Name: rs2067040
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.

rs2067040

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:66730906 (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: G>C / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.302308 (80018/264690, TOPMED)
T=0.289798 (40559/139956, GnomAD)
G=0.38074 (10759/28258, 14KJPN) (+ 17 more)
T=0.32277 (8279/25650, ALFA)
G=0.38347 (6427/16760, 8.3KJPN)
T=0.3346 (2143/6404, 1000G_30x)
T=0.3438 (1722/5008, 1000G)
T=0.3219 (1442/4480, Estonian)
T=0.3303 (1273/3854, ALSPAC)
T=0.3244 (1203/3708, TWINSUK)
G=0.3543 (1038/2930, KOREAN)
T=0.3120 (589/1888, HapMap)
G=0.3777 (692/1832, Korea1K)
T=0.364 (363/998, GoNL)
T=0.288 (173/600, NorthernSweden)
G=0.311 (107/344, SGDP_PRJ)
T=0.380 (82/216, Qatari)
G=0.425 (90/212, Vietnamese)
T=0.35 (14/40, GENOME_DK)
G=0.32 (12/38, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DYNC1LI2 : 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	25650	G=0.67723	T=0.32277
European	Sub	17398	G=0.66467	T=0.33533
African	Sub	3624	G=0.8891	T=0.1109
African Others	Sub	126	G=0.913	T=0.087
African American	Sub	3498	G=0.8882	T=0.1118
Asian	Sub	160	G=0.344	T=0.656
East Asian	Sub	102	G=0.324	T=0.676
Other Asian	Sub	58	G=0.38	T=0.62
Latin American 1	Sub	288	G=0.701	T=0.299
Latin American 2	Sub	2726	G=0.5293	T=0.4707
South Asian	Sub	110	G=0.609	T=0.391
Other	Sub	1344	G=0.6086	T=0.3914

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=0.697692	T=0.302308
gnomAD - Genomes	Global	Study-wide	139956	G=0.710202	T=0.289798
gnomAD - Genomes	European	Sub	75796	G=0.66167	T=0.33833
gnomAD - Genomes	African	Sub	41974	G=0.87690	T=0.12310
gnomAD - Genomes	American	Sub	13612	G=0.58588	T=0.41412
gnomAD - Genomes	Ashkenazi Jewish	Sub	3314	G=0.5260	T=0.4740
gnomAD - Genomes	East Asian	Sub	3110	G=0.4055	T=0.5945
gnomAD - Genomes	Other	Sub	2150	G=0.6786	T=0.3214
14KJPN	JAPANESE	Study-wide	28258	G=0.38074	T=0.61926
Allele Frequency Aggregator	Total	Global	25650	G=0.67723	T=0.32277
Allele Frequency Aggregator	European	Sub	17398	G=0.66467	T=0.33533
Allele Frequency Aggregator	African	Sub	3624	G=0.8891	T=0.1109
Allele Frequency Aggregator	Latin American 2	Sub	2726	G=0.5293	T=0.4707
Allele Frequency Aggregator	Other	Sub	1344	G=0.6086	T=0.3914
Allele Frequency Aggregator	Latin American 1	Sub	288	G=0.701	T=0.299
Allele Frequency Aggregator	Asian	Sub	160	G=0.344	T=0.656
Allele Frequency Aggregator	South Asian	Sub	110	G=0.609	T=0.391
8.3KJPN	JAPANESE	Study-wide	16760	G=0.38347	T=0.61653
1000Genomes_30x	Global	Study-wide	6404	G=0.6654	T=0.3346
1000Genomes_30x	African	Sub	1786	G=0.9334	T=0.0666
1000Genomes_30x	Europe	Sub	1266	G=0.6524	T=0.3476
1000Genomes_30x	South Asian	Sub	1202	G=0.6082	T=0.3918
1000Genomes_30x	East Asian	Sub	1170	G=0.3880	T=0.6120
1000Genomes_30x	American	Sub	980	G=0.595	T=0.405
1000Genomes	Global	Study-wide	5008	G=0.6562	T=0.3438
1000Genomes	African	Sub	1322	G=0.9312	T=0.0688
1000Genomes	East Asian	Sub	1008	G=0.3839	T=0.6161
1000Genomes	Europe	Sub	1006	G=0.6511	T=0.3489
1000Genomes	South Asian	Sub	978	G=0.607	T=0.393
1000Genomes	American	Sub	694	G=0.604	T=0.396
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.6781	T=0.3219
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6697	T=0.3303
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6756	T=0.3244
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.3543	C=0.0000, T=0.6457
HapMap	Global	Study-wide	1888	G=0.6880	T=0.3120
HapMap	American	Sub	766	G=0.624	T=0.376
HapMap	African	Sub	692	G=0.887	T=0.113
HapMap	Asian	Sub	254	G=0.366	T=0.634
HapMap	Europe	Sub	176	G=0.648	T=0.352
Korean Genome Project	KOREAN	Study-wide	1832	G=0.3777	T=0.6223
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.636	T=0.364
Northern Sweden	ACPOP	Study-wide	600	G=0.712	T=0.288
SGDP_PRJ	Global	Study-wide	344	G=0.311	T=0.689
Qatari	Global	Study-wide	216	G=0.620	T=0.380
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.425	T=0.575
The Danish reference pan genome	Danish	Study-wide	40	G=0.65	T=0.35
Siberian	Global	Study-wide	38	G=0.32	T=0.68

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 16	NC_000016.10:g.66730906G>C
GRCh38.p14 chr 16	NC_000016.10:g.66730906G>T
GRCh37.p13 chr 16	NC_000016.9:g.66764809G>C
GRCh37.p13 chr 16	NC_000016.9:g.66764809G>T

Gene: DYNC1LI2, dynein cytoplasmic 1 light intermediate chain 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DYNC1LI2 transcript variant 2	NM_001286157.2:c.699-683C… NM_001286157.2:c.699-683C>G	N/A	Intron Variant
DYNC1LI2 transcript variant 3	NM_001323955.2:c.813-683C… NM_001323955.2:c.813-683C>G	N/A	Intron Variant
DYNC1LI2 transcript variant 1	NM_006141.3:c.930-683C>G	N/A	Intron Variant
DYNC1LI2 transcript variant 4	NR_136658.2:n.	N/A	Intron Variant
DYNC1LI2 transcript variant X1	XM_017023008.2:c.930-683C… XM_017023008.2:c.930-683C>G	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	G=	C	T
GRCh38.p14 chr 16	NC_000016.10:g.66730906=	NC_000016.10:g.66730906G>C	NC_000016.10:g.66730906G>T
GRCh37.p13 chr 16	NC_000016.9:g.66764809=	NC_000016.9:g.66764809G>C	NC_000016.9:g.66764809G>T
DYNC1LI2 transcript variant 2	NM_001286157.2:c.699-683=	NM_001286157.2:c.699-683C>G	NM_001286157.2:c.699-683C>A
DYNC1LI2 transcript variant 3	NM_001323955.2:c.813-683=	NM_001323955.2:c.813-683C>G	NM_001323955.2:c.813-683C>A
DYNC1LI2 transcript variant 1	NM_006141.2:c.930-683=	NM_006141.2:c.930-683C>G	NM_006141.2:c.930-683C>A
DYNC1LI2 transcript variant 1	NM_006141.3:c.930-683=	NM_006141.3:c.930-683C>G	NM_006141.3:c.930-683C>A
DYNC1LI2 transcript variant X1	XM_005255831.1:c.699-683=	XM_005255831.1:c.699-683C>G	XM_005255831.1:c.699-683C>A
DYNC1LI2 transcript variant X1	XM_017023008.2:c.930-683=	XM_017023008.2:c.930-683C>G	XM_017023008.2:c.930-683C>A

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#.

74 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SHGC/AFFYMETRIX	ss2980898	Jun 15, 2001 (96)
2	TSC-CSHL	ss3100601	Jun 15, 2001 (96)
3	YUSUKE	ss4971446	Aug 28, 2002 (108)
4	TSC-CSHL	ss5209373	Oct 08, 2002 (108)
5	SC_JCM	ss5672930	Feb 20, 2003 (111)
6	BCM_SSAHASNP	ss10823349	Jul 11, 2003 (116)
7	PERLEGEN	ss24192158	Sep 20, 2004 (123)
8	ABI	ss43812543	Mar 15, 2006 (126)
9	ILLUMINA	ss65733296	Oct 15, 2006 (127)
10	AFFY	ss66260283	Nov 30, 2006 (127)
11	AFFY	ss76405489	Dec 07, 2007 (129)
12	KRIBB_YJKIM	ss81678495	Dec 16, 2007 (130)
13	HGSV	ss82676899	Dec 16, 2007 (130)
14	HUMANGENOME_JCVI	ss96690160	Feb 06, 2009 (130)
15	ILLUMINA-UK	ss118289001	Feb 14, 2009 (130)
16	GMI	ss157473726	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss168371756	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss171372670	Jul 04, 2010 (132)
19	AFFY	ss173489810	Jul 04, 2010 (132)
20	1000GENOMES	ss227298766	Jul 14, 2010 (132)
21	1000GENOMES	ss237066213	Jul 15, 2010 (132)
22	1000GENOMES	ss243398032	Jul 15, 2010 (132)
23	BL	ss255776679	May 09, 2011 (134)
24	GMI	ss282573275	May 04, 2012 (137)
25	PJP	ss291862655	May 09, 2011 (134)
26	TISHKOFF	ss564966101	Apr 25, 2013 (138)
27	SSMP	ss660742904	Apr 25, 2013 (138)
28	EVA-GONL	ss992601281	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1080705685	Aug 21, 2014 (142)
30	1000GENOMES	ss1356666315	Aug 21, 2014 (142)
31	DDI	ss1427879449	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1577958402	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1634647875	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1677641908	Apr 01, 2015 (144)
35	EVA_DECODE	ss1696636048	Apr 01, 2015 (144)
36	EVA_SVP	ss1713547053	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1808559722	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1936032349	Feb 12, 2016 (147)
39	GENOMED	ss1968286763	Jul 19, 2016 (147)
40	JJLAB	ss2028802194	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2157239617	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2213032307	Dec 20, 2016 (150)
43	SYSTEMSBIOZJU	ss2628892368	Nov 08, 2017 (151)
44	ILLUMINA	ss2633331458	Nov 08, 2017 (151)
45	GRF	ss2701768184	Nov 08, 2017 (151)
46	GNOMAD	ss2944204485	Nov 08, 2017 (151)
47	SWEGEN	ss3014683201	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3028219471	Nov 08, 2017 (151)
49	CSHL	ss3351500222	Nov 08, 2017 (151)
50	URBANLAB	ss3650532082	Oct 12, 2018 (152)
51	EGCUT_WGS	ss3681666748	Jul 13, 2019 (153)
52	EVA_DECODE	ss3699473372	Jul 13, 2019 (153)
53	ACPOP	ss3741603743	Jul 13, 2019 (153)
54	EVA	ss3754067464	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3819351591	Jul 13, 2019 (153)
56	EVA	ss3834623367	Apr 27, 2020 (154)
57	SGDP_PRJ	ss3884660006	Apr 27, 2020 (154)
58	KRGDB	ss3934167735	Apr 27, 2020 (154)
59	KOGIC	ss3977792110	Apr 27, 2020 (154)
60	TOPMED	ss5019077365	Apr 26, 2021 (155)
61	TOMMO_GENOMICS	ss5220053125	Apr 26, 2021 (155)
62	1000G_HIGH_COVERAGE	ss5301328256	Oct 16, 2022 (156)
63	EVA	ss5424395170	Oct 16, 2022 (156)
64	HUGCELL_USP	ss5494645364	Oct 16, 2022 (156)
65	EVA	ss5511644000	Oct 16, 2022 (156)
66	1000G_HIGH_COVERAGE	ss5604172949	Oct 16, 2022 (156)
67	SANFORD_IMAGENETICS	ss5659112885	Oct 16, 2022 (156)
68	TOMMO_GENOMICS	ss5775198721	Oct 16, 2022 (156)
69	YY_MCH	ss5816064936	Oct 16, 2022 (156)
70	EVA	ss5846552816	Oct 16, 2022 (156)
71	EVA	ss5851611902	Oct 16, 2022 (156)
72	EVA	ss5899523456	Oct 16, 2022 (156)
73	EVA	ss5950512397	Oct 16, 2022 (156)
74	EVA	ss5980926753	Oct 16, 2022 (156)
75	1000Genomes	NC_000016.9 - 66764809	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000016.10 - 66730906	Oct 16, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 66764809	Oct 12, 2018 (152)
78	Genetic variation in the Estonian population	NC_000016.9 - 66764809	Oct 12, 2018 (152)
79	The Danish reference pan genome	NC_000016.9 - 66764809	Apr 27, 2020 (154)
80	gnomAD - Genomes	NC_000016.10 - 66730906	Apr 26, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000016.9 - 66764809	Apr 27, 2020 (154)
82	HapMap	NC_000016.10 - 66730906	Apr 27, 2020 (154)
83	KOREAN population from KRGDB	NC_000016.9 - 66764809	Apr 27, 2020 (154)
84	Korean Genome Project	NC_000016.10 - 66730906	Apr 27, 2020 (154)
85	Northern Sweden	NC_000016.9 - 66764809	Jul 13, 2019 (153)
86	Qatari	NC_000016.9 - 66764809	Apr 27, 2020 (154)
87	SGDP_PRJ	NC_000016.9 - 66764809	Apr 27, 2020 (154)
88	Siberian	NC_000016.9 - 66764809	Apr 27, 2020 (154)
89	8.3KJPN	NC_000016.9 - 66764809	Apr 26, 2021 (155)
90	14KJPN	NC_000016.10 - 66730906	Oct 16, 2022 (156)
91	TopMed	NC_000016.10 - 66730906	Apr 26, 2021 (155)
92	UK 10K study - Twins	NC_000016.9 - 66764809	Oct 12, 2018 (152)
93	A Vietnamese Genetic Variation Database	NC_000016.9 - 66764809	Jul 13, 2019 (153)
94	ALFA	NC_000016.10 - 66730906	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).

Associated ID	History Updated (Build)
rs3785090	Oct 09, 2002 (108)
rs17700023	Oct 08, 2004 (123)
rs61429235	May 26, 2008 (130)
rs61658577	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
41345129, ss3934167735	NC_000016.9:66764808:G:C	NC_000016.10:66730905:G:C	(self)
ss82676899, ss118289001, ss168371756, ss171372670, ss255776679, ss282573275, ss291862655, ss1696636048, ss1713547053	NC_000016.8:65322309:G:T	NC_000016.10:66730905:G:T	(self)
69844209, 38746959, 27404996, 4168982, 17278571, 41345129, 14888608, 18074271, 36676986, 9755971, 78022432, 38746959, 8595759, ss227298766, ss237066213, ss243398032, ss564966101, ss660742904, ss992601281, ss1080705685, ss1356666315, ss1427879449, ss1577958402, ss1634647875, ss1677641908, ss1808559722, ss1936032349, ss1968286763, ss2028802194, ss2157239617, ss2628892368, ss2633331458, ss2701768184, ss2944204485, ss3014683201, ss3351500222, ss3681666748, ss3741603743, ss3754067464, ss3834623367, ss3884660006, ss3934167735, ss5220053125, ss5424395170, ss5511644000, ss5659112885, ss5846552816, ss5950512397, ss5980926753	NC_000016.9:66764808:G:T	NC_000016.10:66730905:G:T	(self)
91698884, 492640238, 1403039, 34170111, 109035825, 234623026, 7674809497, ss2213032307, ss3028219471, ss3650532082, ss3699473372, ss3819351591, ss3977792110, ss5019077365, ss5301328256, ss5494645364, ss5604172949, ss5775198721, ss5816064936, ss5851611902, ss5899523456	NC_000016.10:66730905:G:T	NC_000016.10:66730905:G:T	(self)
ss10823349	NT_010498.13:15486366:G:T	NC_000016.10:66730905:G:T	(self)
ss2980898, ss3100601, ss4971446, ss5209373, ss5672930, ss24192158, ss43812543, ss65733296, ss66260283, ss76405489, ss81678495, ss96690160, ss157473726, ss173489810	NT_010498.15:20379007:G:T	NC_000016.10:66730905:G:T	(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 rs2067040

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

rs2067040