Name: rs6044169
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.

rs6044169

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:16618283 (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>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.427477 (113149/264690, TOPMED)
A=0.431348 (57321/132888, GnomAD)
A=0.28262 (7983/28246, 14KJPN) (+ 14 more)
A=0.28403 (4757/16748, 8.3KJPN)
A=0.19323 (2238/11582, ALFA)
A=0.4472 (2864/6404, 1000G_30x)
A=0.4373 (2190/5008, 1000G)
A=0.3175 (1416/4460, Estonian)
A=0.3114 (1200/3854, ALSPAC)
A=0.3083 (1143/3708, TWINSUK)
A=0.2734 (801/2930, KOREAN)
A=0.316 (315/998, GoNL)
A=0.291 (174/598, NorthernSweden)
G=0.324 (103/318, SGDP_PRJ)
A=0.329 (71/216, Qatari)
A=0.45 (18/40, GENOME_DK)
G=0.33 (12/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105372542 : 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	11582	G=0.80677	A=0.19323, C=0.00000
European	Sub	10324	G=0.79969	A=0.20031, C=0.00000
African	Sub	418	G=0.789	A=0.211, C=0.000
African Others	Sub	12	G=0.50	A=0.50, C=0.00
African American	Sub	406	G=0.798	A=0.202, C=0.000
Asian	Sub	42	G=0.93	A=0.07, C=0.00
East Asian	Sub	30	G=0.97	A=0.03, C=0.00
Other Asian	Sub	12	G=0.83	A=0.17, C=0.00
Latin American 1	Sub	52	G=1.00	A=0.00, C=0.00
Latin American 2	Sub	288	G=1.000	A=0.000, C=0.000
South Asian	Sub	60	G=0.97	A=0.03, C=0.00
Other	Sub	398	G=0.807	A=0.193, C=0.000

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.572523	A=0.427477
gnomAD - Genomes	Global	Study-wide	132888	G=0.568652	A=0.431348
gnomAD - Genomes	European	Sub	72716	G=0.68593	A=0.31407
gnomAD - Genomes	African	Sub	39724	G=0.30631	A=0.69369
gnomAD - Genomes	American	Sub	12102	G=0.65270	A=0.34730
gnomAD - Genomes	Ashkenazi Jewish	Sub	3286	G=0.7188	A=0.2812
gnomAD - Genomes	East Asian	Sub	3038	G=0.6715	A=0.3285
gnomAD - Genomes	Other	Sub	2022	G=0.6034	A=0.3966
14KJPN	JAPANESE	Study-wide	28246	G=0.71738	A=0.28262
8.3KJPN	JAPANESE	Study-wide	16748	G=0.71597	A=0.28403
Allele Frequency Aggregator	Total	Global	11582	G=0.80677	A=0.19323, C=0.00000
Allele Frequency Aggregator	European	Sub	10324	G=0.79969	A=0.20031, C=0.00000
Allele Frequency Aggregator	African	Sub	418	G=0.789	A=0.211, C=0.000
Allele Frequency Aggregator	Other	Sub	398	G=0.807	A=0.193, C=0.000
Allele Frequency Aggregator	Latin American 2	Sub	288	G=1.000	A=0.000, C=0.000
Allele Frequency Aggregator	South Asian	Sub	60	G=0.97	A=0.03, C=0.00
Allele Frequency Aggregator	Latin American 1	Sub	52	G=1.00	A=0.00, C=0.00
Allele Frequency Aggregator	Asian	Sub	42	G=0.93	A=0.07, C=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.5528	A=0.4472
1000Genomes_30x	African	Sub	1786	G=0.2464	A=0.7536
1000Genomes_30x	Europe	Sub	1266	G=0.6746	A=0.3254
1000Genomes_30x	South Asian	Sub	1202	G=0.6647	A=0.3353
1000Genomes_30x	East Asian	Sub	1170	G=0.6607	A=0.3393
1000Genomes_30x	American	Sub	980	G=0.688	A=0.312
1000Genomes	Global	Study-wide	5008	G=0.5627	A=0.4373
1000Genomes	African	Sub	1322	G=0.2526	A=0.7474
1000Genomes	East Asian	Sub	1008	G=0.6617	A=0.3383
1000Genomes	Europe	Sub	1006	G=0.6799	A=0.3201
1000Genomes	South Asian	Sub	978	G=0.671	A=0.329
1000Genomes	American	Sub	694	G=0.687	A=0.313
Genetic variation in the Estonian population	Estonian	Study-wide	4460	G=0.6825	A=0.3175
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6886	A=0.3114
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6917	A=0.3083
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.7266	A=0.2734
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.684	A=0.316
Northern Sweden	ACPOP	Study-wide	598	G=0.709	A=0.291
SGDP_PRJ	Global	Study-wide	318	G=0.324	A=0.676
Qatari	Global	Study-wide	216	G=0.671	A=0.329
The Danish reference pan genome	Danish	Study-wide	40	G=0.55	A=0.45
Siberian	Global	Study-wide	36	G=0.33	A=0.67

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 20	NC_000020.11:g.16618283G>A
GRCh38.p14 chr 20	NC_000020.11:g.16618283G>C
GRCh37.p13 chr 20	NC_000020.10:g.16598928G>A
GRCh37.p13 chr 20	NC_000020.10:g.16598928G>C

Gene: LOC105372542, uncharacterized LOC105372542 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372542 transcript	XR_937286.3:n.	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=	A	C
GRCh38.p14 chr 20	NC_000020.11:g.16618283=	NC_000020.11:g.16618283G>A	NC_000020.11:g.16618283G>C
GRCh37.p13 chr 20	NC_000020.10:g.16598928=	NC_000020.10:g.16598928G>A	NC_000020.10:g.16598928G>C

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#.

56 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8354287	Apr 21, 2003 (114)
2	SC_SNP	ss11111402	Jul 11, 2003 (117)
3	HGSV	ss79069470	Dec 06, 2007 (129)
4	HGSV	ss85743117	Dec 15, 2007 (130)
5	IGMI-SNU	ss115463944	Feb 05, 2009 (130)
6	ENSEMBL	ss161308142	Dec 01, 2009 (131)
7	COMPLETE_GENOMICS	ss169208857	Jul 04, 2010 (132)
8	BUSHMAN	ss203845214	Jul 04, 2010 (132)
9	BCM-HGSC-SUB	ss208739728	Jul 04, 2010 (132)
10	1000GENOMES	ss237782668	Jul 15, 2010 (132)
11	BL	ss255510821	May 09, 2011 (134)
12	GMI	ss283318035	May 04, 2012 (137)
13	GMI	ss287430944	Apr 25, 2013 (138)
14	PJP	ss292621253	May 09, 2011 (134)
15	TISHKOFF	ss566164592	Apr 25, 2013 (138)
16	SSMP	ss662038572	Apr 25, 2013 (138)
17	EVA-GONL	ss994588522	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1082110158	Aug 21, 2014 (142)
19	1000GENOMES	ss1364241882	Aug 21, 2014 (142)
20	DDI	ss1429011051	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1579457063	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1638509870	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1681503903	Apr 01, 2015 (144)
24	HAMMER_LAB	ss1809442677	Sep 08, 2015 (146)
25	WEILL_CORNELL_DGM	ss1938096690	Feb 12, 2016 (147)
26	JJLAB	ss2029830391	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2158384130	Dec 20, 2016 (150)
28	HUMAN_LONGEVITY	ss2241698501	Dec 20, 2016 (150)
29	SYSTEMSBIOZJU	ss2629411343	Nov 08, 2017 (151)
30	GRF	ss2704058443	Nov 08, 2017 (151)
31	GNOMAD	ss2965930914	Nov 08, 2017 (151)
32	SWEGEN	ss3017940104	Nov 08, 2017 (151)
33	BIOINF_KMB_FNS_UNIBA	ss3028748871	Nov 08, 2017 (151)
34	CSHL	ss3352441606	Nov 08, 2017 (151)
35	EGCUT_WGS	ss3684660972	Jul 13, 2019 (153)
36	ACPOP	ss3743289566	Jul 13, 2019 (153)
37	EVA	ss3758478965	Jul 13, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3821650211	Jul 13, 2019 (153)
39	EVA	ss3835611978	Apr 27, 2020 (154)
40	EVA	ss3841431951	Apr 27, 2020 (154)
41	EVA	ss3846939891	Apr 27, 2020 (154)
42	SGDP_PRJ	ss3888825115	Apr 27, 2020 (154)
43	KRGDB	ss3939023027	Apr 27, 2020 (154)
44	TOPMED	ss5083830217	Apr 27, 2021 (155)
45	TOMMO_GENOMICS	ss5229038434	Apr 27, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5308238952	Oct 13, 2022 (156)
47	EVA	ss5436547262	Oct 13, 2022 (156)
48	EVA	ss5512170501	Oct 13, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5614401081	Oct 13, 2022 (156)
50	SANFORD_IMAGENETICS	ss5662953973	Oct 13, 2022 (156)
51	TOMMO_GENOMICS	ss5788080851	Oct 13, 2022 (156)
52	YY_MCH	ss5817855434	Oct 13, 2022 (156)
53	EVA	ss5845507804	Oct 13, 2022 (156)
54	EVA	ss5853088718	Oct 13, 2022 (156)
55	EVA	ss5922854623	Oct 13, 2022 (156)
56	EVA	ss5957862323	Oct 13, 2022 (156)
57	1000Genomes	NC_000020.10 - 16598928	Oct 12, 2018 (152)
58	1000Genomes_30x	NC_000020.11 - 16618283	Oct 13, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 16598928	Oct 12, 2018 (152)
60	Genetic variation in the Estonian population	NC_000020.10 - 16598928	Oct 12, 2018 (152)
61	The Danish reference pan genome	NC_000020.10 - 16598928	Apr 27, 2020 (154)
62	gnomAD - Genomes	NC_000020.11 - 16618283	Apr 27, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000020.10 - 16598928	Apr 27, 2020 (154)
64	KOREAN population from KRGDB	NC_000020.10 - 16598928	Apr 27, 2020 (154)
65	Northern Sweden	NC_000020.10 - 16598928	Jul 13, 2019 (153)
66	Qatari	NC_000020.10 - 16598928	Apr 27, 2020 (154)
67	SGDP_PRJ	NC_000020.10 - 16598928	Apr 27, 2020 (154)
68	Siberian	NC_000020.10 - 16598928	Apr 27, 2020 (154)
69	8.3KJPN	NC_000020.10 - 16598928	Apr 27, 2021 (155)
70	14KJPN	NC_000020.11 - 16618283	Oct 13, 2022 (156)
71	TopMed	NC_000020.11 - 16618283	Apr 27, 2021 (155)
72	UK 10K study - Twins	NC_000020.10 - 16598928	Oct 12, 2018 (152)
73	ALFA	NC_000020.11 - 16618283	Apr 27, 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)
rs7348739	Aug 26, 2003 (117)
rs59906857	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss79069470, ss85743117, ss169208857, ss203845214, ss208739728, ss255510821, ss283318035, ss287430944, ss292621253	NC_000020.9:16546927:G:A	NC_000020.11:16618282:G:A	(self)
77687778, 43012029, 30399220, 5622002, 19165850, 46200421, 16574431, 20138612, 40842095, 10900484, 87007741, 43012029, ss237782668, ss566164592, ss662038572, ss994588522, ss1082110158, ss1364241882, ss1429011051, ss1579457063, ss1638509870, ss1681503903, ss1809442677, ss1938096690, ss2029830391, ss2158384130, ss2629411343, ss2704058443, ss2965930914, ss3017940104, ss3352441606, ss3684660972, ss3743289566, ss3758478965, ss3835611978, ss3841431951, ss3888825115, ss3939023027, ss5229038434, ss5436547262, ss5512170501, ss5662953973, ss5845507804, ss5957862323	NC_000020.10:16598927:G:A	NC_000020.11:16618282:G:A	(self)
101927016, 547756421, 121917955, 358939162, 6610594280, ss2241698501, ss3028748871, ss3821650211, ss3846939891, ss5083830217, ss5308238952, ss5614401081, ss5788080851, ss5817855434, ss5853088718, ss5922854623	NC_000020.11:16618282:G:A	NC_000020.11:16618282:G:A	(self)
ss8354287, ss11111402, ss115463944, ss161308142	NT_011387.8:16538927:G:A	NC_000020.11:16618282:G:A	(self)
6610594280	NC_000020.11:16618282:G:C	NC_000020.11:16618282:G:C	(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 rs6044169

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs6044169