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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.

rs1042571

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr2:25161018 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.153566 (19283/125568, TOPMED)
A=0.14736 (4626/31392, GnomAD)
A=0.1156 (579/5008, 1000G) (+ 15 more)
A=0.1437 (644/4480, Estonian)
A=0.1993 (768/3854, ALSPAC)
A=0.1939 (719/3708, TWINSUK)
A=0.0038 (11/2922, KOREAN)
A=0.1924 (421/2188, ALFA Project)
A=0.0044 (8/1832, Korea1K)
A=0.174 (174/998, GoNL)
A=0.180 (163/906, PharmGKB)
A=0.133 (80/600, NorthernSweden)
A=0.227 (121/534, MGP)
A=0.236 (51/216, Qatari)
A=0.024 (5/212, Vietnamese)
G=0.42 (39/92, SGDP_PRJ)
G=0.5 (5/10, Siberian)
A=0.5 (5/10, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
POMC : 3 Prime UTR Variant
Publications
15 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 2 NC_000002.12:g.25161018G>A
GRCh37.p13 chr 2 NC_000002.11:g.25383887G>A
POMC RefSeqGene NG_008997.1:g.12673C>T
Gene: POMC, proopiomelanocortin (minus strand)
Molecule type Change Amino acid[Codon] SO Term
POMC transcript variant 1 NM_001035256.2:c.*63= N/A 3 Prime UTR Variant
POMC transcript variant 2 NM_000939.4:c.*63= N/A 3 Prime UTR Variant
POMC transcript variant 4 NM_001319205.2:c.*63= N/A 3 Prime UTR Variant
POMC transcript variant 3 NM_001319204.2:c.*63= N/A 3 Prime UTR 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.

Allele: A (allele ID: 289041 )
ClinVar Accession Disease Names Clinical Significance
RCV000272308.1 Monogenic Non-Syndromic Obesity Likely-Benign
RCV000329597.1 Proopiomelanocortin deficiency Likely-Benign

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: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 2188 G=0.8076 A=0.1924
European Sub 2072 G=0.8012 A=0.1988
African Sub 82 G=0.93 A=0.07
African Others Sub 6 G=1.0 A=0.0
African American Sub 76 G=0.92 A=0.08
Asian Sub 4 G=0.8 A=0.2
East Asian Sub 2 G=1.0 A=0.0
Other Asian Sub 2 G=0.5 A=0.5
Latin American 1 Sub 0 G=0 A=0
Latin American 2 Sub 0 G=0 A=0
South Asian Sub 4 G=0.8 A=0.2
Other Sub 26 G=0.96 A=0.04


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 G=0.846434 A=0.153566
gnomAD - Genomes Global Study-wide 31392 G=0.85264 A=0.14736
gnomAD - Genomes European Sub 18898 G=0.83342 A=0.16658
gnomAD - Genomes African Sub 8710 G=0.8724 A=0.1276
gnomAD - Genomes East Asian Sub 1560 G=0.9878 A=0.0122
gnomAD - Genomes Other Sub 1086 G=0.8398 A=0.1602
gnomAD - Genomes American Sub 848 G=0.886 A=0.114
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.734 A=0.266
1000Genomes Global Study-wide 5008 G=0.8844 A=0.1156
1000Genomes African Sub 1322 G=0.8873 A=0.1127
1000Genomes East Asian Sub 1008 G=0.9653 A=0.0347
1000Genomes Europe Sub 1006 G=0.7962 A=0.2038
1000Genomes South Asian Sub 978 G=0.925 A=0.075
1000Genomes American Sub 694 G=0.831 A=0.169
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8562 A=0.1437
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8007 A=0.1993
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8061 A=0.1939
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9962 A=0.0038
ALFA Total Global 2188 G=0.8076 A=0.1924
ALFA European Sub 2072 G=0.8012 A=0.1988
ALFA African Sub 82 G=0.93 A=0.07
ALFA Other Sub 26 G=0.96 A=0.04
ALFA South Asian Sub 4 G=0.8 A=0.2
ALFA Asian Sub 4 G=0.8 A=0.2
ALFA Latin American 1 Sub 0 G=0 A=0
ALFA Latin American 2 Sub 0 G=0 A=0
Korean Genome Project KOREAN Study-wide 1832 G=0.9956 A=0.0044
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.826 A=0.174
PharmGKB Aggregated Global Study-wide 906 G=0.820 A=0.180
PharmGKB Aggregated PA141936838 Sub 906 G=0.820 A=0.180
Northern Sweden ACPOP Study-wide 600 G=0.867 A=0.133
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.773 A=0.227
Qatari Global Study-wide 216 G=0.764 A=0.236
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.976 A=0.024
SGDP_PRJ Global Study-wide 92 G=0.42 A=0.58
Siberian Global Study-wide 10 G=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 G= A
GRCh38.p12 chr 2 NC_000002.12:g.25161018= NC_000002.12:g.25161018G>A
GRCh37.p13 chr 2 NC_000002.11:g.25383887= NC_000002.11:g.25383887G>A
POMC RefSeqGene NG_008997.1:g.12673= NG_008997.1:g.12673C>T
POMC transcript variant 2 NM_000939.4:c.*63= NM_000939.4:c.*63C>T
POMC transcript variant 2 NM_000939.3:c.*63= NM_000939.3:c.*63C>T
POMC transcript variant 2 NM_000939.2:c.*63= NM_000939.2:c.*63C>T
POMC transcript variant 1 NM_001035256.2:c.*63= NM_001035256.2:c.*63C>T
POMC transcript variant 1 NM_001035256.1:c.*63= NM_001035256.1:c.*63C>T
POMC transcript variant 3 NM_001319204.2:c.*63= NM_001319204.2:c.*63C>T
POMC transcript variant 3 NM_001319204.1:c.*63= NM_001319204.1:c.*63C>T
POMC transcript variant 4 NM_001319205.2:c.*63= NM_001319205.2:c.*63C>T
POMC transcript variant 4 NM_001319205.1:c.*63= NM_001319205.1:c.*63C>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#.

55 SubSNP, 17 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 LEE ss1509903 Oct 05, 2000 (86)
2 LEE ss4403954 May 29, 2002 (106)
3 HG_BONN_CNS_SNPS ss12586976 Aug 26, 2003 (117)
4 CGAP-GAI ss16264502 Feb 27, 2004 (120)
5 CEPH ss38339122 May 24, 2005 (125)
6 SNP500CANCER ss48296390 Mar 13, 2006 (126)
7 PHARMGKB_PHAT ss69365676 May 17, 2007 (127)
8 BCMHGSC_JDW ss91092135 Mar 24, 2008 (129)
9 1000GENOMES ss109325652 Jan 24, 2009 (130)
10 COMPLETE_GENOMICS ss164026442 Jul 04, 2010 (132)
11 1000GENOMES ss219127204 Jul 14, 2010 (132)
12 1000GENOMES ss231081630 Jul 14, 2010 (132)
13 BL ss252981000 May 09, 2011 (134)
14 TISHKOFF ss555424862 Apr 25, 2013 (138)
15 SSMP ss649004835 Apr 25, 2013 (138)
16 EVA-GONL ss976600578 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1068943315 Aug 21, 2014 (142)
18 1000GENOMES ss1296335237 Aug 21, 2014 (142)
19 DDI ss1428510862 Apr 01, 2015 (144)
20 EVA_DECODE ss1586004427 Apr 01, 2015 (144)
21 EVA_UK10K_ALSPAC ss1603037763 Apr 01, 2015 (144)
22 EVA_UK10K_TWINSUK ss1646031796 Apr 01, 2015 (144)
23 EVA_MGP ss1710956377 Apr 01, 2015 (144)
24 HAMMER_LAB ss1796435656 Sep 08, 2015 (146)
25 WEILL_CORNELL_DGM ss1919832614 Feb 12, 2016 (147)
26 ILLUMINA ss1958398087 Feb 12, 2016 (147)
27 JJLAB ss2020444955 Sep 14, 2016 (149)
28 USC_VALOUEV ss2148488986 Dec 20, 2016 (150)
29 HUMAN_LONGEVITY ss2228396256 Dec 20, 2016 (150)
30 TOPMED ss2394312475 Dec 20, 2016 (150)
31 GRF ss2703049897 Nov 08, 2017 (151)
32 GNOMAD ss2770920090 Nov 08, 2017 (151)
33 AFFY ss2985786624 Nov 08, 2017 (151)
34 SWEGEN ss2989148357 Nov 08, 2017 (151)
35 ILLUMINA ss3021950409 Nov 08, 2017 (151)
36 BIOINF_KMB_FNS_UNIBA ss3023989215 Nov 08, 2017 (151)
37 TOPMED ss3302029497 Nov 08, 2017 (151)
38 CSHL ss3344124619 Nov 08, 2017 (151)
39 OMUKHERJEE_ADBS ss3646258904 Oct 11, 2018 (152)
40 ILLUMINA ss3652379451 Oct 11, 2018 (152)
41 EGCUT_WGS ss3657103528 Jul 12, 2019 (153)
42 EVA_DECODE ss3703460056 Jul 12, 2019 (153)
43 ACPOP ss3728245499 Jul 12, 2019 (153)
44 EVA ss3756486913 Jul 12, 2019 (153)
45 PACBIO ss3783807341 Jul 12, 2019 (153)
46 PACBIO ss3789404164 Jul 12, 2019 (153)
47 PACBIO ss3794276920 Jul 12, 2019 (153)
48 KHV_HUMAN_GENOMES ss3800868652 Jul 12, 2019 (153)
49 EVA ss3825596008 Apr 25, 2020 (154)
50 EVA ss3826873628 Apr 25, 2020 (154)
51 EVA ss3836843923 Apr 25, 2020 (154)
52 EVA ss3842258461 Apr 25, 2020 (154)
53 SGDP_PRJ ss3851813885 Apr 25, 2020 (154)
54 KRGDB ss3897219561 Apr 25, 2020 (154)
55 KOGIC ss3947319848 Apr 25, 2020 (154)
56 1000Genomes NC_000002.11 - 25383887 Oct 11, 2018 (152)
57 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 25383887 Oct 11, 2018 (152)
58 Genetic variation in the Estonian population NC_000002.11 - 25383887 Oct 11, 2018 (152)
59 gnomAD - Genomes NC_000002.11 - 25383887 Jul 12, 2019 (153)
60 Genome of the Netherlands Release 5 NC_000002.11 - 25383887 Apr 25, 2020 (154)
61 KOREAN population from KRGDB NC_000002.11 - 25383887 Apr 25, 2020 (154)
62 Korean Genome Project NC_000002.12 - 25161018 Apr 25, 2020 (154)
63 Medical Genome Project healthy controls from Spanish population NC_000002.11 - 25383887 Apr 25, 2020 (154)
64 Northern Sweden NC_000002.11 - 25383887 Jul 12, 2019 (153)
65 PharmGKB Aggregated NC_000002.12 - 25161018 Apr 25, 2020 (154)
66 Qatari NC_000002.11 - 25383887 Apr 25, 2020 (154)
67 SGDP_PRJ NC_000002.11 - 25383887 Apr 25, 2020 (154)
68 Siberian NC_000002.11 - 25383887 Apr 25, 2020 (154)
69 TopMed NC_000002.12 - 25161018 Oct 11, 2018 (152)
70 UK 10K study - Twins NC_000002.11 - 25383887 Oct 11, 2018 (152)
71 A Vietnamese Genetic Variation Database NC_000002.11 - 25383887 Jul 12, 2019 (153)
72 dbGaP Population Frequency Project NC_000002.12 - 25161018 Apr 25, 2020 (154)
73 ClinVar RCV000272308.1 Oct 11, 2018 (152)
74 ClinVar RCV000329597.1 Oct 11, 2018 (152)
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)
rs3182045 Jul 03, 2002 (106)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss91092135, ss109325652, ss164026442, ss252981000, ss1586004427 NC_000002.10:25237390:G:A NC_000002.12:25161017:G:A (self)
7251323, 4026249, 2841776, 19738151, 1770415, 4396955, 73129, 1530364, 1874544, 3830865, 1005340, 4026249, 879009, ss219127204, ss231081630, ss555424862, ss649004835, ss976600578, ss1068943315, ss1296335237, ss1428510862, ss1603037763, ss1646031796, ss1710956377, ss1796435656, ss1919832614, ss1958398087, ss2020444955, ss2148488986, ss2394312475, ss2703049897, ss2770920090, ss2985786624, ss2989148357, ss3021950409, ss3344124619, ss3646258904, ss3652379451, ss3657103528, ss3728245499, ss3756486913, ss3783807341, ss3789404164, ss3794276920, ss3825596008, ss3826873628, ss3836843923, ss3851813885, ss3897219561 NC_000002.11:25383886:G:A NC_000002.12:25161017:G:A (self)
RCV000272308.1, RCV000329597.1, 3697849, 6158, 188193494, 370570557, ss2228396256, ss3023989215, ss3302029497, ss3703460056, ss3800868652, ss3842258461, ss3947319848 NC_000002.12:25161017:G:A NC_000002.12:25161017:G:A (self)
ss1509903, ss4403954, ss12586976, ss16264502, ss38339122, ss48296390, ss69365676 NT_022184.15:4205773:G:A NC_000002.12:25161017: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.

15 citations for rs1042571
PMID Title Author Year Journal
14513068 Pro-opiomelanocortin gene is associated with serum leptin levels in lean but not in obese individuals. Suviolahti E et al. 2003 International journal of obesity and related metabolic disorders
17357083 Medical sequencing at the extremes of human body mass. Ahituv N et al. 2007 American journal of human genetics
19217079 Pro-opiomelanocortin gene variation related to alcohol or drug dependence: evidence and replications across family- and population-based studies. Zhang H et al. 2009 Biological psychiatry
19384953 Genetic variants in pigmentation genes, pigmentary phenotypes, and risk of skin cancer in Caucasians. Nan H et al. 2009 International journal of cancer
20200332 Family-based analysis of candidate genes for polycystic ovary syndrome. Ewens KG et al. 2010 The Journal of clinical endocrinology and metabolism
21211529 Association study of POMC variants with body composition measures and nutrient choice. Ternouth A et al. 2011 European journal of pharmacology
21691274 Association of a polymorphism in the indoleamine- 2,3-dioxygenase gene and interferon-α-induced depression in patients with chronic hepatitis C. Smith AK et al. 2012 Molecular psychiatry
22547174 The genetics of the opioid system and specific drug addictions. Levran O et al. 2012 Human genetics
22576335 MAP3K7 and GSTZ1 are associated with human longevity: a two-stage case-control study using a multilocus genotyping. Di Cianni F et al. 2013 Age (Dordrecht, Netherlands)
23028917 Identification of POMC exonic variants associated with substance dependence and body mass index. Wang F et al. 2012 PloS one
24691024 Investigation of genetic variants, birthweight and hypothalamic-pituitary-adrenal axis function suggests a genetic variant in the SERPINA6 gene is associated with corticosteroid binding globulin in the western Australia pregnancy cohort (Raine) study. Anderson LN et al. 2014 PloS one
24831852 The role of leptin, melanocortin, and neurotrophin system genes on body weight in anorexia nervosa and bulimia nervosa. Yilmaz Z et al. 2014 Journal of psychiatric research
26226973 Analysis of MC4R rs17782313, POMC rs1042571, APOE-Hha1 and AGRP rs3412352 genetic variants with susceptibility to obesity risk in North Indians. Srivastava A et al. 2016 Annals of human biology
26345846 Association between rs155971 in the PCSK1 gene and the lipid profile of obese Thai children: a family-based study. Kulanuwat S et al. 2015 Genetics and molecular research
27168919 Association of FTO rs9939609 SNP with Obesity and Obesity- Associated Phenotypes in a North Indian Population. Prakash J et al. 2016 Oman medical journal
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.post536+f5d31d6