Skip to main page content
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.

rs869

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr9:33113123 (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
G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.499214 (132137/264690, TOPMED)
A=0.497313 (69587/139926, GnomAD)
A=0.40326 (25241/62592, ALFA) (+ 17 more)
G=0.31480 (5276/16760, 8.3KJPN)
G=0.4465 (2236/5008, 1000G)
A=0.3810 (1707/4480, Estonian)
A=0.4344 (1674/3854, ALSPAC)
A=0.4253 (1577/3708, TWINSUK)
G=0.2983 (874/2930, KOREAN)
G=0.4022 (761/1892, HapMap)
G=0.2767 (507/1832, Korea1K)
A=0.411 (410/998, GoNL)
A=0.369 (231/626, Chileans)
A=0.433 (260/600, NorthernSweden)
A=0.350 (187/534, MGP)
G=0.293 (115/392, SGDP_PRJ)
A=0.454 (98/216, Qatari)
G=0.286 (60/210, Vietnamese)
A=0.40 (16/40, GENOME_DK)
G=0.32 (12/38, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
B4GALT1 : Intron 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 9 NC_000009.12:g.33113123G>A
GRCh38.p13 chr 9 NC_000009.12:g.33113123G>C
GRCh38.p13 chr 9 NC_000009.12:g.33113123G>T
GRCh37.p13 chr 9 NC_000009.11:g.33113121G>A
GRCh37.p13 chr 9 NC_000009.11:g.33113121G>C
GRCh37.p13 chr 9 NC_000009.11:g.33113121G>T
B4GALT1 RefSeqGene NG_008919.1:g.59236C>T
B4GALT1 RefSeqGene NG_008919.1:g.59236C>G
B4GALT1 RefSeqGene NG_008919.1:g.59236C>A
Gene: B4GALT1, beta-1,4-galactosyltransferase 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
B4GALT1 transcript variant 4 NM_001378497.1:c.649-8342…

NM_001378497.1:c.649-8342C>T

N/A Intron Variant
B4GALT1 transcript variant 3 NM_001378496.1:c.*331= N/A 3 Prime UTR Variant
B4GALT1 transcript variant 2 NM_001378495.1:c.*331= N/A 3 Prime UTR Variant
B4GALT1 transcript variant 1 NM_001497.4:c.*331= N/A 3 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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 62592 G=0.59674 A=0.40326, C=0.00000
European Sub 45832 G=0.60224 A=0.39776, C=0.00000
African Sub 3794 G=0.3838 A=0.6162, C=0.0000
African Others Sub 120 G=0.383 A=0.617, C=0.000
African American Sub 3674 G=0.3838 A=0.6162, C=0.0000
Asian Sub 410 G=0.359 A=0.641, C=0.000
East Asian Sub 326 G=0.307 A=0.693, C=0.000
Other Asian Sub 84 G=0.56 A=0.44, C=0.00
Latin American 1 Sub 630 G=0.478 A=0.522, C=0.000
Latin American 2 Sub 6818 G=0.7081 A=0.2919, C=0.0000
South Asian Sub 118 G=0.568 A=0.432, C=0.000
Other Sub 4990 G=0.5912 A=0.4088, C=0.0000


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 G=0.499214 A=0.500786
gnomAD - Genomes Global Study-wide 139926 G=0.502687 A=0.497313
gnomAD - Genomes European Sub 75760 G=0.57954 A=0.42046
gnomAD - Genomes African Sub 41944 G=0.33678 A=0.66322
gnomAD - Genomes American Sub 13634 G=0.61024 A=0.38976
gnomAD - Genomes Ashkenazi Jewish Sub 3320 G=0.5919 A=0.4081
gnomAD - Genomes East Asian Sub 3126 G=0.2879 A=0.7121
gnomAD - Genomes Other Sub 2142 G=0.5238 A=0.4762
8.3KJPN JAPANESE Study-wide 16760 G=0.31480 A=0.68520
1000Genomes Global Study-wide 5008 G=0.4465 A=0.5535
1000Genomes African Sub 1322 G=0.3064 A=0.6936
1000Genomes East Asian Sub 1008 G=0.2827 A=0.7173
1000Genomes Europe Sub 1006 G=0.5666 A=0.4334
1000Genomes South Asian Sub 978 G=0.542 A=0.458
1000Genomes American Sub 694 G=0.643 A=0.357
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.6190 A=0.3810
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.5656 A=0.4344
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5747 A=0.4253
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2983 A=0.7017
HapMap Global Study-wide 1892 G=0.4022 A=0.5978
HapMap American Sub 770 G=0.477 A=0.523
HapMap African Sub 692 G=0.335 A=0.665
HapMap Asian Sub 254 G=0.287 A=0.713
HapMap Europe Sub 176 G=0.506 A=0.494
Korean Genome Project KOREAN Study-wide 1832 G=0.2767 A=0.7233
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.589 A=0.411
Chileans Chilean Study-wide 626 G=0.631 A=0.369
Northern Sweden ACPOP Study-wide 600 G=0.567 A=0.433
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.650 A=0.350
SGDP_PRJ Global Study-wide 392 G=0.293 A=0.707
Qatari Global Study-wide 216 G=0.546 A=0.454
A Vietnamese Genetic Variation Database Global Study-wide 210 G=0.286 A=0.714
The Danish reference pan genome Danish Study-wide 40 G=0.60 A=0.40
Siberian Global Study-wide 38 G=0.32 A=0.68
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 G= A C T
GRCh38.p13 chr 9 NC_000009.12:g.33113123= NC_000009.12:g.33113123G>A NC_000009.12:g.33113123G>C NC_000009.12:g.33113123G>T
GRCh37.p13 chr 9 NC_000009.11:g.33113121= NC_000009.11:g.33113121G>A NC_000009.11:g.33113121G>C NC_000009.11:g.33113121G>T
B4GALT1 RefSeqGene NG_008919.1:g.59236= NG_008919.1:g.59236C>T NG_008919.1:g.59236C>G NG_008919.1:g.59236C>A
B4GALT1 transcript variant 1 NM_001497.4:c.*331= NM_001497.4:c.*331C>T NM_001497.4:c.*331C>G NM_001497.4:c.*331C>A
B4GALT1 transcript NM_001497.3:c.*331= NM_001497.3:c.*331C>T NM_001497.3:c.*331C>G NM_001497.3:c.*331C>A
B4GALT1 transcript variant 3 NM_001378496.1:c.*331= NM_001378496.1:c.*331C>T NM_001378496.1:c.*331C>G NM_001378496.1:c.*331C>A
B4GALT1 transcript variant 2 NM_001378495.1:c.*331= NM_001378495.1:c.*331C>T NM_001378495.1:c.*331C>G NM_001378495.1:c.*331C>A
B4GALT1 transcript variant 4 NM_001378497.1:c.649-8342= NM_001378497.1:c.649-8342C>T NM_001378497.1:c.649-8342C>G NM_001378497.1:c.649-8342C>A
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#.

102 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 WIAF ss891 Sep 19, 2000 (36)
2 CGAP-GAI ss12675 Sep 19, 2000 (52)
3 LEE ss1546190 Oct 04, 2000 (86)
4 SC_JCM ss3916790 Sep 28, 2001 (100)
5 LEE ss4431664 May 29, 2002 (106)
6 BCM_SSAHASNP ss10492710 Jul 11, 2003 (116)
7 SC_SNP ss12931409 Dec 05, 2003 (119)
8 SC_SNP ss16012372 Feb 27, 2004 (120)
9 CGAP-GAI ss16247756 Feb 27, 2004 (120)
10 CSHL-HAPMAP ss18017871 Feb 27, 2004 (120)
11 SSAHASNP ss22874406 Apr 05, 2004 (121)
12 PERLEGEN ss24525984 Sep 20, 2004 (123)
13 ABI ss43761864 Mar 15, 2006 (126)
14 SI_EXO ss52082926 Oct 16, 2006 (127)
15 AFFY ss76642241 Dec 07, 2007 (129)
16 HGSV ss77468772 Dec 07, 2007 (129)
17 HGSV ss83179535 Dec 15, 2007 (130)
18 HGSV ss85336322 Dec 15, 2007 (130)
19 HUMANGENOME_JCVI ss97720519 Feb 05, 2009 (130)
20 KRIBB_YJKIM ss104807690 Feb 05, 2009 (130)
21 BGI ss105676217 Feb 05, 2009 (130)
22 1000GENOMES ss108743998 Jan 23, 2009 (130)
23 1000GENOMES ss114434032 Jan 25, 2009 (130)
24 ILLUMINA-UK ss115724708 Feb 14, 2009 (130)
25 ENSEMBL ss134152383 Dec 01, 2009 (131)
26 GMI ss157417878 Dec 01, 2009 (131)
27 ILLUMINA ss160959856 Dec 01, 2009 (131)
28 COMPLETE_GENOMICS ss164066424 Jul 04, 2010 (132)
29 COMPLETE_GENOMICS ss164986168 Jul 04, 2010 (132)
30 COMPLETE_GENOMICS ss166414899 Jul 04, 2010 (132)
31 ILLUMINA ss169053937 Jul 04, 2010 (132)
32 BUSHMAN ss200334558 Jul 04, 2010 (132)
33 BCM-HGSC-SUB ss206857632 Jul 04, 2010 (132)
34 1000GENOMES ss224224489 Jul 14, 2010 (132)
35 1000GENOMES ss234800308 Jul 15, 2010 (132)
36 1000GENOMES ss241580147 Jul 15, 2010 (132)
37 BL ss254176924 May 09, 2011 (134)
38 GMI ss280188113 May 04, 2012 (137)
39 GMI ss286004938 Apr 25, 2013 (138)
40 PJP ss294436375 May 09, 2011 (134)
41 ILLUMINA ss482808359 Sep 08, 2015 (146)
42 ILLUMINA ss483496729 May 04, 2012 (137)
43 ILLUMINA ss485782796 May 04, 2012 (137)
44 ILLUMINA ss535704994 Sep 08, 2015 (146)
45 TISHKOFF ss561359053 Apr 25, 2013 (138)
46 SSMP ss655800726 Apr 25, 2013 (138)
47 ILLUMINA ss780299475 Sep 08, 2015 (146)
48 ILLUMINA ss782191773 Sep 08, 2015 (146)
49 ILLUMINA ss835786172 Sep 08, 2015 (146)
50 EVA-GONL ss986509018 Aug 21, 2014 (142)
51 JMKIDD_LAB ss1076270270 Aug 21, 2014 (142)
52 1000GENOMES ss1333655805 Aug 21, 2014 (142)
53 DDI ss1431811969 Apr 01, 2015 (144)
54 EVA_GENOME_DK ss1583068878 Apr 01, 2015 (144)
55 EVA_DECODE ss1596147050 Apr 01, 2015 (144)
56 EVA_UK10K_ALSPAC ss1622644922 Apr 01, 2015 (144)
57 EVA_UK10K_TWINSUK ss1665638955 Apr 01, 2015 (144)
58 EVA_MGP ss1711219307 Apr 01, 2015 (144)
59 EVA_SVP ss1713105650 Apr 01, 2015 (144)
60 HAMMER_LAB ss1805965444 Sep 08, 2015 (146)
61 WEILL_CORNELL_DGM ss1929795588 Feb 12, 2016 (147)
62 GENOMED ss1971202320 Jul 19, 2016 (147)
63 JJLAB ss2025611388 Sep 14, 2016 (149)
64 USC_VALOUEV ss2153837308 Dec 20, 2016 (150)
65 HUMAN_LONGEVITY ss2310949500 Dec 20, 2016 (150)
66 TOPMED ss2481063942 Dec 20, 2016 (150)
67 SYSTEMSBIOZJU ss2627280616 Nov 08, 2017 (151)
68 ILLUMINA ss2634860772 Nov 08, 2017 (151)
69 GRF ss2709647070 Nov 08, 2017 (151)
70 GNOMAD ss2877533235 Nov 08, 2017 (151)
71 AFFY ss2985460250 Nov 08, 2017 (151)
72 AFFY ss2986105972 Nov 08, 2017 (151)
73 SWEGEN ss3004680721 Nov 08, 2017 (151)
74 BIOINF_KMB_FNS_UNIBA ss3026595660 Nov 08, 2017 (151)
75 CSHL ss3348613206 Nov 08, 2017 (151)
76 TOPMED ss3586897258 Nov 08, 2017 (151)
77 ILLUMINA ss3630254512 Oct 12, 2018 (152)
78 ILLUMINA ss3632753488 Oct 12, 2018 (152)
79 ILLUMINA ss3636957942 Oct 12, 2018 (152)
80 ILLUMINA ss3638810477 Oct 12, 2018 (152)
81 ILLUMINA ss3642685288 Oct 12, 2018 (152)
82 OMUKHERJEE_ADBS ss3646385841 Oct 12, 2018 (152)
83 URBANLAB ss3649114531 Oct 12, 2018 (152)
84 ILLUMINA ss3654224231 Oct 12, 2018 (152)
85 EGCUT_WGS ss3672435255 Jul 13, 2019 (153)
86 EVA_DECODE ss3723833952 Jul 13, 2019 (153)
87 ACPOP ss3736474040 Jul 13, 2019 (153)
88 EVA ss3769146139 Jul 13, 2019 (153)
89 PACBIO ss3786397020 Jul 13, 2019 (153)
90 PACBIO ss3791616660 Jul 13, 2019 (153)
91 PACBIO ss3796498349 Jul 13, 2019 (153)
92 KHV_HUMAN_GENOMES ss3812304960 Jul 13, 2019 (153)
93 EVA ss3825753670 Apr 26, 2020 (154)
94 EVA ss3831634426 Apr 26, 2020 (154)
95 EVA ss3839334765 Apr 26, 2020 (154)
96 EVA ss3844797948 Apr 26, 2020 (154)
97 SGDP_PRJ ss3871919570 Apr 26, 2020 (154)
98 KRGDB ss3919589171 Apr 26, 2020 (154)
99 KOGIC ss3965640986 Apr 26, 2020 (154)
100 EVA ss3986045859 Apr 26, 2021 (155)
101 TOPMED ss4819247950 Apr 26, 2021 (155)
102 TOMMO_GENOMICS ss5192908816 Apr 26, 2021 (155)
103 1000Genomes NC_000009.11 - 33113121 Oct 12, 2018 (152)
104 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 33113121 Oct 12, 2018 (152)
105 Chileans NC_000009.11 - 33113121 Apr 26, 2020 (154)
106 Genetic variation in the Estonian population NC_000009.11 - 33113121 Oct 12, 2018 (152)
107 The Danish reference pan genome NC_000009.11 - 33113121 Apr 26, 2020 (154)
108 gnomAD - Genomes NC_000009.12 - 33113123 Apr 26, 2021 (155)
109 Genome of the Netherlands Release 5 NC_000009.11 - 33113121 Apr 26, 2020 (154)
110 HapMap NC_000009.12 - 33113123 Apr 26, 2020 (154)
111 KOREAN population from KRGDB NC_000009.11 - 33113121 Apr 26, 2020 (154)
112 Korean Genome Project NC_000009.12 - 33113123 Apr 26, 2020 (154)
113 Medical Genome Project healthy controls from Spanish population NC_000009.11 - 33113121 Apr 26, 2020 (154)
114 Northern Sweden NC_000009.11 - 33113121 Jul 13, 2019 (153)
115 Qatari NC_000009.11 - 33113121 Apr 26, 2020 (154)
116 SGDP_PRJ NC_000009.11 - 33113121 Apr 26, 2020 (154)
117 Siberian NC_000009.11 - 33113121 Apr 26, 2020 (154)
118 8.3KJPN NC_000009.11 - 33113121 Apr 26, 2021 (155)
119 TopMed NC_000009.12 - 33113123 Apr 26, 2021 (155)
120 UK 10K study - Twins NC_000009.11 - 33113121 Oct 12, 2018 (152)
121 A Vietnamese Genetic Variation Database NC_000009.11 - 33113121 Jul 13, 2019 (153)
122 ALFA NC_000009.12 - 33113123 Apr 26, 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)
rs3202448 Jul 03, 2002 (106)
rs17326644 Oct 08, 2004 (123)
rs58855169 May 24, 2008 (130)
rs117834397 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77468772, ss83179535, ss85336322 NC_000009.9:33103120:G:A NC_000009.12:33113122:G:A (self)
ss76642241, ss108743998, ss114434032, ss115724708, ss164066424, ss164986168, ss166414899, ss200334558, ss206857632, ss254176924, ss280188113, ss286004938, ss294436375, ss485782796, ss1596147050, ss1713105650 NC_000009.10:33103120:G:A NC_000009.12:33113122:G:A (self)
45907305, 25535506, 458507, 18173503, 9233815, 11392333, 26766565, 335067, 9758905, 11837518, 23936550, 6353662, 50878123, 25535506, 5676815, ss224224489, ss234800308, ss241580147, ss482808359, ss483496729, ss535704994, ss561359053, ss655800726, ss780299475, ss782191773, ss835786172, ss986509018, ss1076270270, ss1333655805, ss1431811969, ss1583068878, ss1622644922, ss1665638955, ss1711219307, ss1805965444, ss1929795588, ss1971202320, ss2025611388, ss2153837308, ss2481063942, ss2627280616, ss2634860772, ss2709647070, ss2877533235, ss2985460250, ss2986105972, ss3004680721, ss3348613206, ss3630254512, ss3632753488, ss3636957942, ss3638810477, ss3642685288, ss3646385841, ss3654224231, ss3672435255, ss3736474040, ss3769146139, ss3786397020, ss3791616660, ss3796498349, ss3825753670, ss3831634426, ss3839334765, ss3871919570, ss3919589171, ss3986045859, ss5192908816 NC_000009.11:33113120:G:A NC_000009.12:33113122:G:A (self)
323516626, 3822487, 22018987, 410167285, 656625511, 13680484612, ss2310949500, ss3026595660, ss3586897258, ss3649114531, ss3723833952, ss3812304960, ss3844797948, ss3965640986, ss4819247950 NC_000009.12:33113122:G:A NC_000009.12:33113122:G:A (self)
ss10492710, ss12931409 NT_008413.15:33103121:G:A NC_000009.12:33113122:G:A (self)
ss16012372, ss18017871, ss22874406, ss52082926 NT_008413.16:33103120:G:A NC_000009.12:33113122:G:A (self)
ss891, ss12675, ss1546190, ss3916790, ss4431664, ss16247756, ss24525984, ss43761864, ss97720519, ss104807690, ss105676217, ss134152383, ss157417878, ss160959856, ss169053937 NT_008413.18:33103120:G:A NC_000009.12:33113122:G:A (self)
ss200334558 NC_000009.10:33103120:G:C NC_000009.12:33113122:G:C (self)
13680484612 NC_000009.12:33113122:G:C NC_000009.12:33113122:G:C
ss200334558 NC_000009.10:33103120:G:T NC_000009.12:33113122:G: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 rs869

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