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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.

rs9931109

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr16:20047253 (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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.073834 (19543/264690, TOPMED)
A=0.073257 (10262/140082, GnomAD)
A=0.03086 (872/28258, 14KJPN) (+ 15 more)
A=0.06957 (1314/18888, ALFA)
A=0.03258 (546/16760, 8.3KJPN)
A=0.0631 (404/6404, 1000G_30x)
A=0.0621 (311/5008, 1000G)
A=0.0578 (259/4478, Estonian)
A=0.0607 (234/3854, ALSPAC)
A=0.0734 (272/3708, TWINSUK)
A=0.0270 (79/2930, KOREAN)
A=0.0311 (57/1832, Korea1K)
A=0.060 (60/998, GoNL)
A=0.050 (30/600, NorthernSweden)
A=0.049 (27/554, SGDP_PRJ)
A=0.093 (20/216, Qatari)
A=0.02 (1/56, Siberian)
A=0.05 (2/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GPR139 : 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 18888 A=0.06957 G=0.93043
European Sub 14284 A=0.06476 G=0.93524
African Sub 2946 A=0.0957 G=0.9043
African Others Sub 114 A=0.088 G=0.912
African American Sub 2832 A=0.0960 G=0.9040
Asian Sub 112 A=0.009 G=0.991
East Asian Sub 86 A=0.00 G=1.00
Other Asian Sub 26 A=0.04 G=0.96
Latin American 1 Sub 146 A=0.096 G=0.904
Latin American 2 Sub 610 A=0.052 G=0.948
South Asian Sub 98 A=0.12 G=0.88
Other Sub 692 A=0.069 G=0.931


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 A=0.073834 G=0.926166
gnomAD - Genomes Global Study-wide 140082 A=0.073257 G=0.926743
gnomAD - Genomes European Sub 75898 A=0.06208 G=0.93792
gnomAD - Genomes African Sub 41946 A=0.10454 G=0.89546
gnomAD - Genomes American Sub 13638 A=0.04590 G=0.95410
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.0894 G=0.9106
gnomAD - Genomes East Asian Sub 3128 A=0.0301 G=0.9699
gnomAD - Genomes Other Sub 2148 A=0.0689 G=0.9311
14KJPN JAPANESE Study-wide 28258 A=0.03086 G=0.96914
Allele Frequency Aggregator Total Global 18888 A=0.06957 G=0.93043
Allele Frequency Aggregator European Sub 14284 A=0.06476 G=0.93524
Allele Frequency Aggregator African Sub 2946 A=0.0957 G=0.9043
Allele Frequency Aggregator Other Sub 692 A=0.069 G=0.931
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.052 G=0.948
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.096 G=0.904
Allele Frequency Aggregator Asian Sub 112 A=0.009 G=0.991
Allele Frequency Aggregator South Asian Sub 98 A=0.12 G=0.88
8.3KJPN JAPANESE Study-wide 16760 A=0.03258 G=0.96742
1000Genomes_30x Global Study-wide 6404 A=0.0631 G=0.9369
1000Genomes_30x African Sub 1786 A=0.0941 G=0.9059
1000Genomes_30x Europe Sub 1266 A=0.0592 G=0.9408
1000Genomes_30x South Asian Sub 1202 A=0.0591 G=0.9409
1000Genomes_30x East Asian Sub 1170 A=0.0342 G=0.9658
1000Genomes_30x American Sub 980 A=0.051 G=0.949
1000Genomes Global Study-wide 5008 A=0.0621 G=0.9379
1000Genomes African Sub 1322 A=0.0968 G=0.9032
1000Genomes East Asian Sub 1008 A=0.0327 G=0.9673
1000Genomes Europe Sub 1006 A=0.0596 G=0.9404
1000Genomes South Asian Sub 978 A=0.058 G=0.942
1000Genomes American Sub 694 A=0.048 G=0.952
Genetic variation in the Estonian population Estonian Study-wide 4478 A=0.0578 G=0.9422
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.0607 G=0.9393
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.0734 G=0.9266
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.0270 C=0.0000, G=0.9730, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.0311 G=0.9689
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.060 G=0.940
Northern Sweden ACPOP Study-wide 600 A=0.050 G=0.950
SGDP_PRJ Global Study-wide 554 A=0.049 G=0.951
Qatari Global Study-wide 216 A=0.093 G=0.907
Siberian Global Study-wide 56 A=0.02 G=0.98
The Danish reference pan genome Danish Study-wide 40 A=0.05 G=0.95
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 16 NC_000016.10:g.20047253A>C
GRCh38.p14 chr 16 NC_000016.10:g.20047253A>G
GRCh38.p14 chr 16 NC_000016.10:g.20047253A>T
GRCh37.p13 chr 16 NC_000016.9:g.20058575A>C
GRCh37.p13 chr 16 NC_000016.9:g.20058575A>G
GRCh37.p13 chr 16 NC_000016.9:g.20058575A>T
Gene: GPR139, G protein-coupled receptor 139 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GPR139 transcript variant 1 NM_001002911.4:c.128-1458…

NM_001002911.4:c.128-14584T>G

N/A Intron Variant
GPR139 transcript variant 2 NM_001318483.1:c.-152-145…

NM_001318483.1:c.-152-14584T>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
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= C G T
GRCh38.p14 chr 16 NC_000016.10:g.20047253= NC_000016.10:g.20047253A>C NC_000016.10:g.20047253A>G NC_000016.10:g.20047253A>T
GRCh37.p13 chr 16 NC_000016.9:g.20058575= NC_000016.9:g.20058575A>C NC_000016.9:g.20058575A>G NC_000016.9:g.20058575A>T
GPR139 transcript NM_001002911.2:c.128-14584= NM_001002911.2:c.128-14584T>G NM_001002911.2:c.128-14584T>C NM_001002911.2:c.128-14584T>A
GPR139 transcript variant 1 NM_001002911.4:c.128-14584= NM_001002911.4:c.128-14584T>G NM_001002911.4:c.128-14584T>C NM_001002911.4:c.128-14584T>A
GPR139 transcript variant 2 NM_001318483.1:c.-152-14584= NM_001318483.1:c.-152-14584T>G NM_001318483.1:c.-152-14584T>C NM_001318483.1:c.-152-14584T>A
GPR139 transcript variant X1 XM_005255114.1:c.-152-14584= XM_005255114.1:c.-152-14584T>G XM_005255114.1:c.-152-14584T>C XM_005255114.1:c.-152-14584T>A
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#.

70 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss13770088 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss20022592 Feb 27, 2004 (120)
3 SSAHASNP ss21300558 Apr 05, 2004 (121)
4 HGSV ss77503094 Dec 07, 2007 (129)
5 HGSV ss85543732 Dec 14, 2007 (130)
6 BCMHGSC_JDW ss90343515 Mar 24, 2008 (129)
7 HUMANGENOME_JCVI ss96629816 Feb 04, 2009 (130)
8 ENSEMBL ss136625413 Dec 01, 2009 (131)
9 ENSEMBL ss143015392 Dec 01, 2009 (131)
10 GMI ss157178077 Dec 01, 2009 (131)
11 COMPLETE_GENOMICS ss167988655 Jul 04, 2010 (132)
12 COMPLETE_GENOMICS ss171076411 Jul 04, 2010 (132)
13 BUSHMAN ss201532012 Jul 04, 2010 (132)
14 BCM-HGSC-SUB ss207643683 Jul 04, 2010 (132)
15 BL ss255571460 May 09, 2011 (134)
16 GMI ss282467294 May 04, 2012 (137)
17 GMI ss287047586 Apr 25, 2013 (138)
18 PJP ss291932906 May 09, 2011 (134)
19 1000GENOMES ss339164025 May 09, 2011 (134)
20 TISHKOFF ss564829831 Apr 25, 2013 (138)
21 SSMP ss660577903 Apr 25, 2013 (138)
22 EVA-GONL ss992361617 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1080542171 Aug 21, 2014 (142)
24 1000GENOMES ss1355691191 Aug 21, 2014 (142)
25 DDI ss1427802175 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1577868159 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1634164123 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1677158156 Apr 01, 2015 (144)
29 EVA_DECODE ss1696395605 Apr 01, 2015 (144)
30 HAMMER_LAB ss1808457565 Sep 08, 2015 (146)
31 WEILL_CORNELL_DGM ss1935783260 Feb 12, 2016 (147)
32 GENOMED ss1968237102 Jul 19, 2016 (147)
33 JJLAB ss2028678668 Sep 14, 2016 (149)
34 USC_VALOUEV ss2157089123 Dec 20, 2016 (150)
35 HUMAN_LONGEVITY ss2211192390 Dec 20, 2016 (150)
36 SYSTEMSBIOZJU ss2628832333 Nov 08, 2017 (151)
37 GRF ss2701592225 Nov 08, 2017 (151)
38 GNOMAD ss2941229228 Nov 08, 2017 (151)
39 SWEGEN ss3014205381 Nov 08, 2017 (151)
40 BIOINF_KMB_FNS_UNIBA ss3028163676 Nov 08, 2017 (151)
41 CSHL ss3351375409 Nov 08, 2017 (151)
42 URBANLAB ss3650482486 Oct 12, 2018 (152)
43 EGCUT_WGS ss3681302109 Jul 13, 2019 (153)
44 EVA_DECODE ss3698991358 Jul 13, 2019 (153)
45 ACPOP ss3741404256 Jul 13, 2019 (153)
46 EVA ss3753778016 Jul 13, 2019 (153)
47 PACBIO ss3788002572 Jul 13, 2019 (153)
48 PACBIO ss3792992813 Jul 13, 2019 (153)
49 PACBIO ss3797877762 Jul 13, 2019 (153)
50 KHV_HUMAN_GENOMES ss3819073136 Jul 13, 2019 (153)
51 EVA ss3834512832 Apr 27, 2020 (154)
52 EVA ss3840863594 Apr 27, 2020 (154)
53 EVA ss3846354452 Apr 27, 2020 (154)
54 SGDP_PRJ ss3884122661 Apr 27, 2020 (154)
55 KRGDB ss3933441661 Apr 27, 2020 (154)
56 KOGIC ss3977244252 Apr 27, 2020 (154)
57 TOPMED ss5010358316 Apr 27, 2021 (155)
58 TOMMO_GENOMICS ss5218811263 Apr 27, 2021 (155)
59 1000G_HIGH_COVERAGE ss5300420138 Oct 16, 2022 (156)
60 EVA ss5422809371 Oct 16, 2022 (156)
61 HUGCELL_USP ss5493894991 Oct 16, 2022 (156)
62 1000G_HIGH_COVERAGE ss5602782602 Oct 16, 2022 (156)
63 SANFORD_IMAGENETICS ss5658626586 Oct 16, 2022 (156)
64 TOMMO_GENOMICS ss5773404060 Oct 16, 2022 (156)
65 YY_MCH ss5815828976 Oct 16, 2022 (156)
66 EVA ss5846212113 Oct 16, 2022 (156)
67 EVA ss5851522278 Oct 16, 2022 (156)
68 EVA ss5898574573 Oct 16, 2022 (156)
69 EVA ss5950047300 Oct 16, 2022 (156)
70 EVA ss5980910996 Oct 16, 2022 (156)
71 1000Genomes NC_000016.9 - 20058575 Oct 12, 2018 (152)
72 1000Genomes_30x NC_000016.10 - 20047253 Oct 16, 2022 (156)
73 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 20058575 Oct 12, 2018 (152)
74 Genetic variation in the Estonian population NC_000016.9 - 20058575 Oct 12, 2018 (152)
75 The Danish reference pan genome NC_000016.9 - 20058575 Apr 27, 2020 (154)
76 gnomAD - Genomes NC_000016.10 - 20047253 Apr 27, 2021 (155)
77 Genome of the Netherlands Release 5 NC_000016.9 - 20058575 Apr 27, 2020 (154)
78 KOREAN population from KRGDB NC_000016.9 - 20058575 Apr 27, 2020 (154)
79 Korean Genome Project NC_000016.10 - 20047253 Apr 27, 2020 (154)
80 Northern Sweden NC_000016.9 - 20058575 Jul 13, 2019 (153)
81 Qatari NC_000016.9 - 20058575 Apr 27, 2020 (154)
82 SGDP_PRJ NC_000016.9 - 20058575 Apr 27, 2020 (154)
83 Siberian NC_000016.9 - 20058575 Apr 27, 2020 (154)
84 8.3KJPN NC_000016.9 - 20058575 Apr 27, 2021 (155)
85 14KJPN NC_000016.10 - 20047253 Oct 16, 2022 (156)
86 TopMed NC_000016.10 - 20047253 Apr 27, 2021 (155)
87 UK 10K study - Twins NC_000016.9 - 20058575 Oct 12, 2018 (152)
88 ALFA NC_000016.10 - 20047253 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)
rs57097414 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
40619055, ss3933441661 NC_000016.9:20058574:A:C NC_000016.10:20047252:A:C (self)
ss77503094, ss85543732, ss90343515, ss167988655, ss171076411, ss201532012, ss207643683, ss255571460, ss282467294, ss287047586, ss291932906, ss1696395605 NC_000016.8:19966075:A:G NC_000016.10:20047252:A:G (self)
68836106, 38213957, 27040357, 4082379, 17047232, 40619055, 14689121, 17825182, 36139641, 9605477, 76780570, 38213957, ss339164025, ss564829831, ss660577903, ss992361617, ss1080542171, ss1355691191, ss1427802175, ss1577868159, ss1634164123, ss1677158156, ss1808457565, ss1935783260, ss1968237102, ss2028678668, ss2157089123, ss2628832333, ss2701592225, ss2941229228, ss3014205381, ss3351375409, ss3681302109, ss3741404256, ss3753778016, ss3788002572, ss3792992813, ss3797877762, ss3834512832, ss3840863594, ss3884122661, ss3933441661, ss5218811263, ss5422809371, ss5658626586, ss5846212113, ss5950047300, ss5980910996 NC_000016.9:20058574:A:G NC_000016.10:20047252:A:G (self)
90308537, 485100655, 33622253, 107241164, 225903977, 1379500679, ss2211192390, ss3028163676, ss3650482486, ss3698991358, ss3819073136, ss3846354452, ss3977244252, ss5010358316, ss5300420138, ss5493894991, ss5602782602, ss5773404060, ss5815828976, ss5851522278, ss5898574573 NC_000016.10:20047252:A:G NC_000016.10:20047252:A:G (self)
ss13770088, ss20022592, ss21300558 NT_010393.14:11370907:A:G NC_000016.10:20047252:A:G (self)
ss96629816, ss136625413, ss143015392, ss157178077 NT_010393.16:19998574:A:G NC_000016.10:20047252:A:G (self)
40619055, ss3933441661 NC_000016.9:20058574:A:T NC_000016.10:20047252: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.

No publications for rs9931109

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