Name: rs836711
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.

rs836711

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:167809951 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.446312 (62124/139194, GnomAD)
T=0.27796 (7854/28256, 14KJPN)
T=0.27816 (4662/16760, 8.3KJPN) (+ 10 more)
C=0.1662 (1603/9644, ALFA)
T=0.4461 (2857/6404, 1000G_30x)
T=0.4533 (2270/5008, 1000G)
C=0.2500 (1120/4480, Estonian)
T=0.3652 (1070/2930, KOREAN)
T=0.2937 (538/1832, Korea1K)
C=0.319 (318/998, GoNL)
C=0.322 (193/600, NorthernSweden)
T=0.292 (125/428, SGDP_PRJ)
T=0.449 (97/216, Qatari)

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	9644	T=0.8338	A=0.0000, C=0.1662
European	Sub	8504	T=0.8472	A=0.0000, C=0.1528
African	Sub	720	T=0.581	A=0.000, C=0.419
African Others	Sub	32	T=0.53	A=0.00, C=0.47
African American	Sub	688	T=0.583	A=0.000, C=0.417
Asian	Sub	10	T=1.0	A=0.0, C=0.0
East Asian	Sub	4	T=1.0	A=0.0, C=0.0
Other Asian	Sub	6	T=1.0	A=0.0, C=0.0
Latin American 1	Sub	46	T=1.00	A=0.00, C=0.00
Latin American 2	Sub	194	T=1.000	A=0.000, C=0.000
South Asian	Sub	22	T=1.00	A=0.00, C=0.00
Other	Sub	148	T=0.986	A=0.000, C=0.014

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
gnomAD - Genomes	Global	Study-wide	139194	T=0.553688	C=0.446312
gnomAD - Genomes	European	Sub	75654	T=0.68945	C=0.31055
gnomAD - Genomes	African	Sub	41480	T=0.30820	C=0.69180
gnomAD - Genomes	American	Sub	13570	T=0.59167	C=0.40833
gnomAD - Genomes	Ashkenazi Jewish	Sub	3304	T=0.5575	C=0.4425
gnomAD - Genomes	East Asian	Sub	3056	T=0.3442	C=0.6558
gnomAD - Genomes	Other	Sub	2130	T=0.5648	C=0.4352
14KJPN	JAPANESE	Study-wide	28256	T=0.27796	C=0.72204
8.3KJPN	JAPANESE	Study-wide	16760	T=0.27816	C=0.72184
Allele Frequency Aggregator	Total	Global	9644	T=0.8338	A=0.0000, C=0.1662
Allele Frequency Aggregator	European	Sub	8504	T=0.8472	A=0.0000, C=0.1528
Allele Frequency Aggregator	African	Sub	720	T=0.581	A=0.000, C=0.419
Allele Frequency Aggregator	Latin American 2	Sub	194	T=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	Other	Sub	148	T=0.986	A=0.000, C=0.014
Allele Frequency Aggregator	Latin American 1	Sub	46	T=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	South Asian	Sub	22	T=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	Asian	Sub	10	T=1.0	A=0.0, C=0.0
1000Genomes_30x	Global	Study-wide	6404	T=0.4461	C=0.5539
1000Genomes_30x	African	Sub	1786	T=0.2172	C=0.7828
1000Genomes_30x	Europe	Sub	1266	T=0.6469	C=0.3531
1000Genomes_30x	South Asian	Sub	1202	T=0.5790	C=0.4210
1000Genomes_30x	East Asian	Sub	1170	T=0.3171	C=0.6829
1000Genomes_30x	American	Sub	980	T=0.595	C=0.405
1000Genomes	Global	Study-wide	5008	T=0.4533	C=0.5467
1000Genomes	African	Sub	1322	T=0.2209	C=0.7791
1000Genomes	East Asian	Sub	1008	T=0.3214	C=0.6786
1000Genomes	Europe	Sub	1006	T=0.6551	C=0.3449
1000Genomes	South Asian	Sub	978	T=0.591	C=0.409
1000Genomes	American	Sub	694	T=0.601	C=0.399
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.7500	C=0.2500
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3652	A=0.0000, C=0.6348
Korean Genome Project	KOREAN	Study-wide	1832	T=0.2937	C=0.7063
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.681	C=0.319
Northern Sweden	ACPOP	Study-wide	600	T=0.678	C=0.322
SGDP_PRJ	Global	Study-wide	428	T=0.292	C=0.708
Qatari	Global	Study-wide	216	T=0.449	C=0.551

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.167809951T>A
GRCh38.p14 chr 2	NC_000002.12:g.167809951T>C
GRCh37.p13 chr 2	NC_000002.11:g.168666461T>A
GRCh37.p13 chr 2	NC_000002.11:g.168666461T>C
B3GALT1 RefSeqGene	NG_050644.1:g.521891T>A
B3GALT1 RefSeqGene	NG_050644.1:g.521891T>C

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

Molecule type	Change	Amino acid[Codon]	SO Term
B3GALT1 transcript	NM_020981.4:c.-351-8721T>A	N/A	Intron Variant
B3GALT1 transcript variant X2	XM_006712819.4:c.-351-872… XM_006712819.4:c.-351-8721T>A	N/A	Intron Variant
B3GALT1 transcript variant X3	XM_011512085.3:c.-367-872… XM_011512085.3:c.-367-8721T>A	N/A	Intron Variant
B3GALT1 transcript variant X1	XM_047446159.1:c.-351-872… XM_047446159.1:c.-351-8721T>A	N/A	Intron Variant
B3GALT1 transcript variant X4	XM_047446160.1:c.-367-872… XM_047446160.1:c.-367-8721T>A	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	T=	A	C
GRCh38.p14 chr 2	NC_000002.12:g.167809951=	NC_000002.12:g.167809951T>A	NC_000002.12:g.167809951T>C
GRCh37.p13 chr 2	NC_000002.11:g.168666461=	NC_000002.11:g.168666461T>A	NC_000002.11:g.168666461T>C
B3GALT1 RefSeqGene	NG_050644.1:g.521891=	NG_050644.1:g.521891T>A	NG_050644.1:g.521891T>C
B3GALT1 transcript	NM_020981.4:c.-351-8721=	NM_020981.4:c.-351-8721T>A	NM_020981.4:c.-351-8721T>C
B3GALT1 transcript variant X1	XM_005246931.1:c.-351-8721=	XM_005246931.1:c.-351-8721T>A	XM_005246931.1:c.-351-8721T>C
B3GALT1 transcript variant X2	XM_006712819.4:c.-351-8721=	XM_006712819.4:c.-351-8721T>A	XM_006712819.4:c.-351-8721T>C
B3GALT1 transcript variant X3	XM_011512085.3:c.-367-8721=	XM_011512085.3:c.-367-8721T>A	XM_011512085.3:c.-367-8721T>C
B3GALT1 transcript variant X1	XM_047446159.1:c.-351-8721=	XM_047446159.1:c.-351-8721T>A	XM_047446159.1:c.-351-8721T>C
B3GALT1 transcript variant X4	XM_047446160.1:c.-367-8721=	XM_047446160.1:c.-367-8721T>A	XM_047446160.1:c.-367-8721T>C

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#.

49 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1164583	Oct 05, 2000 (86)
2	KWOK	ss1810598	Oct 18, 2000 (87)
3	WI_SSAHASNP	ss11471832	Jul 11, 2003 (116)
4	CSHL-HAPMAP	ss16830289	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss20085452	Feb 27, 2004 (120)
6	SSAHASNP	ss21669531	Apr 05, 2004 (121)
7	HGSV	ss81342077	Dec 14, 2007 (130)
8	HGSV	ss82296139	Dec 14, 2007 (130)
9	BUSHMAN	ss201339531	Jul 04, 2010 (142)
10	BL	ss253658255	May 09, 2011 (134)
11	GMI	ss276776740	May 04, 2012 (137)
12	PJP	ss292420009	May 09, 2011 (134)
13	1000GENOMES	ss330117702	May 09, 2011 (134)
14	SSMP	ss649671165	Apr 25, 2013 (138)
15	EVA-GONL	ss977617079	Aug 21, 2014 (142)
16	1000GENOMES	ss1300326942	Aug 21, 2014 (142)
17	DDI	ss1428812759	Apr 01, 2015 (144)
18	HAMMER_LAB	ss1797876151	Sep 08, 2015 (146)
19	WEILL_CORNELL_DGM	ss1920869119	Feb 12, 2016 (147)
20	JJLAB	ss2020968253	Sep 14, 2016 (149)
21	SYSTEMSBIOZJU	ss2624988142	Nov 08, 2017 (151)
22	GRF	ss2703670156	Nov 08, 2017 (151)
23	GNOMAD	ss2782531950	Nov 08, 2017 (151)
24	SWEGEN	ss2990823150	Nov 08, 2017 (151)
25	CSHL	ss3344593402	Nov 08, 2017 (151)
26	URBANLAB	ss3647200316	Oct 11, 2018 (152)
27	EGCUT_WGS	ss3658692781	Jul 13, 2019 (153)
28	ACPOP	ss3729083438	Jul 13, 2019 (153)
29	EVA	ss3757689284	Jul 13, 2019 (153)
30	PACBIO	ss3784059646	Jul 13, 2019 (153)
31	PACBIO	ss3789612722	Jul 13, 2019 (153)
32	PACBIO	ss3794485716	Jul 13, 2019 (153)
33	KHV_HUMAN_GENOMES	ss3802047719	Jul 13, 2019 (153)
34	EVA	ss3827340343	Apr 25, 2020 (154)
35	EVA	ss3837087913	Apr 25, 2020 (154)
36	EVA	ss3842507675	Apr 25, 2020 (154)
37	SGDP_PRJ	ss3853921170	Apr 25, 2020 (154)
38	KRGDB	ss3899549293	Apr 25, 2020 (154)
39	KOGIC	ss3949449782	Apr 25, 2020 (154)
40	TOMMO_GENOMICS	ss5155002667	Apr 25, 2021 (155)
41	1000G_HIGH_COVERAGE	ss5250880422	Oct 12, 2022 (156)
42	EVA	ss5333938186	Oct 12, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5527624011	Oct 12, 2022 (156)
44	SANFORD_IMAGENETICS	ss5630305223	Oct 12, 2022 (156)
45	TOMMO_GENOMICS	ss5685452645	Oct 12, 2022 (156)
46	YY_MCH	ss5802942363	Oct 12, 2022 (156)
47	EVA	ss5821142526	Oct 12, 2022 (156)
48	EVA	ss5933377514	Oct 12, 2022 (156)
49	EVA	ss5956527265	Oct 12, 2022 (156)
50	1000Genomes	NC_000002.11 - 168666461	Oct 11, 2018 (152)
51	1000Genomes_30x	NC_000002.12 - 167809951	Oct 12, 2022 (156)
52	Genetic variation in the Estonian population	NC_000002.11 - 168666461	Oct 11, 2018 (152)
53	gnomAD - Genomes	NC_000002.12 - 167809951	Apr 25, 2021 (155)
54	Genome of the Netherlands Release 5	NC_000002.11 - 168666461	Apr 25, 2020 (154)
55	KOREAN population from KRGDB	NC_000002.11 - 168666461	Apr 25, 2020 (154)
56	Korean Genome Project	NC_000002.12 - 167809951	Apr 25, 2020 (154)
57	Northern Sweden	NC_000002.11 - 168666461	Jul 13, 2019 (153)
58	Qatari	NC_000002.11 - 168666461	Apr 25, 2020 (154)
59	SGDP_PRJ	NC_000002.11 - 168666461	Apr 25, 2020 (154)
60	8.3KJPN	NC_000002.11 - 168666461	Apr 25, 2021 (155)
61	14KJPN	NC_000002.12 - 167809951	Oct 12, 2022 (156)
62	ALFA	NC_000002.12 - 167809951	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)
rs2927191	Oct 14, 2006 (127)
rs35835470	May 23, 2006 (127)
rs56969288	May 23, 2008 (130)
rs112563634	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
6726687, ss3899549293	NC_000002.11:168666460:T:A	NC_000002.12:167809950:T:A	(self)
957159933	NC_000002.12:167809950:T:A	NC_000002.12:167809950:T:A	(self)
ss81342077, ss82296139	NC_000002.9:168491967:T:C	NC_000002.12:167809950:T:C	(self)
ss201339531, ss253658255, ss276776740, ss292420009	NC_000002.10:168374706:T:C	NC_000002.12:167809950:T:C	(self)
11380467, 4431029, 2758143, 6726687, 2368303, 2911049, 5938150, 12971974, ss330117702, ss649671165, ss977617079, ss1300326942, ss1428812759, ss1797876151, ss1920869119, ss2020968253, ss2624988142, ss2703670156, ss2782531950, ss2990823150, ss3344593402, ss3658692781, ss3729083438, ss3757689284, ss3784059646, ss3789612722, ss3794485716, ss3827340343, ss3837087913, ss3853921170, ss3899549293, ss5155002667, ss5333938186, ss5630305223, ss5821142526, ss5956527265	NC_000002.11:168666460:T:C	NC_000002.12:167809950:T:C	(self)
15149946, 81139323, 5827783, 19289749, 957159933, ss3647200316, ss3802047719, ss3842507675, ss3949449782, ss5250880422, ss5527624011, ss5685452645, ss5802942363, ss5933377514	NC_000002.12:167809950:T:C	NC_000002.12:167809950:T:C	(self)
ss11471832	NT_005403.13:18825798:T:C	NC_000002.12:167809950:T:C	(self)
ss16830289, ss20085452, ss21669531	NT_005403.14:18875877:T:C	NC_000002.12:167809950:T:C	(self)
ss1164583, ss1810598	NT_005403.17:18875878:T:C	NC_000002.12:167809950:T:C	(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 rs836711

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

rs836711