146)
23 ILLUMINA ss484614144 May 04, 2012 (137)
24 ILLUMINA ss536738151 Sep 08, 2015 (146)
25 TISHKOFF ss556896750 Apr 25, 2013 (138)
26 ILLUMINA ss778342321 Aug 21, 2014 (142)
27 ILLUMINA ss782753885 Aug 21, 2014 (142)
28 ILLUMINA ss783720463 Aug 21, 2014 (142)
29 ILLUMINA ss832006054 Apr 01, 2015 (144)
30 ILLUMINA ss833796931 Aug 21, 2014 (142)
31 EVA-GONL ss979078249 Aug 21, 2014 (142)
32 JMKIDD_LAB ss1070773281 Aug 21, 2014 (142)
33 1000GENOMES ss1305837749 Aug 21, 2014 (142)
34 DDI ss1429562469 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1580150333 Apr 01, 2015 (144)
36 EVA_DECODE ss1588559972 Apr 01, 2015 (144)
37 EVA_UK10K_ALSPAC ss1608047375 Apr 01, 2015 (144)
38 EVA_UK10K_TWINSUK ss1651041408 Apr 01, 2015 (144)
39 EVA_MGP ss1711029747 Apr 01, 2015 (144)
40 EVA_SVP ss1712606642 Apr 01, 2015 (144)
41 ILLUMINA ss1752434831 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1922304807 Feb 12, 2016 (147)
43 JJLAB ss2021720154 Sep 14, 2016 (149)
44 USC_VALOUEV ss2149812107 Dec 20, 2016 (150)
45 HUMAN_LONGEVITY ss2255207357 Dec 20, 2016 (150)
46 TOPMED ss2422532311 Dec 20, 2016 (150)
47 ILLUMINA ss2634002659 Nov 08, 2017 (151)
48 GNOMAD ss2798216787 Nov 08, 2017 (151)
49 SWEGEN ss2993065586 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3024626855 Nov 08, 2017 (151)
51 CSHL ss3345229025 Nov 08, 2017 (151)
52 TOPMED ss3403453337 Nov 08, 2017 (151)
53 ILLUMINA ss3628757972 Oct 12, 2018 (152)
54 ILLUMINA ss3631946051 Oct 12, 2018 (152)
55 ILLUMINA ss3633306116 Oct 12, 2018 (152)
56 ILLUMINA ss3634023678 Oct 12, 2018 (152)
57 ILLUMINA ss3634913165 Oct 12, 2018 (152)
58 ILLUMINA ss3635707321 Oct 12, 2018 (152)
59 ILLUMINA ss3636609570 Oct 12, 2018 (152)
60 ILLUMINA ss3637459721 Oct 12, 2018 (152)
61 ILLUMINA ss3638437241 Oct 12, 2018 (152)
62 ILLUMINA ss3640620464 Oct 12, 2018 (152)
63 ILLUMINA ss3643392569 Oct 12, 2018 (152)
64 EGCUT_WGS ss3660992173 Jul 13, 2019 (153)
65 EVA_DECODE ss3710134763 Jul 13, 2019 (153)
66 ACPOP ss3730282151 Jul 13, 2019 (153)
67 ILLUMINA ss3745213128 Jul 13, 2019 (153)
68 EVA ss3760592468 Jul 13, 2019 (153)
69 ILLUMINA ss3772708436 Jul 13, 2019 (153)
70 KHV_HUMAN_GENOMES ss3803729233 Jul 13, 2019 (153)
71 EVA ss3828035604 Apr 25, 2020 (154)
72 SGDP_PRJ ss3856802677 Apr 25, 2020 (154)
73 KRGDB ss3902793454 Apr 25, 2020 (154)
74 KOGIC ss3952249991 Apr 25, 2020 (154)
75 FSA-LAB ss3984259526 Apr 27, 2021 (155)
76 EVA ss3986250614 Apr 27, 2021 (155)
77 EVA ss4017101728 Apr 27, 2021 (155)
78 TOPMED ss4580899157 Apr 27, 2021 (155)
79 TOMMO_GENOMICS ss5161222116 Apr 27, 2021 (155)
80 EVA ss5237178191 Apr 27, 2021 (155)
81 1000Genomes NC_000003.11 - 119535795 Oct 12, 2018 (152)
82 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 119535795 Oct 12, 2018 (152)
83 Genetic variation in the Estonian population NC_000003.11 - 119535795 Oct 12, 2018 (152)
84 The Danish reference pan genome NC_000003.11 - 119535795 Apr 25, 2020 (154)
85 gnomAD - Genomes NC_000003.12 - 119816948 Apr 27, 2021 (155)
86 Genome of the Netherlands Release 5 NC_000003.11 - 119535795 Apr 25, 2020 (154)
87 HapMap NC_000003.12 - 119816948 Apr 25, 2020 (154)
88 KOREAN population from KRGDB NC_000003.11 - 119535795 Apr 25, 2020 (154)
89 Korean Genome Project NC_000003.12 - 119816948 Apr 25, 2020 (154)
90 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 119535795 Apr 25, 2020 (154)
91 Northern Sweden NC_000003.11 - 119535795 Jul 13, 2019 (153)
92 PharmGKB Aggregated NC_000003.12 - 119816948 Apr 25, 2020 (154)
93 Qatari NC_000003.11 - 119535795 Apr 25, 2020 (154)
94 SGDP_PRJ NC_000003.11 - 119535795 Apr 25, 2020 (154)
95 Siberian NC_000003.11 - 119535795 Apr 25, 2020 (154)
96 8.3KJPN NC_000003.11 - 119535795 Apr 27, 2021 (155)
97 TopMed NC_000003.12 - 119816948 Apr 27, 2021 (155)
98 UK 10K study - Twins NC_000003.11 - 119535795 Oct 12, 2018 (152)
99 ALFA NC_000003.12 - 119816948 Apr 27, 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)
rs58718666 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss84912405 NC_000003.9:121018484:C:G NC_000003.12:119816947:C:G (self)
ss76536786, ss110817315, ss112406778, ss117247453, ss164100152, ss167107640, ss203084642, ss479630935, ss1588559972, ss1712606642, ss3643392569 NC_000003.10:121018484:C:G NC_000003.12:119816947:C:G (self)
17089563, 9518967, 6730421, 6315272, 4182396, 9970848, 145594, 3567016, 4346737, 8819657, 2328461, 19191423, 9518967, ss220386638, ss232002165, ss479636085, ss480139294, ss484614144, ss536738151, ss556896750, ss778342321, ss782753885, ss783720463, ss832006054, ss833796931, ss979078249, ss1070773281, ss1305837749, ss1429562469, ss1580150333, ss1608047375, ss1651041408, ss1711029747, ss1752434831, ss1922304807, ss2021720154, ss2149812107, ss2422532311, ss2634002659, ss2798216787, ss2993065586, ss3345229025, ss3628757972, ss3631946051, ss3633306116, ss3634023678, ss3634913165, ss3635707321, ss3636609570, ss3637459721, ss3638437241, ss3640620464, ss3660992173, ss3730282151, ss3745213128, ss3760592468, ss3772708436, ss3828035604, ss3856802677, ss3902793454, ss3984259526, ss3986250614, ss4017101728, ss5161222116 NC_000003.11:119535794:C:G NC_000003.12:119816947:C:G (self)
121505464, 2444624, 8627992, 8672, 261399830, 418276712, 1253683448, ss2255207357, ss3024626855, ss3403453337, ss3710134763, ss3803729233, ss3952249991, ss4580899157, ss5237178191 NC_000003.12:119816947:C:G NC_000003.12:119816947:C:G (self)
ss17773077 NT_005612.14:26030940:C:G NC_000003.12:119816947:C:G (self)
ss44410098, ss68756193, ss75268331, ss119732083, ss160018369, ss161383121, ss171724730, ss244274658 NT_005612.16:26030940:C:G NC_000003.12:119816947:C:G (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 rs11929668
PMID Title Author Year Journal
23064017 Donor ABCB1 variant associates with increased risk for kidney allograft failure. Moore J et al. 2012 Journal of the American Society of Nephrology
23777469 Haplotype association analysis of genes within the WNT signalling pathways in diabetic nephropathy. Kavanagh DH et al. 2013 BMC nephrology
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.post596+ae089ad