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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.

rs12116437

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:209723682 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.189943 (50276/264690, TOPMED)
A=0.194605 (27272/140140, GnomAD)
A=0.12840 (3628/28256, 14KJPN) (+ 18 more)
A=0.20842 (3937/18890, ALFA)
A=0.12512 (2097/16760, 8.3KJPN)
A=0.1928 (1235/6404, 1000G_30x)
A=0.1921 (962/5008, 1000G)
A=0.2257 (1011/4480, Estonian)
A=0.2060 (794/3854, ALSPAC)
A=0.2149 (797/3708, TWINSUK)
A=0.1679 (492/2930, KOREAN)
A=0.1463 (268/1832, Korea1K)
A=0.225 (225/998, GoNL)
A=0.275 (165/600, NorthernSweden)
A=0.148 (32/216, Qatari)
A=0.227 (49/216, Vietnamese)
G=0.435 (87/200, SGDP_PRJ)
A=0.21 (16/76, Ancient Sardinia)
A=0.23 (9/40, GENOME_DK)
G=0.50 (12/24, Siberian)
A=0.50 (12/24, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HSD11B1-AS1 : Intron Variant
HSD11B1 : 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 G=0.79158 A=0.20842
European Sub 14286 G=0.78622 A=0.21378
African Sub 2946 G=0.8232 A=0.1768
African Others Sub 114 G=0.772 A=0.228
African American Sub 2832 G=0.8252 A=0.1748
Asian Sub 112 G=0.804 A=0.196
East Asian Sub 86 G=0.83 A=0.17
Other Asian Sub 26 G=0.73 A=0.27
Latin American 1 Sub 146 G=0.795 A=0.205
Latin American 2 Sub 610 G=0.761 A=0.239
South Asian Sub 98 G=0.81 A=0.19
Other Sub 692 G=0.790 A=0.210


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 G=0.810057 A=0.189943
gnomAD - Genomes Global Study-wide 140140 G=0.805395 A=0.194605
gnomAD - Genomes European Sub 75886 G=0.78785 A=0.21215
gnomAD - Genomes African Sub 41998 G=0.83171 A=0.16829
gnomAD - Genomes American Sub 13656 G=0.82696 A=0.17304
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.7964 A=0.2036
gnomAD - Genomes East Asian Sub 3130 G=0.7958 A=0.2042
gnomAD - Genomes Other Sub 2150 G=0.8014 A=0.1986
14KJPN JAPANESE Study-wide 28256 G=0.87160 A=0.12840
Allele Frequency Aggregator Total Global 18890 G=0.79158 A=0.20842
Allele Frequency Aggregator European Sub 14286 G=0.78622 A=0.21378
Allele Frequency Aggregator African Sub 2946 G=0.8232 A=0.1768
Allele Frequency Aggregator Other Sub 692 G=0.790 A=0.210
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.761 A=0.239
Allele Frequency Aggregator Latin American 1 Sub 146 G=0.795 A=0.205
Allele Frequency Aggregator Asian Sub 112 G=0.804 A=0.196
Allele Frequency Aggregator South Asian Sub 98 G=0.81 A=0.19
8.3KJPN JAPANESE Study-wide 16760 G=0.87488 A=0.12512
1000Genomes_30x Global Study-wide 6404 G=0.8072 A=0.1928
1000Genomes_30x African Sub 1786 G=0.8303 A=0.1697
1000Genomes_30x Europe Sub 1266 G=0.7836 A=0.2164
1000Genomes_30x South Asian Sub 1202 G=0.8328 A=0.1672
1000Genomes_30x East Asian Sub 1170 G=0.7812 A=0.2188
1000Genomes_30x American Sub 980 G=0.795 A=0.205
1000Genomes Global Study-wide 5008 G=0.8079 A=0.1921
1000Genomes African Sub 1322 G=0.8306 A=0.1694
1000Genomes East Asian Sub 1008 G=0.7788 A=0.2212
1000Genomes Europe Sub 1006 G=0.7922 A=0.2078
1000Genomes South Asian Sub 978 G=0.833 A=0.167
1000Genomes American Sub 694 G=0.794 A=0.206
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.7743 A=0.2257
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7940 A=0.2060
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7851 A=0.2149
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.8321 A=0.1679
Korean Genome Project KOREAN Study-wide 1832 G=0.8537 A=0.1463
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.775 A=0.225
Northern Sweden ACPOP Study-wide 600 G=0.725 A=0.275
Qatari Global Study-wide 216 G=0.852 A=0.148
A Vietnamese Genetic Variation Database Global Study-wide 216 G=0.773 A=0.227
SGDP_PRJ Global Study-wide 200 G=0.435 A=0.565
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 76 G=0.79 A=0.21
The Danish reference pan genome Danish Study-wide 40 G=0.78 A=0.23
Siberian Global Study-wide 24 G=0.50 A=0.50
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 1 NC_000001.11:g.209723682G>A
GRCh37.p13 chr 1 NC_000001.10:g.209897027G>A
HSD11B1 RefSeqGene NG_012081.1:g.42478G>A
Gene: HSD11B1, hydroxysteroid 11-beta dehydrogenase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
HSD11B1 transcript variant 3 NM_001206741.2:c.518-8754…

NM_001206741.2:c.518-8754G>A

N/A Intron Variant
HSD11B1 transcript variant 1 NM_005525.4:c.518-8754G>A N/A Intron Variant
HSD11B1 transcript variant 2 NM_181755.3:c.518-8754G>A N/A Intron Variant
Gene: HSD11B1-AS1, HSD11B1 antisense RNA 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HSD11B1-AS1 transcript variant 1 NR_134509.1:n. N/A Intron Variant
HSD11B1-AS1 transcript variant 2 NR_134510.1:n. N/A Intron Variant
HSD11B1-AS1 transcript variant 3 NR_134511.1:n. N/A Genic 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

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 G= A
GRCh38.p14 chr 1 NC_000001.11:g.209723682= NC_000001.11:g.209723682G>A
GRCh37.p13 chr 1 NC_000001.10:g.209897027= NC_000001.10:g.209897027G>A
HSD11B1 RefSeqGene NG_012081.1:g.42478= NG_012081.1:g.42478G>A
HSD11B1 transcript variant 3 NM_001206741.1:c.518-8754= NM_001206741.1:c.518-8754G>A
HSD11B1 transcript variant 3 NM_001206741.2:c.518-8754= NM_001206741.2:c.518-8754G>A
HSD11B1 transcript variant 1 NM_005525.3:c.518-8754= NM_005525.3:c.518-8754G>A
HSD11B1 transcript variant 1 NM_005525.4:c.518-8754= NM_005525.4:c.518-8754G>A
HSD11B1 transcript variant 2 NM_181755.2:c.518-8754= NM_181755.2:c.518-8754G>A
HSD11B1 transcript variant 2 NM_181755.3:c.518-8754= NM_181755.3:c.518-8754G>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#.

60 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss18243027 Feb 28, 2004 (120)
2 BCMHGSC_JDW ss87954111 Mar 23, 2008 (129)
3 1000GENOMES ss108909620 Jan 23, 2009 (130)
4 ENSEMBL ss138145766 Dec 01, 2009 (131)
5 GMI ss156230788 Dec 01, 2009 (131)
6 COMPLETE_GENOMICS ss167470501 Jul 04, 2010 (132)
7 1000GENOMES ss218855978 Jul 14, 2010 (132)
8 1000GENOMES ss230881530 Jul 14, 2010 (132)
9 1000GENOMES ss238498313 Jul 15, 2010 (132)
10 GMI ss276198346 May 04, 2012 (137)
11 GMI ss284219829 Apr 25, 2013 (138)
12 TISHKOFF ss555109153 Apr 25, 2013 (138)
13 SSMP ss648665969 Apr 25, 2013 (138)
14 EVA-GONL ss976090882 Aug 21, 2014 (142)
15 JMKIDD_LAB ss1068562105 Aug 21, 2014 (142)
16 1000GENOMES ss1294453240 Aug 21, 2014 (142)
17 EVA_GENOME_DK ss1574643847 Apr 01, 2015 (144)
18 EVA_DECODE ss1585486445 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1602033960 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1645027993 Apr 01, 2015 (144)
21 HAMMER_LAB ss1795662163 Sep 08, 2015 (146)
22 WEILL_CORNELL_DGM ss1919316909 Feb 12, 2016 (147)
23 JJLAB ss2020180097 Sep 14, 2016 (149)
24 USC_VALOUEV ss2148209869 Dec 20, 2016 (150)
25 HUMAN_LONGEVITY ss2169679681 Dec 20, 2016 (150)
26 GRF ss2698202597 Nov 08, 2017 (151)
27 GNOMAD ss2765660960 Nov 08, 2017 (151)
28 AFFY ss2985537573 Nov 08, 2017 (151)
29 SWEGEN ss2988368888 Nov 08, 2017 (151)
30 BIOINF_KMB_FNS_UNIBA ss3023849752 Nov 08, 2017 (151)
31 CSHL ss3343888354 Nov 08, 2017 (151)
32 EGCUT_WGS ss3656327278 Jul 12, 2019 (153)
33 EVA_DECODE ss3688533061 Jul 12, 2019 (153)
34 ACPOP ss3727818375 Jul 12, 2019 (153)
35 EVA ss3747274313 Jul 12, 2019 (153)
36 PACBIO ss3783674518 Jul 12, 2019 (153)
37 PACBIO ss3789288914 Jul 12, 2019 (153)
38 PACBIO ss3794161185 Jul 12, 2019 (153)
39 KHV_HUMAN_GENOMES ss3800279840 Jul 12, 2019 (153)
40 EVA ss3826617532 Apr 25, 2020 (154)
41 EVA ss3836709026 Apr 25, 2020 (154)
42 EVA ss3842120533 Apr 25, 2020 (154)
43 SGDP_PRJ ss3850795862 Apr 25, 2020 (154)
44 KRGDB ss3896099629 Apr 25, 2020 (154)
45 KOGIC ss3946396441 Apr 25, 2020 (154)
46 EVA ss3984848768 Apr 27, 2021 (155)
47 TOPMED ss4481846064 Apr 27, 2021 (155)
48 TOMMO_GENOMICS ss5148211537 Apr 27, 2021 (155)
49 1000G_HIGH_COVERAGE ss5245625177 Oct 12, 2022 (156)
50 EVA ss5324479911 Oct 12, 2022 (156)
51 HUGCELL_USP ss5446079086 Oct 12, 2022 (156)
52 EVA ss5506168661 Oct 12, 2022 (156)
53 1000G_HIGH_COVERAGE ss5519635707 Oct 12, 2022 (156)
54 SANFORD_IMAGENETICS ss5627350353 Oct 12, 2022 (156)
55 TOMMO_GENOMICS ss5675908832 Oct 12, 2022 (156)
56 YY_MCH ss5801594861 Oct 12, 2022 (156)
57 EVA ss5833192449 Oct 12, 2022 (156)
58 EVA ss5849263048 Oct 12, 2022 (156)
59 EVA ss5911775951 Oct 12, 2022 (156)
60 EVA ss5939182899 Oct 12, 2022 (156)
61 1000Genomes NC_000001.10 - 209897027 Oct 11, 2018 (152)
62 1000Genomes_30x NC_000001.11 - 209723682 Oct 12, 2022 (156)
63 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 209897027 Oct 11, 2018 (152)
64 Genetic variation in the Estonian population NC_000001.10 - 209897027 Oct 11, 2018 (152)
65 The Danish reference pan genome NC_000001.10 - 209897027 Apr 25, 2020 (154)
66 gnomAD - Genomes NC_000001.11 - 209723682 Apr 27, 2021 (155)
67 Genome of the Netherlands Release 5 NC_000001.10 - 209897027 Apr 25, 2020 (154)
68 KOREAN population from KRGDB NC_000001.10 - 209897027 Apr 25, 2020 (154)
69 Korean Genome Project NC_000001.11 - 209723682 Apr 25, 2020 (154)
70 Northern Sweden NC_000001.10 - 209897027 Jul 12, 2019 (153)
71 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000001.10 - 209897027 Apr 27, 2021 (155)
72 Qatari NC_000001.10 - 209897027 Apr 25, 2020 (154)
73 SGDP_PRJ NC_000001.10 - 209897027 Apr 25, 2020 (154)
74 Siberian NC_000001.10 - 209897027 Apr 25, 2020 (154)
75 8.3KJPN NC_000001.10 - 209897027 Apr 27, 2021 (155)
76 14KJPN NC_000001.11 - 209723682 Oct 12, 2022 (156)
77 TopMed NC_000001.11 - 209723682 Apr 27, 2021 (155)
78 UK 10K study - Twins NC_000001.10 - 209897027 Oct 11, 2018 (152)
79 A Vietnamese Genetic Variation Database NC_000001.10 - 209897027 Jul 12, 2019 (153)
80 ALFA NC_000001.11 - 209723682 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss87954111, ss108909620, ss167470501, ss276198346, ss284219829, ss1585486445 NC_000001.9:207963649:G:A NC_000001.11:209723681:G:A (self)
5300406, 2922256, 2065526, 1863833, 1275438, 3277023, 1103240, 74695, 1358839, 2812842, 726223, 6180844, 2922256, 631003, ss218855978, ss230881530, ss238498313, ss555109153, ss648665969, ss976090882, ss1068562105, ss1294453240, ss1574643847, ss1602033960, ss1645027993, ss1795662163, ss1919316909, ss2020180097, ss2148209869, ss2698202597, ss2765660960, ss2985537573, ss2988368888, ss3343888354, ss3656327278, ss3727818375, ss3747274313, ss3783674518, ss3789288914, ss3794161185, ss3826617532, ss3836709026, ss3850795862, ss3896099629, ss3984848768, ss5148211537, ss5324479911, ss5506168661, ss5627350353, ss5833192449, ss5939182899 NC_000001.10:209897026:G:A NC_000001.11:209723681:G:A (self)
7161642, 38160125, 2774442, 9745936, 45452399, 7818639705, ss2169679681, ss3023849752, ss3688533061, ss3800279840, ss3842120533, ss3946396441, ss4481846064, ss5245625177, ss5446079086, ss5519635707, ss5675908832, ss5801594861, ss5849263048, ss5911775951 NC_000001.11:209723681:G:A NC_000001.11:209723681:G:A (self)
ss18243027 NT_021877.16:3355823:G:A NC_000001.11:209723681:G:A (self)
ss138145766, ss156230788 NT_167186.1:3414805:G:A NC_000001.11:209723681:G:A (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 rs12116437

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