Name: rs111517281
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.

rs111517281

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr19:2182104 (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=0.077661 (20556/264690, TOPMED)
G=0.070543 (9877/140014, GnomAD)
G=0.18363 (5188/28252, 14KJPN) (+ 14 more)
G=0.05124 (968/18890, ALFA)
G=0.18409 (3085/16758, 8.3KJPN)
G=0.1060 (679/6404, 1000G_30x)
G=0.1080 (541/5008, 1000G)
G=0.0275 (123/4480, Estonian)
G=0.0215 (83/3854, ALSPAC)
G=0.0189 (70/3708, TWINSUK)
G=0.1738 (509/2928, KOREAN)
G=0.1698 (311/1832, Korea1K)
G=0.035 (21/600, NorthernSweden)
G=0.102 (22/216, Qatari)
A=0.455 (60/132, SGDP_PRJ)
G=0.03 (1/40, GENOME_DK)
A=0.4 (3/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DOT1L : 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	18890	A=0.94876	G=0.05124
European	Sub	14286	A=0.97403	G=0.02597
African	Sub	2946	A=0.8422	G=0.1578
African Others	Sub	114	A=0.816	G=0.184
African American	Sub	2832	A=0.8432	G=0.1568
Asian	Sub	112	A=0.884	G=0.116
East Asian	Sub	86	A=0.88	G=0.12
Other Asian	Sub	26	A=0.88	G=0.12
Latin American 1	Sub	146	A=0.966	G=0.034
Latin American 2	Sub	610	A=0.931	G=0.069
South Asian	Sub	98	A=0.86	G=0.14
Other	Sub	692	A=0.916	G=0.084

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	A=0.922339	G=0.077661
gnomAD - Genomes	Global	Study-wide	140014	A=0.929457	G=0.070543
gnomAD - Genomes	European	Sub	75852	A=0.97636	G=0.02364
gnomAD - Genomes	African	Sub	41944	A=0.84167	G=0.15833
gnomAD - Genomes	American	Sub	13632	A=0.94469	G=0.05531
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.9621	G=0.0379
gnomAD - Genomes	East Asian	Sub	3118	A=0.8711	G=0.1289
gnomAD - Genomes	Other	Sub	2146	A=0.9250	G=0.0750
14KJPN	JAPANESE	Study-wide	28252	A=0.81637	G=0.18363
Allele Frequency Aggregator	Total	Global	18890	A=0.94876	G=0.05124
Allele Frequency Aggregator	European	Sub	14286	A=0.97403	G=0.02597
Allele Frequency Aggregator	African	Sub	2946	A=0.8422	G=0.1578
Allele Frequency Aggregator	Other	Sub	692	A=0.916	G=0.084
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.931	G=0.069
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.966	G=0.034
Allele Frequency Aggregator	Asian	Sub	112	A=0.884	G=0.116
Allele Frequency Aggregator	South Asian	Sub	98	A=0.86	G=0.14
8.3KJPN	JAPANESE	Study-wide	16758	A=0.81591	G=0.18409
1000Genomes_30x	Global	Study-wide	6404	A=0.8940	G=0.1060
1000Genomes_30x	African	Sub	1786	A=0.8477	G=0.1523
1000Genomes_30x	Europe	Sub	1266	A=0.9708	G=0.0292
1000Genomes_30x	South Asian	Sub	1202	A=0.8627	G=0.1373
1000Genomes_30x	East Asian	Sub	1170	A=0.8880	G=0.1120
1000Genomes_30x	American	Sub	980	A=0.924	G=0.076
1000Genomes	Global	Study-wide	5008	A=0.8920	G=0.1080
1000Genomes	African	Sub	1322	A=0.8464	G=0.1536
1000Genomes	East Asian	Sub	1008	A=0.8829	G=0.1171
1000Genomes	Europe	Sub	1006	A=0.9712	G=0.0288
1000Genomes	South Asian	Sub	978	A=0.856	G=0.144
1000Genomes	American	Sub	694	A=0.928	G=0.072
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9725	G=0.0275
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9785	G=0.0215
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9811	G=0.0189
KOREAN population from KRGDB	KOREAN	Study-wide	2928	A=0.8262	G=0.1738
Korean Genome Project	KOREAN	Study-wide	1832	A=0.8302	G=0.1698
Northern Sweden	ACPOP	Study-wide	600	A=0.965	G=0.035
Qatari	Global	Study-wide	216	A=0.898	G=0.102
SGDP_PRJ	Global	Study-wide	132	A=0.455	G=0.545
The Danish reference pan genome	Danish	Study-wide	40	A=0.97	G=0.03
Siberian	Global	Study-wide	8	A=0.4	G=0.6

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 19	NC_000019.10:g.2182104A>G
GRCh37.p13 chr 19	NC_000019.9:g.2182103A>G
DOT1L RefSeqGene	NG_029793.1:g.22956A>G

Gene: DOT1L, DOT1 like histone lysine methyltransferase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DOT1L transcript variant 1	NM_032482.3:c.125+1348A>G	N/A	Intron Variant
DOT1L transcript variant X1	XM_005259659.4:c.125+1348… XM_005259659.4:c.125+1348A>G	N/A	Intron Variant
DOT1L transcript variant X1	XM_011528359.3:c.125+1348… XM_011528359.3:c.125+1348A>G	N/A	Intron Variant
DOT1L transcript variant X2	XM_047439513.1:c.-38+1348… XM_047439513.1:c.-38+1348A>G	N/A	Intron Variant
DOT1L transcript variant X3	XM_047439514.1:c.-179+134… XM_047439514.1:c.-179+1348A>G	N/A	Intron Variant
DOT1L transcript variant X4	XM_047439515.1:c.125+1348… XM_047439515.1:c.125+1348A>G	N/A	Intron Variant
DOT1L transcript variant X5	XM_011528361.3:c.	N/A	Genic Upstream Transcript 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 19	NC_000019.10:g.2182104=	NC_000019.10:g.2182104A>G
GRCh37.p13 chr 19	NC_000019.9:g.2182103=	NC_000019.9:g.2182103A>G
DOT1L RefSeqGene	NG_029793.1:g.22956=	NG_029793.1:g.22956A>G
DOT1L transcript	NM_032482.2:c.125+1348=	NM_032482.2:c.125+1348A>G
DOT1L transcript variant 1	NM_032482.3:c.125+1348=	NM_032482.3:c.125+1348A>G
DOT1L transcript variant X1	XM_005259659.1:c.125+1348=	XM_005259659.1:c.125+1348A>G
DOT1L transcript variant X1	XM_005259659.4:c.125+1348=	XM_005259659.4:c.125+1348A>G
DOT1L transcript variant X2	XM_005259660.1:c.125+1348=	XM_005259660.1:c.125+1348A>G
DOT1L transcript variant X1	XM_011528359.3:c.125+1348=	XM_011528359.3:c.125+1348A>G
DOT1L transcript variant X2	XM_047439513.1:c.-38+1348=	XM_047439513.1:c.-38+1348A>G
DOT1L transcript variant X3	XM_047439514.1:c.-179+1348=	XM_047439514.1:c.-179+1348A>G
DOT1L transcript variant X4	XM_047439515.1:c.125+1348=	XM_047439515.1:c.125+1348A>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#.

45 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	COMPLETE_GENOMICS	ss168868973	Jul 04, 2010 (132)
2	COMPLETE_GENOMICS	ss171389651	Jul 04, 2010 (132)
3	1000GENOMES	ss243806020	Jul 15, 2010 (132)
4	GMI	ss283098355	May 04, 2012 (137)
5	TISHKOFF	ss565809854	Apr 25, 2013 (138)
6	SSMP	ss661662293	Apr 25, 2013 (138)
7	EVA-GONL	ss994015118	Aug 21, 2014 (142)
8	JMKIDD_LAB	ss1081712917	Aug 21, 2014 (142)
9	1000GENOMES	ss1362077490	Aug 21, 2014 (142)
10	DDI	ss1428312326	Apr 01, 2015 (144)
11	EVA_GENOME_DK	ss1578526608	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1637436675	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1680430708	Apr 01, 2015 (144)
14	EVA_DECODE	ss1698078076	Apr 01, 2015 (144)
15	HAMMER_LAB	ss1809174168	Sep 08, 2015 (146)
16	WEILL_CORNELL_DGM	ss1937492383	Feb 12, 2016 (147)
17	GENOMED	ss1968593079	Jul 19, 2016 (147)
18	JJLAB	ss2029521240	Sep 14, 2016 (149)
19	USC_VALOUEV	ss2158034061	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2223734868	Dec 20, 2016 (150)
21	GRF	ss2702637613	Nov 08, 2017 (151)
22	GNOMAD	ss2959646432	Nov 08, 2017 (151)
23	SWEGEN	ss3016967506	Nov 08, 2017 (151)
24	EGCUT_WGS	ss3683816268	Jul 13, 2019 (153)
25	EVA_DECODE	ss3702193476	Jul 13, 2019 (153)
26	ACPOP	ss3742790075	Jul 13, 2019 (153)
27	EVA	ss3755726777	Jul 13, 2019 (153)
28	KHV_HUMAN_GENOMES	ss3820980418	Jul 13, 2019 (153)
29	SGDP_PRJ	ss3887601159	Apr 27, 2020 (154)
30	KRGDB	ss3937531205	Apr 27, 2020 (154)
31	KOGIC	ss3980658484	Apr 27, 2020 (154)
32	TOPMED	ss5065730862	Apr 26, 2021 (155)
33	TOMMO_GENOMICS	ss5226379011	Apr 26, 2021 (155)
34	1000G_HIGH_COVERAGE	ss5306227542	Oct 16, 2022 (156)
35	EVA	ss5433122798	Oct 16, 2022 (156)
36	HUGCELL_USP	ss5498896925	Oct 16, 2022 (156)
37	EVA	ss5512028281	Oct 16, 2022 (156)
38	1000G_HIGH_COVERAGE	ss5611526238	Oct 16, 2022 (156)
39	SANFORD_IMAGENETICS	ss5661833110	Oct 16, 2022 (156)
40	TOMMO_GENOMICS	ss5784530109	Oct 16, 2022 (156)
41	YY_MCH	ss5817341335	Oct 16, 2022 (156)
42	EVA	ss5840152885	Oct 16, 2022 (156)
43	EVA	ss5927024137	Oct 16, 2022 (156)
44	EVA	ss5953263821	Oct 16, 2022 (156)
45	EVA	ss5981023540	Oct 16, 2022 (156)
46	1000Genomes	NC_000019.9 - 2182103	Oct 12, 2018 (152)
47	1000Genomes_30x	NC_000019.10 - 2182104	Oct 16, 2022 (156)
48	The Avon Longitudinal Study of Parents and Children	NC_000019.9 - 2182103	Oct 12, 2018 (152)
49	Genetic variation in the Estonian population	NC_000019.9 - 2182103	Oct 12, 2018 (152)
50	The Danish reference pan genome	NC_000019.9 - 2182103	Apr 27, 2020 (154)
51	gnomAD - Genomes	NC_000019.10 - 2182104	Apr 26, 2021 (155)
52	KOREAN population from KRGDB	NC_000019.9 - 2182103	Apr 27, 2020 (154)
53	Korean Genome Project	NC_000019.10 - 2182104	Apr 27, 2020 (154)
54	Northern Sweden	NC_000019.9 - 2182103	Jul 13, 2019 (153)
55	Qatari	NC_000019.9 - 2182103	Apr 27, 2020 (154)
56	SGDP_PRJ	NC_000019.9 - 2182103	Apr 27, 2020 (154)
57	Siberian	NC_000019.9 - 2182103	Apr 27, 2020 (154)
58	8.3KJPN	NC_000019.9 - 2182103	Apr 26, 2021 (155)
59	14KJPN	NC_000019.10 - 2182104	Oct 16, 2022 (156)
60	TopMed	NC_000019.10 - 2182104	Apr 26, 2021 (155)
61	UK 10K study - Twins	NC_000019.9 - 2182103	Oct 12, 2018 (152)
62	ALFA	NC_000019.10 - 2182104	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
ss168868973, ss171389651, ss283098355, ss1698078076	NC_000019.8:2133102:A:G	NC_000019.10:2182103:A:G	(self)
75444247, 41816221, 29554516, 4713725, 44708599, 16074940, 19534305, 39618139, 10550415, 84348318, 41816221, ss243806020, ss565809854, ss661662293, ss994015118, ss1081712917, ss1362077490, ss1428312326, ss1578526608, ss1637436675, ss1680430708, ss1809174168, ss1937492383, ss1968593079, ss2029521240, ss2158034061, ss2702637613, ss2959646432, ss3016967506, ss3683816268, ss3742790075, ss3755726777, ss3887601159, ss3937531205, ss5226379011, ss5433122798, ss5512028281, ss5661833110, ss5840152885, ss5953263821, ss5981023540	NC_000019.9:2182102:A:G	NC_000019.10:2182103:A:G	(self)
99052173, 532048636, 37036485, 118367213, 281276526, 1211566415, ss2223734868, ss3702193476, ss3820980418, ss3980658484, ss5065730862, ss5306227542, ss5498896925, ss5611526238, ss5784530109, ss5817341335, ss5927024137	NC_000019.10:2182103:A:G	NC_000019.10:2182103: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 rs111517281

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs111517281