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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.

rs1041939

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:236548318 (GRCh38.p13) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.101613 (26896/264690, TOPMED)
C=0.054423 (8599/158002, ALFA)
C=0.089965 (12614/140210, GnomAD) (+ 16 more)
C=0.12255 (2054/16760, 8.3KJPN)
C=0.1380 (691/5008, 1000G)
C=0.0192 (86/4480, Estonian)
C=0.0353 (136/3854, ALSPAC)
C=0.0307 (114/3708, TWINSUK)
C=0.1539 (451/2930, KOREAN)
C=0.1531 (289/1888, HapMap)
C=0.1463 (268/1832, Korea1K)
C=0.0757 (86/1136, Daghestan)
C=0.034 (34/998, GoNL)
C=0.023 (14/600, NorthernSweden)
C=0.116 (25/216, Qatari)
C=0.149 (31/208, Vietnamese)
A=0.419 (52/124, SGDP_PRJ)
C=0.03 (1/40, GENOME_DK)
A=0.2 (1/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LGALS8 : 3 Prime UTR Variant
Publications
0 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.p13 chr 1 NC_000001.11:g.236548318A>C
GRCh37.p13 chr 1 NC_000001.10:g.236711618A>C
Gene: LGALS8, galectin 8 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LGALS8 transcript variant 4 NM_201545.2:c.*157= N/A 3 Prime UTR Variant
LGALS8 transcript variant 3 NM_201544.4:c.*157= N/A 3 Prime UTR Variant
LGALS8 transcript variant 1 NM_006499.5:c.*157= N/A 3 Prime UTR Variant
LGALS8 transcript variant 2 NM_201543.4:c.*157= N/A 3 Prime UTR Variant
LGALS8 transcript variant X1 XM_011544188.3:c. N/A Genic Downstream Transcript Variant
LGALS8 transcript variant X2 XM_017001274.2:c. N/A Genic Downstream Transcript Variant
LGALS8 transcript variant X3 XM_017001275.2:c. N/A Genic Downstream 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 158002 A=0.945577 C=0.054423
European Sub 130772 A=0.960970 C=0.039030
African Sub 9984 A=0.8113 C=0.1887
African Others Sub 338 A=0.757 C=0.243
African American Sub 9646 A=0.8132 C=0.1868
Asian Sub 680 A=0.851 C=0.149
East Asian Sub 516 A=0.831 C=0.169
Other Asian Sub 164 A=0.915 C=0.085
Latin American 1 Sub 898 A=0.899 C=0.101
Latin American 2 Sub 8486 A=0.8908 C=0.1092
South Asian Sub 198 A=0.859 C=0.141
Other Sub 6984 A=0.9336 C=0.0664


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=0.898387 C=0.101613
Allele Frequency Aggregator Total Global 158002 A=0.945577 C=0.054423
Allele Frequency Aggregator European Sub 130772 A=0.960970 C=0.039030
Allele Frequency Aggregator African Sub 9984 A=0.8113 C=0.1887
Allele Frequency Aggregator Latin American 2 Sub 8486 A=0.8908 C=0.1092
Allele Frequency Aggregator Other Sub 6984 A=0.9336 C=0.0664
Allele Frequency Aggregator Latin American 1 Sub 898 A=0.899 C=0.101
Allele Frequency Aggregator Asian Sub 680 A=0.851 C=0.149
Allele Frequency Aggregator South Asian Sub 198 A=0.859 C=0.141
gnomAD - Genomes Global Study-wide 140210 A=0.910035 C=0.089965
gnomAD - Genomes European Sub 75960 A=0.96959 C=0.03041
gnomAD - Genomes African Sub 41992 A=0.80815 C=0.19185
gnomAD - Genomes American Sub 13652 A=0.90155 C=0.09845
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9260 C=0.0740
gnomAD - Genomes East Asian Sub 3130 A=0.8569 C=0.1431
gnomAD - Genomes Other Sub 2152 A=0.9024 C=0.0976
8.3KJPN JAPANESE Study-wide 16760 A=0.87745 C=0.12255
1000Genomes Global Study-wide 5008 A=0.8620 C=0.1380
1000Genomes African Sub 1322 A=0.7784 C=0.2216
1000Genomes East Asian Sub 1008 A=0.8194 C=0.1806
1000Genomes Europe Sub 1006 A=0.9682 C=0.0318
1000Genomes South Asian Sub 978 A=0.899 C=0.101
1000Genomes American Sub 694 A=0.878 C=0.122
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9808 C=0.0192
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9647 C=0.0353
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9693 C=0.0307
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.8461 C=0.1539
HapMap Global Study-wide 1888 A=0.8469 C=0.1531
HapMap American Sub 768 A=0.917 C=0.083
HapMap African Sub 690 A=0.749 C=0.251
HapMap Asian Sub 254 A=0.823 C=0.177
HapMap Europe Sub 176 A=0.960 C=0.040
Korean Genome Project KOREAN Study-wide 1832 A=0.8537 C=0.1463
Genome-wide autozygosity in Daghestan Global Study-wide 1136 A=0.9243 C=0.0757
Genome-wide autozygosity in Daghestan Daghestan Sub 628 A=0.927 C=0.073
Genome-wide autozygosity in Daghestan Near_East Sub 144 A=0.910 C=0.090
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.951 C=0.049
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.981 C=0.019
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=0.84 C=0.16
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.92 C=0.08
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.966 C=0.034
Northern Sweden ACPOP Study-wide 600 A=0.977 C=0.023
Qatari Global Study-wide 216 A=0.884 C=0.116
A Vietnamese Genetic Variation Database Global Study-wide 208 A=0.851 C=0.149
SGDP_PRJ Global Study-wide 124 A=0.419 C=0.581
The Danish reference pan genome Danish Study-wide 40 A=0.97 C=0.03
Siberian Global Study-wide 4 A=0.2 C=0.8
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
GRCh38.p13 chr 1 NC_000001.11:g.236548318= NC_000001.11:g.236548318A>C
GRCh37.p13 chr 1 NC_000001.10:g.236711618= NC_000001.10:g.236711618A>C
LGALS8 transcript variant 1 NM_006499.5:c.*157= NM_006499.5:c.*157A>C
LGALS8 transcript variant 1 NM_006499.4:c.*157= NM_006499.4:c.*157A>C
LGALS8 transcript variant 2 NM_201543.4:c.*157= NM_201543.4:c.*157A>C
LGALS8 transcript variant 2 NM_201543.3:c.*157= NM_201543.3:c.*157A>C
LGALS8 transcript variant 2 NM_201543.2:c.*157= NM_201543.2:c.*157A>C
LGALS8 transcript variant 3 NM_201544.4:c.*157= NM_201544.4:c.*157A>C
LGALS8 transcript variant 3 NM_201544.3:c.*157= NM_201544.3:c.*157A>C
LGALS8 transcript variant 3 NM_201544.2:c.*157= NM_201544.2:c.*157A>C
LGALS8 transcript variant 4 NM_201545.2:c.*157= NM_201545.2:c.*157A>C
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#.

88 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 LEE ss1508762 Oct 05, 2000 (86)
2 LEE ss4403188 May 29, 2002 (106)
3 PERLEGEN ss38338876 May 24, 2005 (125)
4 AFFY ss65983142 Dec 02, 2006 (127)
5 AFFY ss66359539 Dec 02, 2006 (127)
6 ILLUMINA ss74880739 Dec 07, 2007 (129)
7 AFFY ss76077127 Dec 07, 2007 (129)
8 KRIBB_YJKIM ss81452697 Dec 15, 2007 (130)
9 KRIBB_YJKIM ss102644703 Feb 06, 2009 (130)
10 1000GENOMES ss111982484 Jan 25, 2009 (130)
11 ILLUMINA-UK ss119257016 Feb 15, 2009 (130)
12 ILLUMINA ss159891703 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss165467832 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss167571664 Jul 04, 2010 (132)
15 ILLUMINA ss170052117 Jul 04, 2010 (132)
16 AFFY ss172421420 Jul 04, 2010 (132)
17 BUSHMAN ss199789739 Jul 04, 2010 (132)
18 1000GENOMES ss218957927 Jul 14, 2010 (132)
19 1000GENOMES ss230959332 Jul 14, 2010 (132)
20 1000GENOMES ss238562301 Jul 15, 2010 (132)
21 GMI ss276274085 May 04, 2012 (137)
22 ILLUMINA ss479261880 May 04, 2012 (137)
23 ILLUMINA ss479264827 May 04, 2012 (137)
24 ILLUMINA ss479632648 Sep 08, 2015 (146)
25 ILLUMINA ss484431643 May 04, 2012 (137)
26 ILLUMINA ss536603355 Sep 08, 2015 (146)
27 TISHKOFF ss555229518 Apr 25, 2013 (138)
28 SSMP ss648803087 Apr 25, 2013 (138)
29 ILLUMINA ss778730892 Sep 08, 2015 (146)
30 ILLUMINA ss782662280 Sep 08, 2015 (146)
31 ILLUMINA ss783631220 Sep 08, 2015 (146)
32 ILLUMINA ss831912804 Sep 08, 2015 (146)
33 ILLUMINA ss834190380 Sep 08, 2015 (146)
34 EVA-GONL ss976292682 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1068713784 Aug 21, 2014 (142)
36 1000GENOMES ss1295204002 Aug 21, 2014 (142)
37 HAMMER_LAB ss1397276762 Sep 08, 2015 (146)
38 DDI ss1426154597 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1574774333 Apr 01, 2015 (144)
40 EVA_DECODE ss1585694471 Apr 01, 2015 (144)
41 EVA_UK10K_ALSPAC ss1602436658 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1645430691 Apr 01, 2015 (144)
43 EVA_SVP ss1712416692 Apr 01, 2015 (144)
44 ILLUMINA ss1751907024 Sep 08, 2015 (146)
45 HAMMER_LAB ss1795939891 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1919514273 Feb 12, 2016 (147)
47 GENOMED ss1967008011 Jul 19, 2016 (147)
48 JJLAB ss2020283455 Sep 14, 2016 (149)
49 USC_VALOUEV ss2148320709 Nov 08, 2017 (151)
50 HUMAN_LONGEVITY ss2171226984 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2624654559 Nov 08, 2017 (151)
52 ILLUMINA ss2632647912 Nov 08, 2017 (151)
53 ILLUMINA ss2635008693 Nov 08, 2017 (151)
54 GRF ss2698322903 Nov 08, 2017 (151)
55 GNOMAD ss2767780326 Nov 08, 2017 (151)
56 SWEGEN ss2988680588 Nov 08, 2017 (151)
57 TOPMED ss3106973419 Nov 08, 2017 (151)
58 CSHL ss3343978421 Nov 08, 2017 (151)
59 ILLUMINA ss3626341680 Oct 11, 2018 (152)
60 ILLUMINA ss3630676832 Oct 11, 2018 (152)
61 ILLUMINA ss3632930844 Oct 11, 2018 (152)
62 ILLUMINA ss3633627157 Oct 11, 2018 (152)
63 ILLUMINA ss3634380484 Oct 11, 2018 (152)
64 ILLUMINA ss3635320133 Oct 11, 2018 (152)
65 ILLUMINA ss3636059490 Oct 11, 2018 (152)
66 ILLUMINA ss3637070686 Oct 11, 2018 (152)
67 ILLUMINA ss3637822584 Oct 11, 2018 (152)
68 ILLUMINA ss3640087837 Oct 11, 2018 (152)
69 ILLUMINA ss3642828203 Oct 11, 2018 (152)
70 EGCUT_WGS ss3656639479 Jul 12, 2019 (153)
71 EVA_DECODE ss3688905735 Jul 12, 2019 (153)
72 ACPOP ss3727985399 Jul 12, 2019 (153)
73 ILLUMINA ss3744681392 Jul 12, 2019 (153)
74 EVA ss3747510889 Jul 12, 2019 (153)
75 ILLUMINA ss3772182166 Jul 12, 2019 (153)
76 KHV_HUMAN_GENOMES ss3800513284 Jul 12, 2019 (153)
77 EVA ss3825591709 Apr 25, 2020 (154)
78 EVA ss3826718012 Apr 25, 2020 (154)
79 SGDP_PRJ ss3851188551 Apr 25, 2020 (154)
80 KRGDB ss3896544750 Apr 25, 2020 (154)
81 KOGIC ss3946781213 Apr 25, 2020 (154)
82 FSA-LAB ss3983968171 Apr 25, 2021 (155)
83 FSA-LAB ss3983968172 Apr 25, 2021 (155)
84 EVA ss3986165194 Apr 25, 2021 (155)
85 EVA ss4016970073 Apr 25, 2021 (155)
86 TOPMED ss4488385918 Apr 25, 2021 (155)
87 TOMMO_GENOMICS ss5149069095 Apr 25, 2021 (155)
88 EVA ss5237284533 Apr 25, 2021 (155)
89 1000Genomes NC_000001.10 - 236711618 Oct 11, 2018 (152)
90 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 236711618 Oct 11, 2018 (152)
91 Genome-wide autozygosity in Daghestan NC_000001.9 - 234778241 Apr 25, 2020 (154)
92 Genetic variation in the Estonian population NC_000001.10 - 236711618 Oct 11, 2018 (152)
93 The Danish reference pan genome NC_000001.10 - 236711618 Apr 25, 2020 (154)
94 gnomAD - Genomes NC_000001.11 - 236548318 Apr 25, 2021 (155)
95 Genome of the Netherlands Release 5 NC_000001.10 - 236711618 Apr 25, 2020 (154)
96 HapMap NC_000001.11 - 236548318 Apr 25, 2020 (154)
97 KOREAN population from KRGDB NC_000001.10 - 236711618 Apr 25, 2020 (154)
98 Korean Genome Project NC_000001.11 - 236548318 Apr 25, 2020 (154)
99 Northern Sweden NC_000001.10 - 236711618 Jul 12, 2019 (153)
100 Qatari NC_000001.10 - 236711618 Apr 25, 2020 (154)
101 SGDP_PRJ NC_000001.10 - 236711618 Apr 25, 2020 (154)
102 Siberian NC_000001.10 - 236711618 Apr 25, 2020 (154)
103 8.3KJPN NC_000001.10 - 236711618 Apr 25, 2021 (155)
104 TopMed NC_000001.11 - 236548318 Apr 25, 2021 (155)
105 UK 10K study - Twins NC_000001.10 - 236711618 Oct 11, 2018 (152)
106 A Vietnamese Genetic Variation Database NC_000001.10 - 236711618 Jul 12, 2019 (153)
107 ALFA NC_000001.11 - 236548318 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)
rs3181404 Jul 03, 2002 (106)
rs59827383 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
37849, ss66359539, ss76077127, ss111982484, ss119257016, ss165467832, ss167571664, ss172421420, ss199789739, ss276274085, ss479261880, ss1397276762, ss1585694471, ss1712416692, ss2635008693, ss3642828203 NC_000001.9:234778240:A:C NC_000001.11:236548317:A:C (self)
6078938, 3365532, 2377727, 1944376, 1471779, 3722144, 1270264, 1556203, 3205531, 837063, 7038402, 3365532, 732222, ss218957927, ss230959332, ss238562301, ss479264827, ss479632648, ss484431643, ss536603355, ss555229518, ss648803087, ss778730892, ss782662280, ss783631220, ss831912804, ss834190380, ss976292682, ss1068713784, ss1295204002, ss1426154597, ss1574774333, ss1602436658, ss1645430691, ss1751907024, ss1795939891, ss1919514273, ss1967008011, ss2020283455, ss2148320709, ss2624654559, ss2632647912, ss2698322903, ss2767780326, ss2988680588, ss3343978421, ss3626341680, ss3630676832, ss3632930844, ss3633627157, ss3634380484, ss3635320133, ss3636059490, ss3637070686, ss3637822584, ss3640087837, ss3656639479, ss3727985399, ss3744681392, ss3747510889, ss3772182166, ss3825591709, ss3826718012, ss3851188551, ss3896544750, ss3983968171, ss3983968172, ss3986165194, ss4016970073, ss5149069095, ss5237284533 NC_000001.10:236711617:A:C NC_000001.11:236548317:A:C (self)
43556001, 297380, 3159214, 32680013, 51992253, 321186522, ss2171226984, ss3106973419, ss3688905735, ss3800513284, ss3946781213, ss4488385918 NC_000001.11:236548317:A:C NC_000001.11:236548317:A:C (self)
ss1508762, ss4403188, ss38338876, ss65983142, ss74880739, ss81452697, ss102644703, ss159891703, ss170052117 NT_167186.1:30229396:A:C NC_000001.11:236548317:A:C (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 rs1041939

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.post596+ae089ad