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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.

rs11114654

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:76603765 (GRCh38.p14) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.151755 (40168/264690, TOPMED)
T=0.153400 (21429/139694, GnomAD)
T=0.44228 (12498/28258, 14KJPN) (+ 16 more)
T=0.14447 (2729/18890, ALFA)
T=0.44278 (7421/16760, 8.3KJPN)
T=0.2024 (1296/6404, 1000G_30x)
T=0.2081 (1042/5008, 1000G)
T=0.1491 (668/4480, Estonian)
T=0.1170 (451/3854, ALSPAC)
T=0.1305 (484/3708, TWINSUK)
T=0.4058 (1189/2930, KOREAN)
T=0.133 (133/998, GoNL)
T=0.200 (120/600, NorthernSweden)
T=0.232 (76/328, HapMap)
C=0.409 (94/230, SGDP_PRJ)
T=0.157 (34/216, Qatari)
T=0.299 (64/214, Vietnamese)
T=0.15 (6/40, GENOME_DK)
C=0.43 (13/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LOC105369850 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 18890 C=0.85553 T=0.14447
European Sub 14286 C=0.86329 T=0.13671
African Sub 2946 C=0.8262 T=0.1738
African Others Sub 114 C=0.833 T=0.167
African American Sub 2832 C=0.8259 T=0.1741
Asian Sub 112 C=0.634 T=0.366
East Asian Sub 86 C=0.58 T=0.42
Other Asian Sub 26 C=0.81 T=0.19
Latin American 1 Sub 146 C=0.842 T=0.158
Latin American 2 Sub 610 C=0.890 T=0.110
South Asian Sub 98 C=0.85 T=0.15
Other Sub 692 C=0.829 T=0.171


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=0.848245 T=0.151755
gnomAD - Genomes Global Study-wide 139694 C=0.846600 T=0.153400
gnomAD - Genomes European Sub 75674 C=0.86263 T=0.13737
gnomAD - Genomes African Sub 41824 C=0.82307 T=0.17693
gnomAD - Genomes American Sub 13608 C=0.86897 T=0.13103
gnomAD - Genomes Ashkenazi Jewish Sub 3318 C=0.8662 T=0.1338
gnomAD - Genomes East Asian Sub 3126 C=0.6561 T=0.3439
gnomAD - Genomes Other Sub 2144 C=0.8451 T=0.1549
14KJPN JAPANESE Study-wide 28258 C=0.55772 T=0.44228
Allele Frequency Aggregator Total Global 18890 C=0.85553 T=0.14447
Allele Frequency Aggregator European Sub 14286 C=0.86329 T=0.13671
Allele Frequency Aggregator African Sub 2946 C=0.8262 T=0.1738
Allele Frequency Aggregator Other Sub 692 C=0.829 T=0.171
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.890 T=0.110
Allele Frequency Aggregator Latin American 1 Sub 146 C=0.842 T=0.158
Allele Frequency Aggregator Asian Sub 112 C=0.634 T=0.366
Allele Frequency Aggregator South Asian Sub 98 C=0.85 T=0.15
8.3KJPN JAPANESE Study-wide 16760 C=0.55722 T=0.44278
1000Genomes_30x Global Study-wide 6404 C=0.7976 T=0.2024
1000Genomes_30x African Sub 1786 C=0.8404 T=0.1596
1000Genomes_30x Europe Sub 1266 C=0.8657 T=0.1343
1000Genomes_30x South Asian Sub 1202 C=0.7754 T=0.2246
1000Genomes_30x East Asian Sub 1170 C=0.6239 T=0.3761
1000Genomes_30x American Sub 980 C=0.866 T=0.134
1000Genomes Global Study-wide 5008 C=0.7919 T=0.2081
1000Genomes African Sub 1322 C=0.8404 T=0.1596
1000Genomes East Asian Sub 1008 C=0.6250 T=0.3750
1000Genomes Europe Sub 1006 C=0.8668 T=0.1332
1000Genomes South Asian Sub 978 C=0.770 T=0.230
1000Genomes American Sub 694 C=0.865 T=0.135
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8509 T=0.1491
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8830 T=0.1170
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8695 T=0.1305
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5942 T=0.4058
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.867 T=0.133
Northern Sweden ACPOP Study-wide 600 C=0.800 T=0.200
HapMap Global Study-wide 328 C=0.768 T=0.232
HapMap African Sub 120 C=0.883 T=0.117
HapMap American Sub 118 C=0.856 T=0.144
HapMap Asian Sub 90 C=0.50 T=0.50
SGDP_PRJ Global Study-wide 230 C=0.409 T=0.591
Qatari Global Study-wide 216 C=0.843 T=0.157
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.701 T=0.299
The Danish reference pan genome Danish Study-wide 40 C=0.85 T=0.15
Siberian Global Study-wide 30 C=0.43 T=0.57
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.p14 chr 12 NC_000012.12:g.76603765C>T
GRCh37.p13 chr 12 NC_000012.11:g.76997545C>T
Gene: LOC105369850, uncharacterized LOC105369850 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC105369850 transcript variant X3 XR_001749220.2:n. N/A Intron Variant
LOC105369850 transcript variant X1 XR_945113.4:n. N/A Intron Variant
LOC105369850 transcript variant X2 XR_945114.3: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.

Not Reported in ClinVar
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= T
GRCh38.p14 chr 12 NC_000012.12:g.76603765= NC_000012.12:g.76603765C>T
GRCh37.p13 chr 12 NC_000012.11:g.76997545= NC_000012.11:g.76997545C>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#.

51 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15935039 Feb 27, 2004 (120)
2 SC_SNP ss18960690 Feb 27, 2004 (120)
3 HGSV ss83686766 Dec 15, 2007 (130)
4 GMI ss157666072 Dec 01, 2009 (131)
5 1000GENOMES ss225841207 Jul 14, 2010 (132)
6 1000GENOMES ss235998715 Jul 15, 2010 (132)
7 1000GENOMES ss242545309 Jul 15, 2010 (132)
8 GMI ss281462475 May 04, 2012 (137)
9 PJP ss291286021 May 09, 2011 (134)
10 TISHKOFF ss563265897 Apr 25, 2013 (138)
11 SSMP ss658834262 Apr 25, 2013 (138)
12 EVA-GONL ss989711349 Aug 21, 2014 (142)
13 JMKIDD_LAB ss1078591173 Aug 21, 2014 (142)
14 1000GENOMES ss1345702796 Aug 21, 2014 (142)
15 DDI ss1426985627 Apr 01, 2015 (144)
16 EVA_GENOME_DK ss1576386161 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1628946652 Apr 01, 2015 (144)
18 EVA_DECODE ss1641808177 Apr 01, 2015 (144)
19 EVA_UK10K_TWINSUK ss1671940685 Apr 01, 2015 (144)
20 WEILL_CORNELL_DGM ss1933075112 Feb 12, 2016 (147)
21 GENOMED ss1967628245 Jul 19, 2016 (147)
22 JJLAB ss2027288383 Sep 14, 2016 (149)
23 USC_VALOUEV ss2155632236 Dec 20, 2016 (150)
24 HUMAN_LONGEVITY ss2191209226 Dec 20, 2016 (150)
25 GRF ss2699983541 Nov 08, 2017 (151)
26 GNOMAD ss2912494200 Nov 08, 2017 (151)
27 SWEGEN ss3009971226 Nov 08, 2017 (151)
28 BIOINF_KMB_FNS_UNIBA ss3027454458 Nov 08, 2017 (151)
29 CSHL ss3350142455 Nov 08, 2017 (151)
30 EGCUT_WGS ss3677245859 Jul 13, 2019 (153)
31 EVA_DECODE ss3694006562 Jul 13, 2019 (153)
32 ACPOP ss3739172246 Jul 13, 2019 (153)
33 EVA ss3750684821 Jul 13, 2019 (153)
34 KHV_HUMAN_GENOMES ss3816019401 Jul 13, 2019 (153)
35 EVA ss3833210138 Apr 27, 2020 (154)
36 SGDP_PRJ ss3878631203 Apr 27, 2020 (154)
37 KRGDB ss3927311865 Apr 27, 2020 (154)
38 TOPMED ss4924417562 Apr 26, 2021 (155)
39 TOMMO_GENOMICS ss5207105753 Apr 26, 2021 (155)
40 1000G_HIGH_COVERAGE ss5291414989 Oct 16, 2022 (156)
41 EVA ss5406729836 Oct 16, 2022 (156)
42 HUGCELL_USP ss5486096570 Oct 16, 2022 (156)
43 EVA ss5510763242 Oct 16, 2022 (156)
44 1000G_HIGH_COVERAGE ss5589213363 Oct 16, 2022 (156)
45 SANFORD_IMAGENETICS ss5653494897 Oct 16, 2022 (156)
46 TOMMO_GENOMICS ss5757125323 Oct 16, 2022 (156)
47 YY_MCH ss5813446325 Oct 16, 2022 (156)
48 EVA ss5838196348 Oct 16, 2022 (156)
49 EVA ss5850450634 Oct 16, 2022 (156)
50 EVA ss5905077677 Oct 16, 2022 (156)
51 EVA ss5944870819 Oct 16, 2022 (156)
52 1000Genomes NC_000012.11 - 76997545 Oct 12, 2018 (152)
53 1000Genomes_30x NC_000012.12 - 76603765 Oct 16, 2022 (156)
54 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 76997545 Oct 12, 2018 (152)
55 Genetic variation in the Estonian population NC_000012.11 - 76997545 Oct 12, 2018 (152)
56 The Danish reference pan genome NC_000012.11 - 76997545 Apr 27, 2020 (154)
57 gnomAD - Genomes NC_000012.12 - 76603765 Apr 26, 2021 (155)
58 Genome of the Netherlands Release 5 NC_000012.11 - 76997545 Apr 27, 2020 (154)
59 HapMap NC_000012.12 - 76603765 Apr 27, 2020 (154)
60 KOREAN population from KRGDB NC_000012.11 - 76997545 Apr 27, 2020 (154)
61 Northern Sweden NC_000012.11 - 76997545 Jul 13, 2019 (153)
62 Qatari NC_000012.11 - 76997545 Apr 27, 2020 (154)
63 SGDP_PRJ NC_000012.11 - 76997545 Apr 27, 2020 (154)
64 Siberian NC_000012.11 - 76997545 Apr 27, 2020 (154)
65 8.3KJPN NC_000012.11 - 76997545 Apr 26, 2021 (155)
66 14KJPN NC_000012.12 - 76603765 Oct 16, 2022 (156)
67 TopMed NC_000012.12 - 76603765 Apr 26, 2021 (155)
68 UK 10K study - Twins NC_000012.11 - 76997545 Oct 12, 2018 (152)
69 A Vietnamese Genetic Variation Database NC_000012.11 - 76997545 Jul 13, 2019 (153)
70 ALFA NC_000012.12 - 76603765 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)
rs59026584 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83686766 NC_000012.9:75500012:C:T NC_000012.12:76603764:C:T (self)
ss281462475, ss291286021, ss1641808177 NC_000012.10:75521675:C:T NC_000012.12:76603764:C:T (self)
58477669, 32467200, 22984107, 3032385, 14485880, 34489259, 12457111, 15117042, 30648183, 8148590, 65075060, 32467200, 7206495, ss225841207, ss235998715, ss242545309, ss563265897, ss658834262, ss989711349, ss1078591173, ss1345702796, ss1426985627, ss1576386161, ss1628946652, ss1671940685, ss1933075112, ss1967628245, ss2027288383, ss2155632236, ss2699983541, ss2912494200, ss3009971226, ss3350142455, ss3677245859, ss3739172246, ss3750684821, ss3833210138, ss3878631203, ss3927311865, ss5207105753, ss5406729836, ss5510763242, ss5653494897, ss5838196348, ss5944870819 NC_000012.11:76997544:C:T NC_000012.12:76603764:C:T (self)
76739298, 412416286, 854206, 90962427, 139963219, 1225513055, ss2191209226, ss3027454458, ss3694006562, ss3816019401, ss4924417562, ss5291414989, ss5486096570, ss5589213363, ss5757125323, ss5813446325, ss5850450634, ss5905077677 NC_000012.12:76603764:C:T NC_000012.12:76603764:C:T (self)
ss15935039, ss18960690 NT_019546.15:479735:C:T NC_000012.12:76603764:C:T (self)
ss157666072 NT_029419.12:39140850:C:T NC_000012.12:76603764:C:T (self)
Help

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

No publications for rs11114654

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.post761+d5e8e07