Name: rs1041941
Published: September 21, 2022
License: Open Access

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.

rs1041941

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:236548586 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.409237 (108321/264690, TOPMED)
C=0.382538 (53485/139816, GnomAD)
C=0.33827 (19890/58800, ALFA) (+ 16 more)
T=0.47477 (13415/28256, 14KJPN)
T=0.47291 (7926/16760, 8.3KJPN)
C=0.4989 (3195/6404, 1000G_30x)
C=0.5000 (2504/5008, 1000G)
T=0.5000 (2504/5008, 1000G)
C=0.2690 (1205/4480, Estonian)
C=0.3085 (1189/3854, ALSPAC)
C=0.2988 (1108/3708, TWINSUK)
T=0.4891 (1433/2930, KOREAN)
T=0.4820 (883/1832, Korea1K)
C=0.306 (305/998, GoNL)
C=0.283 (170/600, NorthernSweden)
C=0.316 (132/418, SGDP_PRJ)
C=0.412 (89/216, Qatari)
C=0.24 (11/46, Siberian)
C=0.23 (9/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LGALS8 : 3 Prime UTR Variant
HEATR1 : 500B Downstream 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	58800	C=0.33827	T=0.66173
European	Sub	43016	C=0.30486	T=0.69514
African	Sub	5160	C=0.4868	T=0.5132
African Others	Sub	190	C=0.537	T=0.463
African American	Sub	4970	C=0.4849	T=0.5151
Asian	Sub	454	C=0.485	T=0.515
East Asian	Sub	386	C=0.495	T=0.505
Other Asian	Sub	68	C=0.43	T=0.57
Latin American 1	Sub	596	C=0.371	T=0.629
Latin American 2	Sub	4986	C=0.4477	T=0.5523
South Asian	Sub	178	C=0.506	T=0.494
Other	Sub	4410	C=0.3404	T=0.6596

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.409237	T=0.590763
gnomAD - Genomes	Global	Study-wide	139816	C=0.382538	T=0.617462
gnomAD - Genomes	European	Sub	75756	C=0.30155	T=0.69845
gnomAD - Genomes	African	Sub	41862	C=0.50506	T=0.49494
gnomAD - Genomes	American	Sub	13624	C=0.42381	T=0.57619
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.3898	T=0.6102
gnomAD - Genomes	East Asian	Sub	3110	C=0.5039	T=0.4961
gnomAD - Genomes	Other	Sub	2144	C=0.4025	T=0.5975
Allele Frequency Aggregator	Total	Global	58800	C=0.33827	T=0.66173
Allele Frequency Aggregator	European	Sub	43016	C=0.30486	T=0.69514
Allele Frequency Aggregator	African	Sub	5160	C=0.4868	T=0.5132
Allele Frequency Aggregator	Latin American 2	Sub	4986	C=0.4477	T=0.5523
Allele Frequency Aggregator	Other	Sub	4410	C=0.3404	T=0.6596
Allele Frequency Aggregator	Latin American 1	Sub	596	C=0.371	T=0.629
Allele Frequency Aggregator	Asian	Sub	454	C=0.485	T=0.515
Allele Frequency Aggregator	South Asian	Sub	178	C=0.506	T=0.494
14KJPN	JAPANESE	Study-wide	28256	C=0.52523	T=0.47477
8.3KJPN	JAPANESE	Study-wide	16760	C=0.52709	T=0.47291
1000Genomes_30x	Global	Study-wide	6404	C=0.4989	T=0.5011
1000Genomes_30x	African	Sub	1786	C=0.5582	T=0.4418
1000Genomes_30x	Europe	Sub	1266	C=0.3294	T=0.6706
1000Genomes_30x	South Asian	Sub	1202	C=0.5857	T=0.4143
1000Genomes_30x	East Asian	Sub	1170	C=0.5154	T=0.4846
1000Genomes_30x	American	Sub	980	C=0.484	T=0.516
1000Genomes	Global	Study-wide	5008	C=0.5000	T=0.5000
1000Genomes	African	Sub	1322	C=0.5545	T=0.4455
1000Genomes	East Asian	Sub	1008	C=0.5228	T=0.4772
1000Genomes	Europe	Sub	1006	C=0.3260	T=0.6740
1000Genomes	South Asian	Sub	978	C=0.588	T=0.412
1000Genomes	American	Sub	694	C=0.491	T=0.509
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.2690	T=0.7310
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.3085	T=0.6915
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.2988	T=0.7012
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.5109	T=0.4891
Korean Genome Project	KOREAN	Study-wide	1832	C=0.5180	T=0.4820
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.306	T=0.694
Northern Sweden	ACPOP	Study-wide	600	C=0.283	T=0.717
SGDP_PRJ	Global	Study-wide	418	C=0.316	T=0.684
Qatari	Global	Study-wide	216	C=0.412	T=0.588
Siberian	Global	Study-wide	46	C=0.24	T=0.76
The Danish reference pan genome	Danish	Study-wide	40	C=0.23	T=0.78

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.236548586C>T
GRCh37.p13 chr 1	NC_000001.10:g.236711886C>T

Gene: LGALS8, galectin 8 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LGALS8 transcript variant 4	NM_201545.2:c.*425=	N/A	3 Prime UTR Variant
LGALS8 transcript variant 3	NM_201544.4:c.*425=	N/A	3 Prime UTR Variant
LGALS8 transcript variant 1	NM_006499.5:c.*425=	N/A	3 Prime UTR Variant
LGALS8 transcript variant 2	NM_201543.4:c.*425=	N/A	3 Prime UTR Variant
LGALS8 transcript variant X1	XM_047420409.1:c.*425=	N/A	3 Prime UTR Variant
LGALS8 transcript variant X2	XM_047420410.1:c.*425=	N/A	3 Prime UTR Variant
LGALS8 transcript variant X3	XM_047420411.1:c.*425=	N/A	3 Prime UTR Variant
LGALS8 transcript variant X5	XM_047420416.1:c.*425=	N/A	3 Prime UTR Variant
LGALS8 transcript variant X4	XM_011544188.4:c.	N/A	Genic Downstream Transcript Variant
LGALS8 transcript variant X6	XM_017001274.3:c.	N/A	Genic Downstream Transcript Variant

Gene: HEATR1, HEAT repeat containing 1 (minus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
HEATR1 transcript	NM_018072.6:c.	N/A	Downstream Transcript Variant

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

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=	T
GRCh38.p14 chr 1	NC_000001.11:g.236548586=	NC_000001.11:g.236548586C>T
GRCh37.p13 chr 1	NC_000001.10:g.236711886=	NC_000001.10:g.236711886C>T
LGALS8 transcript variant 1	NM_006499.5:c.*425=	NM_006499.5:c.*425C>T
LGALS8 transcript variant 1	NM_006499.4:c.*425=	NM_006499.4:c.*425C>T
LGALS8 transcript variant 2	NM_201543.4:c.*425=	NM_201543.4:c.*425C>T
LGALS8 transcript variant 2	NM_201543.3:c.*425=	NM_201543.3:c.*425C>T
LGALS8 transcript variant 2	NM_201543.2:c.*425=	NM_201543.2:c.*425C>T
LGALS8 transcript variant 3	NM_201544.4:c.*425=	NM_201544.4:c.*425C>T
LGALS8 transcript variant 3	NM_201544.3:c.*425=	NM_201544.3:c.*425C>T
LGALS8 transcript variant 3	NM_201544.2:c.*425=	NM_201544.2:c.*425C>T
LGALS8 transcript variant 4	NM_201545.2:c.*425=	NM_201545.2:c.*425C>T
LGALS8 transcript variant X2	XM_047420410.1:c.*425=	XM_047420410.1:c.*425C>T
LGALS8 transcript variant X3	XM_047420411.1:c.*425=	XM_047420411.1:c.*425C>T
LGALS8 transcript variant X1	XM_047420409.1:c.*425=	XM_047420409.1:c.*425C>T
LGALS8 transcript variant X5	XM_047420416.1:c.*425=	XM_047420416.1:c.*425C>T

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, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3965438	Sep 28, 2001 (100)
2	LEE	ss4403191	May 29, 2002 (106)
3	BCM_SSAHASNP	ss9878368	Jul 11, 2003 (116)
4	HGSV	ss83789707	Dec 15, 2007 (130)
5	BGI	ss106641624	Feb 06, 2009 (130)
6	1000GENOMES	ss109060108	Jan 23, 2009 (130)
7	GMI	ss156455736	Dec 01, 2009 (131)
8	ILLUMINA	ss159891706	Dec 01, 2009 (131)
9	COMPLETE_GENOMICS	ss165916051	Jul 04, 2010 (132)
10	BUSHMAN	ss199789751	Jul 04, 2010 (132)
11	BCM-HGSC-SUB	ss205162151	Jul 04, 2010 (132)
12	1000GENOMES	ss218957931	Jul 14, 2010 (132)
13	1000GENOMES	ss230959335	Jul 14, 2010 (132)
14	1000GENOMES	ss238562304	Jul 15, 2010 (132)
15	BL	ss253904212	May 09, 2011 (134)
16	GMI	ss276274088	May 04, 2012 (137)
17	GMI	ss284253066	Apr 25, 2013 (138)
18	ILLUMINA	ss479632660	Sep 08, 2015 (146)
19	ILLUMINA	ss482270806	May 04, 2012 (137)
20	ILLUMINA	ss484323309	May 04, 2012 (137)
21	ILLUMINA	ss536506772	Sep 08, 2015 (146)
22	TISHKOFF	ss555229521	Apr 25, 2013 (138)
23	SSMP	ss648803092	Apr 25, 2013 (138)
24	ILLUMINA	ss779531798	Sep 08, 2015 (146)
25	ILLUMINA	ss782607868	Sep 08, 2015 (146)
26	ILLUMINA	ss835002367	Sep 08, 2015 (146)
27	EVA-GONL	ss976292686	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1068713789	Aug 21, 2014 (142)
29	1000GENOMES	ss1295204012	Aug 21, 2014 (142)
30	DDI	ss1426154600	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1574774336	Apr 01, 2015 (144)
32	EVA_DECODE	ss1585694481	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1602436663	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1645430696	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1795939899	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1919514276	Feb 12, 2016 (147)
37	GENOMED	ss1967008014	Jul 19, 2016 (147)
38	JJLAB	ss2020283458	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2148320712	Nov 08, 2017 (151)
40	HUMAN_LONGEVITY	ss2171226994	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2624654562	Nov 08, 2017 (151)
42	ILLUMINA	ss2632647916	Nov 08, 2017 (151)
43	GRF	ss2698322906	Nov 08, 2017 (151)
44	GNOMAD	ss2767780351	Nov 08, 2017 (151)
45	SWEGEN	ss2988680592	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3023903250	Nov 08, 2017 (151)
47	CSHL	ss3343978424	Nov 08, 2017 (151)
48	ILLUMINA	ss3626341685	Oct 11, 2018 (152)
49	ILLUMINA	ss3630676836	Oct 11, 2018 (152)
50	ILLUMINA	ss3636059493	Oct 11, 2018 (152)
51	OMUKHERJEE_ADBS	ss3646255781	Oct 11, 2018 (152)
52	EGCUT_WGS	ss3656639485	Jul 12, 2019 (153)
53	EVA_DECODE	ss3688905745	Jul 12, 2019 (153)
54	ACPOP	ss3727985402	Jul 12, 2019 (153)
55	EVA	ss3747510897	Jul 12, 2019 (153)
56	PACBIO	ss3783726076	Jul 12, 2019 (153)
57	PACBIO	ss3789332063	Jul 12, 2019 (153)
58	PACBIO	ss3794204472	Jul 12, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3800513289	Jul 12, 2019 (153)
60	EVA	ss3826718015	Apr 25, 2020 (154)
61	EVA	ss3836761560	Apr 25, 2020 (154)
62	EVA	ss3842174303	Apr 25, 2020 (154)
63	SGDP_PRJ	ss3851188560	Apr 25, 2020 (154)
64	KRGDB	ss3896544758	Apr 25, 2020 (154)
65	KOGIC	ss3946781217	Apr 25, 2020 (154)
66	FSA-LAB	ss3983968176	Apr 25, 2021 (155)
67	EVA	ss3986016152	Apr 25, 2021 (155)
68	TOPMED	ss4488386001	Apr 25, 2021 (155)
69	TOMMO_GENOMICS	ss5149069108	Apr 25, 2021 (155)
70	1000G_HIGH_COVERAGE	ss5246282076	Oct 12, 2022 (156)
71	EVA	ss5314693972	Oct 12, 2022 (156)
72	EVA	ss5325673885	Oct 12, 2022 (156)
73	HUGCELL_USP	ss5446670341	Oct 12, 2022 (156)
74	EVA	ss5506237587	Oct 12, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5520617990	Oct 12, 2022 (156)
76	SANFORD_IMAGENETICS	ss5627722892	Oct 12, 2022 (156)
77	TOMMO_GENOMICS	ss5677015569	Oct 12, 2022 (156)
78	YY_MCH	ss5801763876	Oct 12, 2022 (156)
79	EVA	ss5833459431	Oct 12, 2022 (156)
80	EVA	ss5849349061	Oct 12, 2022 (156)
81	EVA	ss5912533066	Oct 12, 2022 (156)
82	EVA	ss5939573805	Oct 12, 2022 (156)
83	1000Genomes	NC_000001.10 - 236711886	Oct 11, 2018 (152)
84	1000Genomes_30x	NC_000001.11 - 236548586	Oct 12, 2022 (156)
85	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 236711886	Oct 11, 2018 (152)
86	Genetic variation in the Estonian population	NC_000001.10 - 236711886	Oct 11, 2018 (152)
87	The Danish reference pan genome	NC_000001.10 - 236711886	Apr 25, 2020 (154)
88	gnomAD - Genomes	NC_000001.11 - 236548586	Apr 25, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000001.10 - 236711886	Apr 25, 2020 (154)
90	KOREAN population from KRGDB	NC_000001.10 - 236711886	Apr 25, 2020 (154)
91	Korean Genome Project	NC_000001.11 - 236548586	Apr 25, 2020 (154)
92	Northern Sweden	NC_000001.10 - 236711886	Jul 12, 2019 (153)
93	Qatari	NC_000001.10 - 236711886	Apr 25, 2020 (154)
94	SGDP_PRJ	NC_000001.10 - 236711886	Apr 25, 2020 (154)
95	Siberian	NC_000001.10 - 236711886	Apr 25, 2020 (154)
96	8.3KJPN	NC_000001.10 - 236711886	Apr 25, 2021 (155)
97	14KJPN	NC_000001.11 - 236548586	Oct 12, 2022 (156)
98	TopMed	NC_000001.11 - 236548586	Apr 25, 2021 (155)
99	UK 10K study - Twins	NC_000001.10 - 236711886	Oct 11, 2018 (152)
100	ALFA	NC_000001.11 - 236548586	Apr 25, 2021 (155)

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)
rs3181407	Jul 03, 2002 (106)
rs60595899	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss83789707	NC_000001.8:233037926:C:T	NC_000001.11:236548585:C:T	(self)
ss109060108, ss165916051, ss199789751, ss205162151, ss253904212, ss276274088, ss284253066, ss482270806, ss1585694481	NC_000001.9:234778508:C:T	NC_000001.11:236548585:C:T	(self)
6078948, 3365537, 2377733, 1944379, 1471783, 3722152, 1270267, 1556206, 3205540, 837066, 7038415, 3365537, ss218957931, ss230959335, ss238562304, ss479632660, ss484323309, ss536506772, ss555229521, ss648803092, ss779531798, ss782607868, ss835002367, ss976292686, ss1068713789, ss1295204012, ss1426154600, ss1574774336, ss1602436663, ss1645430696, ss1795939899, ss1919514276, ss1967008014, ss2020283458, ss2148320712, ss2624654562, ss2632647916, ss2698322906, ss2767780351, ss2988680592, ss3343978424, ss3626341685, ss3630676836, ss3636059493, ss3646255781, ss3656639485, ss3727985402, ss3747510897, ss3783726076, ss3789332063, ss3794204472, ss3826718015, ss3836761560, ss3851188560, ss3896544758, ss3983968176, ss3986016152, ss5149069108, ss5314693972, ss5325673885, ss5506237587, ss5627722892, ss5833459431, ss5939573805	NC_000001.10:236711885:C:T	NC_000001.11:236548585:C:T	(self)
8143925, 43556060, 3159218, 10852673, 51992336, 5039407573, ss2171226994, ss3023903250, ss3688905745, ss3800513289, ss3842174303, ss3946781217, ss4488386001, ss5246282076, ss5446670341, ss5520617990, ss5677015569, ss5801763876, ss5849349061, ss5912533066	NC_000001.11:236548585:C:T	NC_000001.11:236548585:C:T	(self)
ss9878368	NT_004836.14:1455244:C:T	NC_000001.11:236548585:C:T	(self)
ss3965438, ss4403191, ss106641624, ss156455736, ss159891706	NT_167186.1:30229664:C:T	NC_000001.11:236548585:C:T	(self)

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

No publications for rs1041941

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs1041941