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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs956237

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr4:108125804 (GRCh38.p7) 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=0.44382 (55730/125568, TOPMED)
A=0.4495 (13813/30728, GnomAD)
A=0.391 (1960/5008, 1000G) (+ 2 more)
G=0.436 (1682/3854, ALSPAC)
G=0.437 (1621/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LEF1 : 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.p7 chr 4 NC_000004.12:g.108125804G>A
GRCh37.p13 chr 4 NC_000004.11:g.109046960G>A
LEF1 RefSeqGene NG_015798.1:g.48153C>T
Gene: LEF1, lymphoid enhancer binding factor 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
LEF1 transcript variant 2 NM_001130713.2:c. N/A Intron Variant
LEF1 transcript variant 3 NM_001130714.2:c. N/A Intron Variant
LEF1 transcript variant 4 NM_001166119.1:c. N/A Intron Variant
LEF1 transcript variant 1 NM_016269.4:c. N/A Intron Variant
LEF1 transcript variant X1 XM_005263046.3:c. N/A Intron Variant
LEF1 transcript variant X2 XM_005263047.1:c. N/A Intron Variant
LEF1 transcript variant X3 XM_005263048.1:c. N/A Intron Variant
LEF1 transcript variant X4 XM_006714233.1:c. N/A Intron 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
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
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.55618 A=0.44382
The Genome Aggregation Database Global Study-wide 30728 G=0.5505 A=0.4495
The Genome Aggregation Database European Sub 18326 G=0.4463 A=0.5537
The Genome Aggregation Database African Sub 8686 G=0.766 A=0.234
The Genome Aggregation Database East Asian Sub 1616 G=0.678 A=0.322
The Genome Aggregation Database Other Sub 978 G=0.47 A=0.53
The Genome Aggregation Database American Sub 824 G=0.54 A=0.46
The Genome Aggregation Database Ashkenazi Jewish Sub 298 G=0.27 A=0.73
1000Genomes Global Study-wide 5008 G=0.609 A=0.391
1000Genomes African Sub 1322 G=0.809 A=0.191
1000Genomes East Asian Sub 1008 G=0.665 A=0.335
1000Genomes Europe Sub 1006 G=0.441 A=0.559
1000Genomes South Asian Sub 978 G=0.48 A=0.52
1000Genomes American Sub 694 G=0.56 A=0.44
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.436 A=0.564
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.437 A=0.563
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.p7 chr 4 NC_000004.12:g.108125804G= NC_000004.12:g.10812580...

NC_000004.12:g.108125804G>A

GRCh37.p13 chr 4 NC_000004.11:g.109046960G= NC_000004.11:g.10904696...

NC_000004.11:g.109046960G>A

LEF1 RefSeqGene NG_015798.1:g.48153C= NG_015798.1:g.48153C>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#.

5 Frequency, 69 SubSNP submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1401459 Oct 05, 2000 (86)
2 WI_SSAHASNP ss14616190 Dec 05, 2003 (119)
3 PERLEGEN ss24362055 Sep 20, 2004 (123)
4 ABI ss44550772 Mar 14, 2006 (126)
5 AFFY ss65957981 Dec 02, 2006 (127)
6 ILLUMINA ss66855438 Dec 02, 2006 (127)
7 ILLUMINA ss67931405 Dec 02, 2006 (127)
8 ILLUMINA ss68051145 Dec 02, 2006 (127)
9 ILLUMINA ss71615832 May 18, 2007 (127)
10 ILLUMINA ss75870346 Dec 07, 2007 (129)
11 ILLUMINA ss79300128 Dec 14, 2007 (130)
12 KRIBB_YJKIM ss83631025 Dec 14, 2007 (130)
13 BCMHGSC_JDW ss92722216 Mar 24, 2008 (129)
14 ILLUMINA ss98272988 May 23, 2008 (130)
15 1000GENOMES ss108212063 Jan 23, 2009 (130)
16 ILLUMINA ss123014362 Dec 01, 2009 (131)
17 ILLUMINA ss154501305 Dec 01, 2009 (131)
18 GMI ss157715314 Dec 01, 2009 (131)
19 ILLUMINA ss159675163 Dec 01, 2009 (131)
20 COMPLETE_GENOMICS ss162422797 Jul 04, 2010 (132)
21 ILLUMINA ss172481144 Jul 04, 2010 (132)
22 ILLUMINA ss174867823 Jul 04, 2010 (132)
23 BCM-HGSC-SUB ss206350516 Jul 04, 2010 (132)
24 1000GENOMES ss211466644 Jul 14, 2010 (132)
25 1000GENOMES ss221129963 Jul 14, 2010 (132)
26 1000GENOMES ss232537373 Jul 14, 2010 (132)
27 1000GENOMES ss239796278 Jul 15, 2010 (132)
28 BL ss253410594 May 09, 2011 (134)
29 GMI ss277865728 May 04, 2012 (137)
30 ILLUMINA ss410958991 Sep 17, 2011 (135)
31 ILLUMINA ss537612129 Sep 08, 2015 (146)
32 SSMP ss651559965 Apr 25, 2013 (138)
33 ILLUMINA ss825630646 Apr 01, 2015 (144)
34 EVA-GONL ss980516100 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1071833653 Aug 21, 2014 (142)
36 1000GENOMES ss1311218357 Aug 21, 2014 (142)
37 DDI ss1430000728 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1580710890 Apr 01, 2015 (144)
39 EVA_DECODE ss1590020909 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1610866103 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1653860136 Apr 01, 2015 (144)
42 EVA_SVP ss1712696988 Apr 01, 2015 (144)
43 HAMMER_LAB ss1801989994 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1923753246 Feb 12, 2016 (147)
45 ILLUMINA ss1946124263 Feb 12, 2016 (147)
46 ILLUMINA ss1958711056 Feb 12, 2016 (147)
47 GENOMED ss1969830283 Jul 19, 2016 (147)
48 JJLAB ss2022461140 Sep 14, 2016 (149)
49 USC_VALOUEV ss2150590700 Dec 20, 2016 (150)
50 HUMAN_LONGEVITY ss2265925939 Dec 20, 2016 (150)
51 TOPMED ss2433758425 Dec 20, 2016 (150)
52 SYSTEMSBIOZJU ss2625727664 Nov 08, 2017 (151)
53 ILLUMINA ss2634161086 Nov 08, 2017 (151)
54 ILLUMINA ss2635135978 Nov 08, 2017 (151)
55 GRF ss2706068787 Nov 08, 2017 (151)
56 ILLUMINA ss2711013312 Nov 08, 2017 (151)
57 GNOMAD ss2813546913 Nov 08, 2017 (151)
58 SWEGEN ss2995308292 Nov 08, 2017 (151)
59 ILLUMINA ss3022403390 Nov 08, 2017 (151)
60 BIOINF_KMB_FNS_UNIBA ss3025005935 Nov 08, 2017 (151)
61 CSHL ss3345889043 Nov 08, 2017 (151)
62 TOPMED ss3438835536 Nov 08, 2017 (151)
63 ILLUMINA ss3625851194 Jul 20, 2018 (151)
64 ILLUMINA ss3629037099 Jul 20, 2018 (151)
65 ILLUMINA ss3638504724 Jul 20, 2018 (151)
66 ILLUMINA ss3639254597 Jul 20, 2018 (151)
67 ILLUMINA ss3639648815 Jul 20, 2018 (151)
68 ILLUMINA ss3643454704 Jul 20, 2018 (151)
69 ILLUMINA ss3644857073 Jul 20, 2018 (151)
70 1000Genomes NC_000004.11 - 109046960 Jul 20, 2018 (151)
71 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 109046960 Jul 20, 2018 (151)
72 The Genome Aggregation Database NC_000004.11 - 109046960 Jul 20, 2018 (151)
73 Trans-Omics for Precision Medicine NC_000004.12 - 108125804 Jul 20, 2018 (151)
74 UK 10K study - Twins NC_000004.11 - 109046960 Jul 20, 2018 (151)
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)
rs17566175 Oct 07, 2004 (123)
rs56952316 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3639254597, ss3639648815 NC_000004.9:109404563:G= NC_000004.12:108125803:G=
ss92722216, ss108212063, ss162422797, ss206350516, ss211466644, ss253410594, ss277865728, ss825630646, ss1590020909, ss1712696988, ss2635135978, ss3643454704 NC_000004.10:109266408:G= NC_000004.12:108125803:G= (self)
22669558, 12614499, 154174668, 12614499, ss221129963, ss232537373, ss239796278, ss537612129, ss651559965, ss980516100, ss1071833653, ss1311218357, ss1430000728, ss1580710890, ss1610866103, ss1653860136, ss1801989994, ss1923753246, ss1946124263, ss1958711056, ss1969830283, ss2022461140, ss2150590700, ss2433758425, ss2625727664, ss2634161086, ss2706068787, ss2711013312, ss2813546913, ss2995308292, ss3022403390, ss3345889043, ss3625851194, ss3629037099, ss3638504724, ss3644857073 NC_000004.11:109046959:G= NC_000004.12:108125803:G= (self)
290147174, ss2265925939, ss3025005935, ss3438835536 NC_000004.12:108125803:G= NC_000004.12:108125803:G= (self)
ss14616190 NT_016354.16:33542089:G= NC_000004.12:108125803:G= (self)
ss1401459, ss24362055, ss44550772, ss65957981, ss66855438, ss67931405, ss68051145, ss71615832, ss75870346, ss79300128, ss83631025, ss98272988, ss123014362, ss154501305, ss157715314, ss159675163, ss172481144, ss174867823, ss410958991 NT_016354.19:33594680:G= NC_000004.12:108125803:G= (self)
ss3639254597, ss3639648815 NC_000004.9:109404563:G>A NC_000004.12:108125803:G>A
ss92722216, ss108212063, ss162422797, ss206350516, ss211466644, ss253410594, ss277865728, ss825630646, ss1590020909, ss1712696988, ss2635135978, ss3643454704 NC_000004.10:109266408:G>A NC_000004.12:108125803:G>A (self)
22669558, 12614499, 154174668, 12614499, ss221129963, ss232537373, ss239796278, ss537612129, ss651559965, ss980516100, ss1071833653, ss1311218357, ss1430000728, ss1580710890, ss1610866103, ss1653860136, ss1801989994, ss1923753246, ss1946124263, ss1958711056, ss1969830283, ss2022461140, ss2150590700, ss2433758425, ss2625727664, ss2634161086, ss2706068787, ss2711013312, ss2813546913, ss2995308292, ss3022403390, ss3345889043, ss3625851194, ss3629037099, ss3638504724, ss3644857073 NC_000004.11:109046959:G>A NC_000004.12:108125803:G>A (self)
290147174, ss2265925939, ss3025005935, ss3438835536 NC_000004.12:108125803:G>A NC_000004.12:108125803:G>A (self)
ss14616190 NT_016354.16:33542089:G>A NC_000004.12:108125803:G>A (self)
ss1401459, ss24362055, ss44550772, ss65957981, ss66855438, ss67931405, ss68051145, ss71615832, ss75870346, ss79300128, ss83631025, ss98272988, ss123014362, ss154501305, ss157715314, ss159675163, ss172481144, ss174867823, ss410958991 NT_016354.19:33594680:G>A NC_000004.12:108125803: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 rs956237

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: 0.1.4.post833+d3ba21e