Name: rs34155024
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.

rs34155024

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:167795117 (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: A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.036367 (9626/264690, TOPMED)
G=0.039233 (5501/140212, GnomAD)
G=0.06087 (1720/28256, 14KJPN) (+ 15 more)
G=0.03900 (857/21974, ALFA)
G=0.05979 (1002/16760, 8.3KJPN)
G=0.0536 (343/6404, 1000G_30x)
G=0.0571 (286/5008, 1000G)
G=0.0449 (201/4480, Estonian)
G=0.0635 (186/2930, KOREAN)
G=0.0731 (134/1832, Korea1K)
G=0.0537 (61/1136, Daghestan)
G=0.044 (44/998, GoNL)
G=0.050 (30/600, NorthernSweden)
G=0.051 (11/216, Qatari)
G=0.089 (19/214, Vietnamese)
A=0.45 (35/78, SGDP_PRJ)
A=0.5 (4/8, Siberian)
G=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: B3GALT1 : 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	21974	A=0.96100	G=0.03900
European	Sub	14366	A=0.95482	G=0.04518
African	Sub	5604	A=0.9775	G=0.0225
African Others	Sub	198	A=0.980	G=0.020
African American	Sub	5406	A=0.9774	G=0.0226
Asian	Sub	118	A=0.915	G=0.085
East Asian	Sub	90	A=0.91	G=0.09
Other Asian	Sub	28	A=0.93	G=0.07
Latin American 1	Sub	154	A=0.961	G=0.039
Latin American 2	Sub	616	A=0.974	G=0.026
South Asian	Sub	100	A=0.93	G=0.07
Other	Sub	1016	A=0.9577	G=0.0423

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	A=0.963633	G=0.036367
gnomAD - Genomes	Global	Study-wide	140212	A=0.960767	G=0.039233
gnomAD - Genomes	European	Sub	75936	A=0.95235	G=0.04765
gnomAD - Genomes	African	Sub	42026	A=0.97647	G=0.02353
gnomAD - Genomes	American	Sub	13648	A=0.96490	G=0.03510
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	A=0.9560	G=0.0440
gnomAD - Genomes	East Asian	Sub	3130	A=0.9435	G=0.0565
gnomAD - Genomes	Other	Sub	2154	A=0.9573	G=0.0427
14KJPN	JAPANESE	Study-wide	28256	A=0.93913	G=0.06087
Allele Frequency Aggregator	Total	Global	21974	A=0.96100	G=0.03900
Allele Frequency Aggregator	European	Sub	14366	A=0.95482	G=0.04518
Allele Frequency Aggregator	African	Sub	5604	A=0.9775	G=0.0225
Allele Frequency Aggregator	Other	Sub	1016	A=0.9577	G=0.0423
Allele Frequency Aggregator	Latin American 2	Sub	616	A=0.974	G=0.026
Allele Frequency Aggregator	Latin American 1	Sub	154	A=0.961	G=0.039
Allele Frequency Aggregator	Asian	Sub	118	A=0.915	G=0.085
Allele Frequency Aggregator	South Asian	Sub	100	A=0.93	G=0.07
8.3KJPN	JAPANESE	Study-wide	16760	A=0.94021	G=0.05979
1000Genomes_30x	Global	Study-wide	6404	A=0.9464	G=0.0536
1000Genomes_30x	African	Sub	1786	A=0.9765	G=0.0235
1000Genomes_30x	Europe	Sub	1266	A=0.9534	G=0.0466
1000Genomes_30x	South Asian	Sub	1202	A=0.8927	G=0.1073
1000Genomes_30x	East Asian	Sub	1170	A=0.9291	G=0.0709
1000Genomes_30x	American	Sub	980	A=0.969	G=0.031
1000Genomes	Global	Study-wide	5008	A=0.9429	G=0.0571
1000Genomes	African	Sub	1322	A=0.9750	G=0.0250
1000Genomes	East Asian	Sub	1008	A=0.9276	G=0.0724
1000Genomes	Europe	Sub	1006	A=0.9493	G=0.0507
1000Genomes	South Asian	Sub	978	A=0.891	G=0.109
1000Genomes	American	Sub	694	A=0.968	G=0.032
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9551	G=0.0449
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.9365	G=0.0635
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9269	G=0.0731
Genome-wide autozygosity in Daghestan	Global	Study-wide	1136	A=0.9463	G=0.0537
Genome-wide autozygosity in Daghestan	Daghestan	Sub	628	A=0.962	G=0.038
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	A=0.938	G=0.062
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	A=0.959	G=0.041
Genome-wide autozygosity in Daghestan	Europe	Sub	108	A=0.954	G=0.046
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	A=0.87	G=0.13
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	A=0.86	G=0.14
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.956	G=0.044
Northern Sweden	ACPOP	Study-wide	600	A=0.950	G=0.050
Qatari	Global	Study-wide	216	A=0.949	G=0.051
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.911	G=0.089
SGDP_PRJ	Global	Study-wide	78	A=0.45	G=0.55
Siberian	Global	Study-wide	8	A=0.5	G=0.5

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 2	NC_000002.12:g.167795117A>G
GRCh37.p13 chr 2	NC_000002.11:g.168651627A>G
B3GALT1 RefSeqGene	NG_050644.1:g.507057A>G

Gene: B3GALT1, beta-1,3-galactosyltransferase 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
B3GALT1 transcript	NM_020981.4:c.-351-23555A… NM_020981.4:c.-351-23555A>G	N/A	Intron Variant
B3GALT1 transcript variant X2	XM_006712819.4:c.-351-235… XM_006712819.4:c.-351-23555A>G	N/A	Intron Variant
B3GALT1 transcript variant X3	XM_011512085.3:c.-367-235… XM_011512085.3:c.-367-23555A>G	N/A	Intron Variant
B3GALT1 transcript variant X1	XM_047446159.1:c.-351-235… XM_047446159.1:c.-351-23555A>G	N/A	Intron Variant
B3GALT1 transcript variant X4	XM_047446160.1:c.-367-235… XM_047446160.1:c.-367-23555A>G	N/A	Intron 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	A=	G
GRCh38.p14 chr 2	NC_000002.12:g.167795117=	NC_000002.12:g.167795117A>G
GRCh37.p13 chr 2	NC_000002.11:g.168651627=	NC_000002.11:g.168651627A>G
B3GALT1 RefSeqGene	NG_050644.1:g.507057=	NG_050644.1:g.507057A>G
B3GALT1 transcript	NM_020981.4:c.-351-23555=	NM_020981.4:c.-351-23555A>G
B3GALT1 transcript variant X1	XM_005246931.1:c.-351-23555=	XM_005246931.1:c.-351-23555A>G
B3GALT1 transcript variant X2	XM_006712819.4:c.-351-23555=	XM_006712819.4:c.-351-23555A>G
B3GALT1 transcript variant X3	XM_011512085.3:c.-367-23555=	XM_011512085.3:c.-367-23555A>G
B3GALT1 transcript variant X1	XM_047446159.1:c.-351-23555=	XM_047446159.1:c.-351-23555A>G
B3GALT1 transcript variant X4	XM_047446160.1:c.-367-23555=	XM_047446160.1:c.-367-23555A>G

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#.

51 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss41786862	Mar 13, 2006 (126)
2	HUMANGENOME_JCVI	ss97097338	Feb 04, 2009 (130)
3	1000GENOMES	ss110220611	Jan 24, 2009 (130)
4	1000GENOMES	ss219640128	Jul 14, 2010 (132)
5	1000GENOMES	ss231458255	Jul 14, 2010 (132)
6	1000GENOMES	ss238948896	Jul 15, 2010 (132)
7	GMI	ss276776662	May 04, 2012 (137)
8	GMI	ss284480731	Apr 25, 2013 (138)
9	ILLUMINA	ss534236404	Sep 08, 2015 (146)
10	TISHKOFF	ss556019615	Apr 25, 2013 (138)
11	SSMP	ss649671037	Apr 25, 2013 (138)
12	EVA-GONL	ss977616902	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1069685067	Aug 21, 2014 (142)
14	1000GENOMES	ss1300326417	Aug 21, 2014 (142)
15	HAMMER_LAB	ss1397311196	Sep 08, 2015 (146)
16	EVA_DECODE	ss1587054237	Apr 01, 2015 (144)
17	WEILL_CORNELL_DGM	ss1920868916	Feb 12, 2016 (147)
18	JJLAB	ss2020968141	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2149032950	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2236369341	Dec 20, 2016 (150)
21	SYSTEMSBIOZJU	ss2624988081	Nov 08, 2017 (151)
22	GRF	ss2703670058	Nov 08, 2017 (151)
23	GNOMAD	ss2782530463	Nov 08, 2017 (151)
24	SWEGEN	ss2990822843	Nov 08, 2017 (151)
25	BIOINF_KMB_FNS_UNIBA	ss3024244528	Nov 08, 2017 (151)
26	CSHL	ss3344593296	Nov 08, 2017 (151)
27	ILLUMINA	ss3628215687	Oct 11, 2018 (152)
28	URBANLAB	ss3647200268	Oct 11, 2018 (152)
29	EGCUT_WGS	ss3658692469	Jul 13, 2019 (153)
30	EVA_DECODE	ss3705372249	Jul 13, 2019 (153)
31	ACPOP	ss3729083266	Jul 13, 2019 (153)
32	EVA	ss3757689114	Jul 13, 2019 (153)
33	KHV_HUMAN_GENOMES	ss3802047493	Jul 13, 2019 (153)
34	EVA	ss3827340264	Apr 25, 2020 (154)
35	SGDP_PRJ	ss3853920841	Apr 25, 2020 (154)
36	KRGDB	ss3899548884	Apr 25, 2020 (154)
37	KOGIC	ss3949449587	Apr 25, 2020 (154)
38	TOPMED	ss4532869954	Apr 26, 2021 (155)
39	TOMMO_GENOMICS	ss5155002128	Apr 26, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5250879922	Oct 12, 2022 (156)
41	EVA	ss5333937440	Oct 12, 2022 (156)
42	HUGCELL_USP	ss5450606507	Oct 12, 2022 (156)
43	EVA	ss5506679587	Oct 12, 2022 (156)
44	1000G_HIGH_COVERAGE	ss5527623318	Oct 12, 2022 (156)
45	SANFORD_IMAGENETICS	ss5630304892	Oct 12, 2022 (156)
46	TOMMO_GENOMICS	ss5685451987	Oct 12, 2022 (156)
47	YY_MCH	ss5802942212	Oct 12, 2022 (156)
48	EVA	ss5821142291	Oct 12, 2022 (156)
49	EVA	ss5852819867	Oct 12, 2022 (156)
50	EVA	ss5933377092	Oct 12, 2022 (156)
51	EVA	ss5956526986	Oct 12, 2022 (156)
52	1000Genomes	NC_000002.11 - 168651627	Oct 11, 2018 (152)
53	1000Genomes_30x	NC_000002.12 - 167795117	Oct 12, 2022 (156)
54	Genome-wide autozygosity in Daghestan	NC_000002.10 - 168359873	Apr 25, 2020 (154)
55	Genetic variation in the Estonian population	NC_000002.11 - 168651627	Oct 11, 2018 (152)
56	gnomAD - Genomes	NC_000002.12 - 167795117	Apr 26, 2021 (155)
57	Genome of the Netherlands Release 5	NC_000002.11 - 168651627	Apr 25, 2020 (154)
58	KOREAN population from KRGDB	NC_000002.11 - 168651627	Apr 25, 2020 (154)
59	Korean Genome Project	NC_000002.12 - 167795117	Apr 25, 2020 (154)
60	Northern Sweden	NC_000002.11 - 168651627	Jul 13, 2019 (153)
61	Qatari	NC_000002.11 - 168651627	Apr 25, 2020 (154)
62	SGDP_PRJ	NC_000002.11 - 168651627	Apr 25, 2020 (154)
63	Siberian	NC_000002.11 - 168651627	Apr 25, 2020 (154)
64	8.3KJPN	NC_000002.11 - 168651627	Apr 26, 2021 (155)
65	14KJPN	NC_000002.12 - 167795117	Oct 12, 2022 (156)
66	TopMed	NC_000002.12 - 167795117	Apr 26, 2021 (155)
67	A Vietnamese Genetic Variation Database	NC_000002.11 - 168651627	Jul 13, 2019 (153)
68	ALFA	NC_000002.12 - 167795117	Apr 26, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
261075, ss110220611, ss276776662, ss284480731, ss1397311196, ss1587054237	NC_000002.10:168359872:A:G	NC_000002.12:167795116:A:G	(self)
11379930, 4430717, 2757976, 6726278, 2368131, 2910846, 5937821, 1549304, 12971435, 1364198, ss219640128, ss231458255, ss238948896, ss534236404, ss556019615, ss649671037, ss977616902, ss1069685067, ss1300326417, ss1920868916, ss2020968141, ss2149032950, ss2624988081, ss2703670058, ss2782530463, ss2990822843, ss3344593296, ss3628215687, ss3658692469, ss3729083266, ss3757689114, ss3827340264, ss3853920841, ss3899548884, ss5155002128, ss5333937440, ss5506679587, ss5630304892, ss5821142291, ss5956526986	NC_000002.11:168651626:A:G	NC_000002.12:167795116:A:G	(self)
15149253, 81135989, 5827588, 19289091, 336692833, 12891602468, ss2236369341, ss3024244528, ss3647200268, ss3705372249, ss3802047493, ss3949449587, ss4532869954, ss5250879922, ss5450606507, ss5527623318, ss5685451987, ss5802942212, ss5852819867, ss5933377092	NC_000002.12:167795116:A:G	NC_000002.12:167795116:A:G	(self)
ss41786862, ss97097338	NT_005403.17:18861044:A:G	NC_000002.12:167795116:A:G	(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 rs34155024

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

rs34155024