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dbSNP Short Genetic Variations

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.

rs6774

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr3:119212037 (GRCh38.p12) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.16718 (20993/125568, TOPMED)
A=0.1551 (4797/30928, GnomAD)
A=0.175 (877/5008, 1000G) (+ 3 more)
A=0.114 (512/4480, Estonian)
A=0.112 (431/3854, ALSPAC)
A=0.115 (426/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
B4GALT4 : Non Coding Transcript 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.p12 chr 3 NC_000003.12:g.119212037G>A
GRCh37.p13 chr 3 NC_000003.11:g.118930884G>A
Gene: B4GALT4, beta-1,4-galactosyltransferase 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
B4GALT4 transcript variant 2 NM_003778.3:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant 1 NM_212543.1:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X4 XM_005247855.1:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X5 XM_011513260.1:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X11 XM_017007401.1:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X1 XM_006713798.3:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X2 XM_006713799.3:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X3 XM_006713800.2:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X6 XM_006713801.3:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X7 XM_024453804.1:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X8 XM_024453805.1:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X9 XM_024453806.1:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X10 XM_024453807.1:c. N/A 3 Prime UTR Variant
B4GALT4 transcript variant X12 XR_001740340.1:n.1877C>T N/A Non Coding Transcript Variant
B4GALT4 transcript variant X16 XR_001740343.1:n.2027C>T N/A Non Coding Transcript Variant
B4GALT4 transcript variant X18 XR_001740345.1:n.1965C>T N/A Non Coding Transcript Variant
B4GALT4 transcript variant X13 XR_001740341.2:n.1948C>T N/A Non Coding Transcript Variant
B4GALT4 transcript variant X14 XR_001740342.2:n.1960C>T N/A Non Coding Transcript Variant
B4GALT4 transcript variant X15 XR_002959604.1:n.2025C>T N/A Non Coding Transcript Variant
B4GALT4 transcript variant X17 XR_001740344.2:n.2110C>T N/A Non Coding Transcript Variant
B4GALT4 transcript variant X19 XR_001740346.2:n.2048C>T N/A Non Coding 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
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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 125568 G=0.83282 A=0.16718
gnomAD - Genomes Global Study-wide 30928 G=0.8449 A=0.1551
gnomAD - Genomes European Sub 18484 G=0.8878 A=0.1122
gnomAD - Genomes African Sub 8708 G=0.747 A=0.253
gnomAD - Genomes East Asian Sub 1614 G=0.880 A=0.120
gnomAD - Genomes Other Sub 982 G=0.89 A=0.11
gnomAD - Genomes American Sub 838 G=0.75 A=0.25
gnomAD - Genomes Ashkenazi Jewish Sub 302 G=0.96 A=0.04
1000Genomes Global Study-wide 5008 G=0.825 A=0.175
1000Genomes African Sub 1322 G=0.744 A=0.256
1000Genomes East Asian Sub 1008 G=0.926 A=0.074
1000Genomes Europe Sub 1006 G=0.909 A=0.091
1000Genomes South Asian Sub 978 G=0.82 A=0.18
1000Genomes American Sub 694 G=0.72 A=0.28
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.886 A=0.114
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.888 A=0.112
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.885 A=0.115
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 Note
GRCh38.p12 chr 3 NC_000003.12:g.119212037G= NC_000003.12:g.11921203...

NC_000003.12:g.119212037G>A

GRCh37.p13 chr 3 NC_000003.11:g.118930884G= NC_000003.11:g.11893088...

NC_000003.11:g.118930884G>A

B4GALT4 transcript variant X6 XM_006713801.3:c.*512C= XM_006713801.3:c.*512C>T
B4GALT4 transcript variant X2 XM_006713799.3:c.*512C= XM_006713799.3:c.*512C>T
B4GALT4 transcript variant X1 XM_006713798.3:c.*512C= XM_006713798.3:c.*512C>T
B4GALT4 transcript variant 2 NM_003778.3:c.*512C= NM_003778.3:c.*512C>T
B4GALT4 transcript variant X17 XR_001740344.2:n.2110C= XR_001740344.2:n.2110C>T
B4GALT4 transcript variant X19 XR_001740346.2:n.2048C= XR_001740346.2:n.2048C>T
B4GALT4 transcript variant X3 XM_006713800.2:c.*512C= XM_006713800.2:c.*512C>T
B4GALT4 transcript variant X14 XR_001740342.2:n.1960C= XR_001740342.2:n.1960C>T
B4GALT4 transcript variant X13 XR_001740341.2:n.1948C= XR_001740341.2:n.1948C>T
B4GALT4 transcript variant X7 XM_024453804.1:c.*512C= XM_024453804.1:c.*512C>T
B4GALT4 transcript variant X10 XM_024453807.1:c.*512C= XM_024453807.1:c.*512C>T
B4GALT4 transcript variant X5 XM_011513260.1:c.*512C= XM_011513260.1:c.*512C>T
B4GALT4 transcript variant X9 XM_024453806.1:c.*512C= XM_024453806.1:c.*512C>T
B4GALT4 transcript variant X8 XM_024453805.1:c.*512C= XM_024453805.1:c.*512C>T
B4GALT4 transcript variant 1 NM_212543.1:c.*512C= NM_212543.1:c.*512C>T
B4GALT4 transcript variant X16 XR_001740343.1:n.2027C= XR_001740343.1:n.2027C>T
B4GALT4 transcript variant X15 XR_002959604.1:n.2025C= XR_002959604.1:n.2025C>T
B4GALT4 transcript variant X4 XM_005247855.1:c.*512C= XM_005247855.1:c.*512C>T
B4GALT4 transcript variant X18 XR_001740345.1:n.1965C= XR_001740345.1:n.1965C>T
B4GALT4 transcript variant X12 XR_001740340.1:n.1877C= XR_001740340.1:n.1877C>T
B4GALT4 transcript variant X11 XM_017007401.1:c.*512C= XM_017007401.1:c.*512C>T
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#.

82 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 CGAP-GAI ss8489 Sep 19, 2000 (52)
2 LEE ss1514352 Oct 13, 2000 (92)
3 BCM_SSAHASNP ss10051741 Jul 11, 2003 (116)
4 WI_SSAHASNP ss11565964 Jul 11, 2003 (116)
5 BCM_SSAHASNP ss14223461 Dec 05, 2003 (119)
6 PERLEGEN ss23673217 Sep 20, 2004 (123)
7 ILLUMINA ss65735253 Oct 16, 2006 (127)
8 AFFY ss66080836 Nov 30, 2006 (127)
9 PERLEGEN ss68873257 May 17, 2007 (127)
10 ILLUMINA ss74896845 Dec 06, 2007 (129)
11 AFFY ss76021718 Dec 08, 2007 (130)
12 KRIBB_YJKIM ss81404202 Dec 14, 2007 (130)
13 RSG_UW ss107936652 Feb 03, 2009 (130)
14 1000GENOMES ss110809438 Jan 25, 2009 (130)
15 1000GENOMES ss112404053 Jan 25, 2009 (130)
16 ILLUMINA-UK ss117245687 Feb 14, 2009 (130)
17 ILLUMINA ss160808529 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss164088812 Jul 04, 2010 (132)
19 AFFY ss170521096 Jul 04, 2010 (132)
20 ILLUMINA ss174107832 Jul 04, 2010 (132)
21 BUSHMAN ss203078689 Jul 04, 2010 (132)
22 1000GENOMES ss220383963 Jul 14, 2010 (132)
23 1000GENOMES ss232000094 Jul 14, 2010 (132)
24 1000GENOMES ss239378067 Jul 15, 2010 (132)
25 ILLUMINA ss244306405 Jul 04, 2010 (132)
26 GMI ss277316366 May 04, 2012 (137)
27 PJP ss292897180 May 09, 2011 (134)
28 ILLUMINA ss410943576 Sep 17, 2011 (135)
29 ILLUMINA ss481350659 May 04, 2012 (137)
30 ILLUMINA ss481376364 May 04, 2012 (137)
31 ILLUMINA ss482355599 Sep 08, 2015 (146)
32 ILLUMINA ss485470517 May 04, 2012 (137)
33 ILLUMINA ss535983523 Sep 08, 2015 (146)
34 ILLUMINA ss537391131 Sep 08, 2015 (146)
35 TISHKOFF ss556893827 Apr 25, 2013 (138)
36 SSMP ss650605306 Apr 25, 2013 (138)
37 ILLUMINA ss778580074 Aug 21, 2014 (142)
38 ILLUMINA ss783180733 Aug 21, 2014 (142)
39 ILLUMINA ss784136059 Aug 21, 2014 (142)
40 ILLUMINA ss832440386 Apr 01, 2015 (144)
41 ILLUMINA ss834037182 Aug 21, 2014 (142)
42 EVA-GONL ss979073670 Aug 21, 2014 (142)
43 JMKIDD_LAB ss1070769494 Aug 21, 2014 (142)
44 1000GENOMES ss1305820708 Aug 21, 2014 (142)
45 HAMMER_LAB ss1397350002 Sep 08, 2015 (146)
46 DDI ss1429560904 Apr 01, 2015 (144)
47 EVA_GENOME_DK ss1580148339 Apr 01, 2015 (144)
48 EVA_DECODE ss1588555196 Apr 01, 2015 (144)
49 EVA_UK10K_ALSPAC ss1608037944 Apr 01, 2015 (144)
50 EVA_UK10K_TWINSUK ss1651031977 Apr 01, 2015 (144)
51 EVA_MGP ss1711029314 Apr 01, 2015 (144)
52 EVA_SVP ss1712606209 Apr 01, 2015 (144)
53 ILLUMINA ss1752434411 Sep 08, 2015 (146)
54 HAMMER_LAB ss1799918676 Sep 08, 2015 (146)
55 WEILL_CORNELL_DGM ss1922300092 Feb 12, 2016 (147)
56 GENOMED ss1969503677 Jul 19, 2016 (147)
57 JJLAB ss2021717622 Sep 14, 2016 (149)
58 USC_VALOUEV ss2149809432 Dec 20, 2016 (150)
59 HUMAN_LONGEVITY ss2255172467 Dec 20, 2016 (150)
60 TOPMED ss2422498465 Dec 20, 2016 (150)
61 SYSTEMSBIOZJU ss2625360771 Nov 08, 2017 (151)
62 ILLUMINA ss2634001814 Nov 08, 2017 (151)
63 ILLUMINA ss2634001815 Nov 08, 2017 (151)
64 GRF ss2705212590 Nov 08, 2017 (151)
65 GNOMAD ss2798171212 Nov 08, 2017 (151)
66 SWEGEN ss2993058697 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3024625477 Nov 08, 2017 (151)
68 CSHL ss3345226817 Nov 08, 2017 (151)
69 TOPMED ss3403348118 Nov 08, 2017 (151)
70 ILLUMINA ss3628756658 Oct 12, 2018 (152)
71 ILLUMINA ss3628756659 Oct 12, 2018 (152)
72 ILLUMINA ss3631945326 Oct 12, 2018 (152)
73 ILLUMINA ss3633305869 Oct 12, 2018 (152)
74 ILLUMINA ss3634023420 Oct 12, 2018 (152)
75 ILLUMINA ss3634912765 Oct 12, 2018 (152)
76 ILLUMINA ss3635707069 Oct 12, 2018 (152)
77 ILLUMINA ss3636609226 Oct 12, 2018 (152)
78 ILLUMINA ss3637459469 Oct 12, 2018 (152)
79 ILLUMINA ss3638436903 Oct 12, 2018 (152)
80 ILLUMINA ss3640620064 Oct 12, 2018 (152)
81 ILLUMINA ss3643392249 Oct 12, 2018 (152)
82 OMUKHERJEE_ADBS ss3646291278 Oct 12, 2018 (152)
83 1000Genomes NC_000003.11 - 118930884 Oct 12, 2018 (152)
84 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 118930884 Oct 12, 2018 (152)
85 Genetic variation in the Estonian population NC_000003.11 - 118930884 Oct 12, 2018 (152)
86 gnomAD - Genomes NC_000003.11 - 118930884 Oct 12, 2018 (152)
87 TopMed NC_000003.12 - 119212037 Oct 12, 2018 (152)
88 UK 10K study - Twins NC_000003.11 - 118930884 Oct 12, 2018 (152)
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)
rs1128057 Jan 18, 2001 (92)
rs56418705 May 27, 2008 (130)
rs57662256 Feb 26, 2009 (130)
rs386605001 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss66080836, ss76021718, ss110809438, ss112404053, ss117245687, ss164088812, ss170521096, ss203078689, ss277316366, ss292897180, ss410943576, ss481350659, ss1397350002, ss1588555196, ss1712606209, ss3643392249 NC_000003.10:120413573:G:A NC_000003.12:119212036:G:A (self)
17071812, 9508513, 6723344, 138798966, 9508513, ss220383963, ss232000094, ss239378067, ss481376364, ss482355599, ss485470517, ss535983523, ss537391131, ss556893827, ss650605306, ss778580074, ss783180733, ss784136059, ss832440386, ss834037182, ss979073670, ss1070769494, ss1305820708, ss1429560904, ss1580148339, ss1608037944, ss1651031977, ss1711029314, ss1752434411, ss1799918676, ss1922300092, ss1969503677, ss2021717622, ss2149809432, ss2422498465, ss2625360771, ss2634001814, ss2634001815, ss2705212590, ss2798171212, ss2993058697, ss3345226817, ss3628756658, ss3628756659, ss3631945326, ss3633305869, ss3634023420, ss3634912765, ss3635707069, ss3636609226, ss3637459469, ss3638436903, ss3640620064, ss3646291278 NC_000003.11:118930883:G:A NC_000003.12:119212036:G:A (self)
261311380, ss2255172467, ss3024625477, ss3403348118 NC_000003.12:119212036:G:A NC_000003.12:119212036:G:A (self)
ss10051741, ss11565964 NT_005612.13:25330037:G:A NC_000003.12:119212036:G:A (self)
ss14223461 NT_005612.14:25426029:G:A NC_000003.12:119212036:G:A (self)
ss8489, ss1514352, ss23673217, ss65735253, ss68873257, ss74896845, ss81404202, ss107936652, ss160808529, ss174107832, ss244306405 NT_005612.16:25426029:G:A NC_000003.12:119212036:G:A (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 rs6774

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.post104+4a6ee9c