Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs1015979

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:54983600 (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>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.277721 (73510/264690, TOPMED)
C=0.43715 (12353/28258, 14KJPN)
C=0.43437 (7280/16760, 8.3KJPN) (+ 16 more)
C=0.24417 (3602/14752, ALFA)
C=0.3303 (2115/6404, 1000G_30x)
C=0.3345 (1675/5008, 1000G)
C=0.1882 (843/4480, Estonian)
C=0.2141 (825/3854, ALSPAC)
C=0.2044 (758/3708, TWINSUK)
C=0.4812 (1410/2930, KOREAN)
C=0.3626 (686/1892, HapMap)
C=0.4765 (873/1832, Korea1K)
C=0.223 (223/998, GoNL)
C=0.232 (139/600, NorthernSweden)
C=0.211 (103/488, SGDP_PRJ)
C=0.333 (72/216, Qatari)
C=0.481 (103/214, Vietnamese)
C=0.18 (9/50, Siberian)
C=0.17 (7/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TMEM61 : 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 14752 C=0.24417 A=0.00000, T=0.75583
European Sub 10080 C=0.20456 A=0.00000, T=0.79544
African Sub 1342 C=0.6505 A=0.0000, T=0.3495
African Others Sub 34 C=0.65 A=0.00, T=0.35
African American Sub 1308 C=0.6506 A=0.0000, T=0.3494
Asian Sub 70 C=0.59 A=0.00, T=0.41
East Asian Sub 32 C=0.66 A=0.00, T=0.34
Other Asian Sub 38 C=0.53 A=0.00, T=0.47
Latin American 1 Sub 156 C=0.224 A=0.000, T=0.776
Latin American 2 Sub 2172 C=0.1685 A=0.0000, T=0.8315
South Asian Sub 22 C=0.50 A=0.00, T=0.50
Other Sub 910 C=0.235 A=0.000, T=0.765


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=0.277721 T=0.722279
14KJPN JAPANESE Study-wide 28258 C=0.43715 T=0.56285
8.3KJPN JAPANESE Study-wide 16760 C=0.43437 T=0.56563
Allele Frequency Aggregator Total Global 14752 C=0.24417 A=0.00000, T=0.75583
Allele Frequency Aggregator European Sub 10080 C=0.20456 A=0.00000, T=0.79544
Allele Frequency Aggregator Latin American 2 Sub 2172 C=0.1685 A=0.0000, T=0.8315
Allele Frequency Aggregator African Sub 1342 C=0.6505 A=0.0000, T=0.3495
Allele Frequency Aggregator Other Sub 910 C=0.235 A=0.000, T=0.765
Allele Frequency Aggregator Latin American 1 Sub 156 C=0.224 A=0.000, T=0.776
Allele Frequency Aggregator Asian Sub 70 C=0.59 A=0.00, T=0.41
Allele Frequency Aggregator South Asian Sub 22 C=0.50 A=0.00, T=0.50
1000Genomes_30x Global Study-wide 6404 C=0.3303 T=0.6697
1000Genomes_30x African Sub 1786 C=0.4496 T=0.5504
1000Genomes_30x Europe Sub 1266 C=0.2227 T=0.7773
1000Genomes_30x South Asian Sub 1202 C=0.2629 T=0.7371
1000Genomes_30x East Asian Sub 1170 C=0.4795 T=0.5205
1000Genomes_30x American Sub 980 C=0.156 T=0.844
1000Genomes Global Study-wide 5008 C=0.3345 T=0.6655
1000Genomes African Sub 1322 C=0.4493 T=0.5507
1000Genomes East Asian Sub 1008 C=0.4782 T=0.5218
1000Genomes Europe Sub 1006 C=0.2247 T=0.7753
1000Genomes South Asian Sub 978 C=0.269 T=0.731
1000Genomes American Sub 694 C=0.159 T=0.841
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.1882 T=0.8118
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.2141 T=0.7859
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.2044 T=0.7956
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.4812 G=0.0000, T=0.5188
HapMap Global Study-wide 1892 C=0.3626 T=0.6374
HapMap American Sub 770 C=0.277 T=0.723
HapMap African Sub 692 C=0.457 T=0.543
HapMap Asian Sub 254 C=0.449 T=0.551
HapMap Europe Sub 176 C=0.244 T=0.756
Korean Genome Project KOREAN Study-wide 1832 C=0.4765 T=0.5235
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.223 T=0.777
Northern Sweden ACPOP Study-wide 600 C=0.232 T=0.768
SGDP_PRJ Global Study-wide 488 C=0.211 T=0.789
Qatari Global Study-wide 216 C=0.333 T=0.667
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.481 T=0.519
Siberian Global Study-wide 50 C=0.18 T=0.82
The Danish reference pan genome Danish Study-wide 40 C=0.17 T=0.82
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.54983600C>A
GRCh38.p14 chr 1 NC_000001.11:g.54983600C>G
GRCh38.p14 chr 1 NC_000001.11:g.54983600C>T
GRCh37.p13 chr 1 NC_000001.10:g.55449273C>A
GRCh37.p13 chr 1 NC_000001.10:g.55449273C>G
GRCh37.p13 chr 1 NC_000001.10:g.55449273C>T
Gene: TMEM61, transmembrane protein 61 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TMEM61 transcript NM_182532.3:c.16-2497C>A N/A Intron Variant
TMEM61 transcript variant X2 XM_005270586.5:c.1-2497C>A N/A Intron Variant
TMEM61 transcript variant X1 XM_011540911.3:c.16-2497C…

XM_011540911.3:c.16-2497C>A

N/A Intron Variant
TMEM61 transcript variant X3 XM_011540912.3:c.-805= N/A 5 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.

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= A G T
GRCh38.p14 chr 1 NC_000001.11:g.54983600= NC_000001.11:g.54983600C>A NC_000001.11:g.54983600C>G NC_000001.11:g.54983600C>T
GRCh37.p13 chr 1 NC_000001.10:g.55449273= NC_000001.10:g.55449273C>A NC_000001.10:g.55449273C>G NC_000001.10:g.55449273C>T
TMEM61 transcript variant X3 XM_011540912.3:c.-805= XM_011540912.3:c.-805C>A XM_011540912.3:c.-805C>G XM_011540912.3:c.-805C>T
TMEM61 transcript variant X3 XM_011540912.2:c.-805= XM_011540912.2:c.-805C>A XM_011540912.2:c.-805C>G XM_011540912.2:c.-805C>T
TMEM61 transcript variant X3 XM_011540912.1:c.-805= XM_011540912.1:c.-805C>A XM_011540912.1:c.-805C>G XM_011540912.1:c.-805C>T
TMEM61 transcript NM_182532.1:c.16-2497= NM_182532.1:c.16-2497C>A NM_182532.1:c.16-2497C>G NM_182532.1:c.16-2497C>T
TMEM61 transcript NM_182532.3:c.16-2497= NM_182532.3:c.16-2497C>A NM_182532.3:c.16-2497C>G NM_182532.3:c.16-2497C>T
TMEM61 transcript variant X1 XM_005270586.1:c.1-2497= XM_005270586.1:c.1-2497C>A XM_005270586.1:c.1-2497C>G XM_005270586.1:c.1-2497C>T
TMEM61 transcript variant X2 XM_005270586.5:c.1-2497= XM_005270586.5:c.1-2497C>A XM_005270586.5:c.1-2497C>G XM_005270586.5:c.1-2497C>T
TMEM61 transcript variant X1 XM_011540911.3:c.16-2497= XM_011540911.3:c.16-2497C>A XM_011540911.3:c.16-2497C>G XM_011540911.3:c.16-2497C>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#.

82 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1479627 Oct 05, 2000 (86)
2 SC_JCM ss3501469 Sep 28, 2001 (100)
3 SC_SNP ss13036743 Dec 05, 2003 (119)
4 SSAHASNP ss20573371 Apr 05, 2004 (121)
5 ABI ss41245098 Mar 14, 2006 (126)
6 AFFY ss66139913 Nov 29, 2006 (127)
7 AFFY ss76156439 Dec 08, 2007 (130)
8 KRIBB_YJKIM ss81450846 Dec 14, 2007 (130)
9 BCMHGSC_JDW ss87437403 Mar 23, 2008 (129)
10 HUMANGENOME_JCVI ss97937494 Feb 03, 2009 (130)
11 BGI ss106566755 Feb 03, 2009 (130)
12 1000GENOMES ss108204045 Jan 23, 2009 (130)
13 ILLUMINA-UK ss118697662 Feb 14, 2009 (130)
14 ENSEMBL ss137939915 Dec 01, 2009 (131)
15 ENSEMBL ss138941010 Dec 01, 2009 (131)
16 GMI ss155005946 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss163393905 Jul 04, 2010 (132)
18 COMPLETE_GENOMICS ss164295596 Jul 04, 2010 (132)
19 AFFY ss172663285 Jul 04, 2010 (132)
20 BUSHMAN ss198457426 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss205259987 Jul 04, 2010 (132)
22 1000GENOMES ss210526146 Jul 14, 2010 (132)
23 1000GENOMES ss218384953 Jul 14, 2010 (132)
24 1000GENOMES ss230534464 Jul 14, 2010 (132)
25 1000GENOMES ss238228929 Jul 15, 2010 (132)
26 ILLUMINA ss244255306 Jul 04, 2010 (132)
27 BL ss253098648 May 09, 2011 (134)
28 GMI ss275826694 May 04, 2012 (137)
29 GMI ss284050141 Apr 25, 2013 (138)
30 PJP ss290511333 May 09, 2011 (134)
31 TISHKOFF ss554113014 Apr 25, 2013 (138)
32 SSMP ss647943581 Apr 25, 2013 (138)
33 EVA-GONL ss975160359 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1067886206 Aug 21, 2014 (142)
35 1000GENOMES ss1290893383 Aug 21, 2014 (142)
36 DDI ss1425808171 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1574058921 Apr 01, 2015 (144)
38 EVA_DECODE ss1584526684 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1600173681 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1643167714 Apr 01, 2015 (144)
41 EVA_SVP ss1712332847 Apr 01, 2015 (144)
42 HAMMER_LAB ss1794363978 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1918369145 Feb 12, 2016 (147)
44 GENOMED ss1966745106 Jul 19, 2016 (147)
45 JJLAB ss2019700150 Sep 14, 2016 (149)
46 USC_VALOUEV ss2147714481 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2162506620 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2624362971 Nov 08, 2017 (151)
49 GRF ss2697626802 Nov 08, 2017 (151)
50 GNOMAD ss2755155623 Nov 08, 2017 (151)
51 SWEGEN ss2986818050 Nov 08, 2017 (151)
52 BIOINF_KMB_FNS_UNIBA ss3023610112 Nov 08, 2017 (151)
53 CSHL ss3343453616 Nov 08, 2017 (151)
54 URBANLAB ss3646662862 Oct 11, 2018 (152)
55 EGCUT_WGS ss3654881680 Jul 12, 2019 (153)
56 EVA_DECODE ss3686772574 Jul 12, 2019 (153)
57 ACPOP ss3727047158 Jul 12, 2019 (153)
58 EVA ss3746203971 Jul 12, 2019 (153)
59 PACBIO ss3783408864 Jul 12, 2019 (153)
60 PACBIO ss3789066859 Jul 12, 2019 (153)
61 PACBIO ss3793939556 Jul 12, 2019 (153)
62 KHV_HUMAN_GENOMES ss3799213181 Jul 12, 2019 (153)
63 EVA ss3826171670 Apr 25, 2020 (154)
64 EVA ss3836472446 Apr 25, 2020 (154)
65 EVA ss3841878511 Apr 25, 2020 (154)
66 SGDP_PRJ ss3848846968 Apr 25, 2020 (154)
67 KRGDB ss3893857738 Apr 25, 2020 (154)
68 KOGIC ss3944513427 Apr 25, 2020 (154)
69 TOPMED ss4449750446 Apr 25, 2021 (155)
70 TOMMO_GENOMICS ss5143953070 Apr 25, 2021 (155)
71 1000G_HIGH_COVERAGE ss5242270812 Oct 12, 2022 (156)
72 EVA ss5318726052 Oct 12, 2022 (156)
73 HUGCELL_USP ss5443332491 Oct 12, 2022 (156)
74 1000G_HIGH_COVERAGE ss5514546594 Oct 12, 2022 (156)
75 SANFORD_IMAGENETICS ss5625529546 Oct 12, 2022 (156)
76 TOMMO_GENOMICS ss5668727383 Oct 12, 2022 (156)
77 YY_MCH ss5800596188 Oct 12, 2022 (156)
78 EVA ss5831959285 Oct 12, 2022 (156)
79 EVA ss5848905352 Oct 12, 2022 (156)
80 EVA ss5908260337 Oct 12, 2022 (156)
81 EVA ss5937360985 Oct 12, 2022 (156)
82 EVA ss5979958688 Oct 12, 2022 (156)
83 1000Genomes NC_000001.10 - 55449273 Oct 11, 2018 (152)
84 1000Genomes_30x NC_000001.11 - 54983600 Oct 12, 2022 (156)
85 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 55449273 Oct 11, 2018 (152)
86 Genetic variation in the Estonian population NC_000001.10 - 55449273 Oct 11, 2018 (152)
87 The Danish reference pan genome NC_000001.10 - 55449273 Apr 25, 2020 (154)
88 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 11408792 (NC_000001.11:54983599:C:A 1/139958)
Row 11408793 (NC_000001.11:54983599:C:T 101656/139892)

- Apr 25, 2021 (155)
89 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 11408792 (NC_000001.11:54983599:C:A 1/139958)
Row 11408793 (NC_000001.11:54983599:C:T 101656/139892)

- Apr 25, 2021 (155)
90 Genome of the Netherlands Release 5 NC_000001.10 - 55449273 Apr 25, 2020 (154)
91 HapMap NC_000001.11 - 54983600 Apr 25, 2020 (154)
92 KOREAN population from KRGDB NC_000001.10 - 55449273 Apr 25, 2020 (154)
93 Korean Genome Project NC_000001.11 - 54983600 Apr 25, 2020 (154)
94 Northern Sweden NC_000001.10 - 55449273 Jul 12, 2019 (153)
95 Qatari NC_000001.10 - 55449273 Apr 25, 2020 (154)
96 SGDP_PRJ NC_000001.10 - 55449273 Apr 25, 2020 (154)
97 Siberian NC_000001.10 - 55449273 Apr 25, 2020 (154)
98 8.3KJPN NC_000001.10 - 55449273 Apr 25, 2021 (155)
99 14KJPN NC_000001.11 - 54983600 Oct 12, 2022 (156)
100 TopMed NC_000001.11 - 54983600 Apr 25, 2021 (155)
101 UK 10K study - Twins NC_000001.10 - 55449273 Oct 11, 2018 (152)
102 A Vietnamese Genetic Variation Database NC_000001.10 - 55449273 Jul 12, 2019 (153)
103 ALFA NC_000001.11 - 54983600 Apr 25, 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)
rs56543462 May 23, 2008 (130)
rs57901849 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
8725219156 NC_000001.11:54983599:C:A NC_000001.11:54983599:C:A (self)
1035132, ss3893857738 NC_000001.10:55449272:C:G NC_000001.11:54983599:C:G (self)
ss87437403, ss108204045, ss118697662, ss163393905, ss164295596, ss198457426, ss205259987, ss210526146, ss253098648, ss275826694, ss284050141, ss290511333, ss1584526684, ss1712332847 NC_000001.9:55221860:C:T NC_000001.11:54983599:C:T (self)
1611859, 876797, 619928, 1501497, 371764, 1035132, 332023, 411075, 863948, 230835, 1922377, 876797, 179823, ss218384953, ss230534464, ss238228929, ss554113014, ss647943581, ss975160359, ss1067886206, ss1290893383, ss1425808171, ss1574058921, ss1600173681, ss1643167714, ss1794363978, ss1918369145, ss1966745106, ss2019700150, ss2147714481, ss2624362971, ss2697626802, ss2755155623, ss2986818050, ss3343453616, ss3654881680, ss3727047158, ss3746203971, ss3783408864, ss3789066859, ss3793939556, ss3826171670, ss3836472446, ss3848846968, ss3893857738, ss5143953070, ss5318726052, ss5625529546, ss5831959285, ss5937360985, ss5979958688 NC_000001.10:55449272:C:T NC_000001.11:54983599:C:T (self)
2072529, 68049, 891428, 2564487, 13356781, 8725219156, ss2162506620, ss3023610112, ss3646662862, ss3686772574, ss3799213181, ss3841878511, ss3944513427, ss4449750446, ss5242270812, ss5443332491, ss5514546594, ss5668727383, ss5800596188, ss5848905352, ss5908260337 NC_000001.11:54983599:C:T NC_000001.11:54983599:C:T (self)
ss13036743 NT_032977.5:7898184:C:T NC_000001.11:54983599:C:T (self)
ss20573371 NT_032977.6:17012343:C:T NC_000001.11:54983599:C:T (self)
ss1479627, ss3501469, ss41245098, ss66139913, ss76156439, ss81450846, ss97937494, ss106566755, ss137939915, ss138941010, ss155005946, ss172663285, ss244255306 NT_032977.9:25421190:C:T NC_000001.11:54983599: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 rs1015979

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