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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.

rs791620

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr7:128241090 (GRCh38.p12) 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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.072104 (9054/125568, TOPMED)
A=0.07754 (2425/31276, GnomAD)
A=0.0559 (280/5008, 1000G) (+ 14 more)
A=0.0658 (295/4480, Estonian)
A=0.0758 (292/3854, ALSPAC)
A=0.0661 (245/3708, TWINSUK)
A=0.0731 (160/2188, ALFA Project)
A=0.0006 (1/1776, Korea1K)
A=0.062 (37/600, NorthernSweden)
A=0.014 (3/216, Qatari)
A=0.005 (1/214, Vietnamese)
A=0.000 (0/186, HapMap)
A=0.05 (2/40, GENOME_DK)
C=0.50 (15/30, SGDP_PRJ)
A=0.50 (15/30, SGDP_PRJ)
C=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LEP : 2KB Upstream Variant
Publications
5 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.p12 chr 7 NC_000007.14:g.128241090C>A
GRCh37.p13 chr 7 NC_000007.13:g.127881143C>A
LEP RefSeqGene NG_007450.1:g.4813C>A
LOC106728418 genomic region NG_044977.1:g.2835C>A
Gene: LEP, leptin (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
LEP transcript NM_000230.3:c. N/A Upstream Transcript Variant
LEP transcript variant X1 XM_005250340.5:c. N/A 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

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 18890 C=0.92811 A=0.07189
European Sub 14286 C=0.93497 A=0.06503
African Sub 2946 C=0.8809 A=0.1191
African Others Sub 114 C=0.930 A=0.070
African American Sub 2832 C=0.8789 A=0.1211
Asian Sub 112 C=1.000 A=0.000
East Asian Sub 86 C=1.00 A=0.00
Other Asian Sub 26 C=1.00 A=0.00
Latin American 1 Sub 146 C=0.945 A=0.055
Latin American 2 Sub 610 C=0.970 A=0.030
South Asian Sub 98 C=1.00 A=0.00
Other Sub 692 C=0.925 A=0.075


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 125568 C=0.927896 A=0.072104
gnomAD - Genomes Global Study-wide 31276 C=0.92246 A=0.07754
gnomAD - Genomes European Sub 18826 C=0.93366 A=0.06634
gnomAD - Genomes African Sub 8668 C=0.8774 A=0.1226
gnomAD - Genomes East Asian Sub 1560 C=0.9994 A=0.0006
gnomAD - Genomes Other Sub 1084 C=0.9419 A=0.0581
gnomAD - Genomes American Sub 848 C=0.958 A=0.042
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=0.955 A=0.045
1000Genomes Global Study-wide 5008 C=0.9441 A=0.0559
1000Genomes African Sub 1322 C=0.8790 A=0.1210
1000Genomes East Asian Sub 1008 C=0.9970 A=0.0030
1000Genomes Europe Sub 1006 C=0.9334 A=0.0666
1000Genomes South Asian Sub 978 C=0.985 A=0.015
1000Genomes American Sub 694 C=0.950 A=0.050
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9342 A=0.0658
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9242 A=0.0758
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9339 A=0.0661
ALFA Total Global 2188 C=0.9269 A=0.0731
ALFA European Sub 2072 C=0.9276 A=0.0724
ALFA African Sub 82 C=0.90 A=0.10
ALFA Other Sub 26 C=0.92 A=0.08
ALFA South Asian Sub 4 C=1.0 A=0.0
ALFA Asian Sub 4 C=1.0 A=0.0
ALFA Latin American 1 Sub 0 C=0 A=0
ALFA Latin American 2 Sub 0 C=0 A=0
Korean Genome Project KOREAN Study-wide 1776 C=0.9994 A=0.0006
Northern Sweden ACPOP Study-wide 600 C=0.938 A=0.062
Qatari Global Study-wide 216 C=0.986 A=0.014
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.995 A=0.005
HapMap Global Study-wide 186 C=1.000 A=0.000
HapMap African Sub 100 C=1.00 A=0.00
HapMap Asian Sub 86 C=1.00 A=0.00
The Danish reference pan genome Danish Study-wide 40 C=0.95 A=0.05
SGDP_PRJ Global Study-wide 30 C=0.50 A=0.50
Siberian Global Study-wide 4 C=0.5 A=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= A
GRCh38.p12 chr 7 NC_000007.14:g.128241090= NC_000007.14:g.128241090C>A
GRCh37.p13 chr 7 NC_000007.13:g.127881143= NC_000007.13:g.127881143C>A
LEP RefSeqGene NG_007450.1:g.4813= NG_007450.1:g.4813C>A
LOC106728418 genomic region NG_044977.1:g.2835= NG_044977.1:g.2835C>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#.

38 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss967549 Oct 05, 2000 (86)
2 KWOK ss1684769 Oct 18, 2000 (87)
3 HGBASE ss2420567 Nov 14, 2000 (89)
4 TSC-CSHL ss3045061 Jun 15, 2001 (96)
5 SC_JCM ss3653702 Sep 28, 2001 (100)
6 BCM_SSAHASNP ss10350656 Jul 11, 2003 (116)
7 WUGSC_SSAHASNP ss14549476 Dec 05, 2003 (120)
8 CSHL-HAPMAP ss19704260 Feb 27, 2004 (120)
9 SSAHASNP ss22575374 Apr 05, 2004 (121)
10 SSAHASNP ss22958242 Apr 05, 2004 (121)
11 SNP500CANCER ss48295359 Mar 13, 2006 (126)
12 1000GENOMES ss223327145 Jul 14, 2010 (132)
13 1000GENOMES ss234163775 Jul 15, 2010 (132)
14 SSMP ss654707640 Apr 25, 2013 (138)
15 EVA-GONL ss984790035 Aug 21, 2014 (142)
16 1000GENOMES ss1327110433 Aug 21, 2014 (142)
17 EVA_GENOME_DK ss1582398305 Apr 01, 2015 (144)
18 EVA_DECODE ss1594378916 Apr 01, 2015 (144)
19 EVA_UK10K_ALSPAC ss1619201951 Apr 01, 2015 (144)
20 EVA_UK10K_TWINSUK ss1662195984 Apr 01, 2015 (144)
21 WEILL_CORNELL_DGM ss1928048032 Feb 12, 2016 (147)
22 JJLAB ss2024711855 Sep 14, 2016 (149)
23 USC_VALOUEV ss2152932792 Dec 20, 2016 (150)
24 HUMAN_LONGEVITY ss2297811178 Dec 20, 2016 (150)
25 TOPMED ss2467284589 Dec 20, 2016 (150)
26 GNOMAD ss2859034728 Nov 08, 2017 (151)
27 SWEGEN ss3002021252 Nov 08, 2017 (151)
28 BIOINF_KMB_FNS_UNIBA ss3026145189 Nov 08, 2017 (151)
29 CSHL ss3347839566 Nov 08, 2017 (151)
30 TOPMED ss3544239606 Nov 08, 2017 (151)
31 EGCUT_WGS ss3669780656 Jul 13, 2019 (153)
32 EVA_DECODE ss3720676935 Jul 13, 2019 (153)
33 ACPOP ss3735064637 Jul 13, 2019 (153)
34 EVA ss3767152085 Jul 13, 2019 (153)
35 KHV_HUMAN_GENOMES ss3810322138 Jul 13, 2019 (153)
36 EVA ss3830816137 Apr 26, 2020 (154)
37 SGDP_PRJ ss3868383543 Apr 26, 2020 (154)
38 KOGIC ss3962563440 Apr 26, 2020 (154)
39 1000Genomes NC_000007.13 - 127881143 Oct 12, 2018 (152)
40 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 127881143 Oct 12, 2018 (152)
41 Genetic variation in the Estonian population NC_000007.13 - 127881143 Oct 12, 2018 (152)
42 The Danish reference pan genome NC_000007.13 - 127881143 Apr 26, 2020 (154)
43 gnomAD - Genomes NC_000007.13 - 127881143 Jul 13, 2019 (153)
44 HapMap NC_000007.14 - 128241090 Apr 26, 2020 (154)
45 Korean Genome Project NC_000007.14 - 128241090 Apr 26, 2020 (154)
46 Northern Sweden NC_000007.13 - 127881143 Jul 13, 2019 (153)
47 Qatari NC_000007.13 - 127881143 Apr 26, 2020 (154)
48 SGDP_PRJ NC_000007.13 - 127881143 Apr 26, 2020 (154)
49 Siberian NC_000007.13 - 127881143 Apr 26, 2020 (154)
50 TopMed NC_000007.14 - 128241090 Oct 12, 2018 (152)
51 UK 10K study - Twins NC_000007.13 - 127881143 Oct 12, 2018 (152)
52 A Vietnamese Genetic Variation Database NC_000007.13 - 127881143 Jul 13, 2019 (153)
53 dbGaP Population Frequency Project NC_000007.14 - 128241090 Apr 26, 2020 (154)
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)
rs10344223 Feb 27, 2004 (120)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1594378916 NC_000007.12:127668378:C:A NC_000007.14:128241089:C:A (self)
39153163, 21784665, 15518904, 8563243, 107037143, 8349502, 10089962, 20400523, 5449146, 21784665, 4853709, ss223327145, ss234163775, ss654707640, ss984790035, ss1327110433, ss1582398305, ss1619201951, ss1662195984, ss1928048032, ss2024711855, ss2152932792, ss2467284589, ss2859034728, ss3002021252, ss3347839566, ss3669780656, ss3735064637, ss3767152085, ss3830816137, ss3868383543 NC_000007.13:127881142:C:A NC_000007.14:128241089:C:A (self)
3492534, 18941441, 375775195, 111654654, ss2297811178, ss3026145189, ss3544239606, ss3720676935, ss3810322138, ss3962563440 NC_000007.14:128241089:C:A NC_000007.14:128241089:C:A (self)
ss10350656 NT_007933.12:53057291:A:A NC_000007.14:128241089:C:A (self)
ss14549476, ss19704260, ss22575374, ss22958242 NT_007933.13:53057291:A:A NC_000007.14:128241089:C:A (self)
ss967549, ss1684769, ss2420567, ss3045061, ss3653702, ss48295359 NT_007933.15:65913985:C:A NC_000007.14:128241089:C:A (self)
Help

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

5 citations for rs791620
PMID Title Author Year Journal
17879022 Are common leptin promoter polymorphisms associated with restenosis after coronary stenting? Bienertová-Vasků JA et al. 2007 Heart and vessels
19035456 Adipokine genes and prostate cancer risk. Moore SC et al. 2009 International journal of cancer
20140086 Genetic variation at selected SNPs in the leptin gene and association of alleles with markers of kidney disease in a Xhosa population of South Africa. Okpechi IG et al. 2010 PloS one
29904569 The rs2167270 polymorphism of leptin gene is associated with atopic dermatitis. Banihani SA et al. 2018 Dermato-endocrinology
30137462 Candidate genes linking maternal nutrient exposure to offspring health via DNA methylation: a review of existing evidence in humans with specific focus on one-carbon metabolism. James P et al. 2018 International journal of epidemiology
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.post565+e32b82c