Name: rs6044171
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.

rs6044171

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:16618692 (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: T>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.331463 (87735/264690, TOPMED)
A=0.334312 (45982/137542, GnomAD)
A=0.28328 (8005/28258, 14KJPN) (+ 14 more)
A=0.31110 (5761/18518, ALFA)
A=0.28381 (4755/16754, 8.3KJPN)
A=0.3562 (2281/6404, 1000G_30x)
A=0.3506 (1756/5008, 1000G)
A=0.3097 (1387/4478, Estonian)
A=0.2849 (1098/3854, ALSPAC)
A=0.2807 (1041/3708, TWINSUK)
A=0.2691 (788/2928, KOREAN)
A=0.285 (284/998, GoNL)
A=0.275 (165/600, NorthernSweden)
T=0.369 (107/290, SGDP_PRJ)
A=0.259 (56/216, Qatari)
A=0.40 (16/40, GENOME_DK)
T=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	18518	T=0.68890	A=0.31110
European	Sub	14150	T=0.71548	A=0.28452
African	Sub	2898	T=0.5483	A=0.4517
African Others	Sub	114	T=0.491	A=0.509
African American	Sub	2784	T=0.5506	A=0.4494
Asian	Sub	112	T=0.580	A=0.420
East Asian	Sub	86	T=0.59	A=0.41
Other Asian	Sub	26	T=0.54	A=0.46
Latin American 1	Sub	146	T=0.699	A=0.301
Latin American 2	Sub	610	T=0.734	A=0.266
South Asian	Sub	98	T=0.78	A=0.22
Other	Sub	504	T=0.700	A=0.300

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	T=0.668537	A=0.331463
gnomAD - Genomes	Global	Study-wide	137542	T=0.665688	A=0.334312
gnomAD - Genomes	European	Sub	74592	T=0.71525	A=0.28475
gnomAD - Genomes	African	Sub	41328	T=0.54743	A=0.45257
gnomAD - Genomes	American	Sub	13180	T=0.72815	A=0.27185
gnomAD - Genomes	Ashkenazi Jewish	Sub	3276	T=0.7515	A=0.2485
gnomAD - Genomes	East Asian	Sub	3076	T=0.6788	A=0.3212
gnomAD - Genomes	Other	Sub	2090	T=0.6876	A=0.3124
14KJPN	JAPANESE	Study-wide	28258	T=0.71672	A=0.28328
Allele Frequency Aggregator	Total	Global	18518	T=0.68890	A=0.31110
Allele Frequency Aggregator	European	Sub	14150	T=0.71548	A=0.28452
Allele Frequency Aggregator	African	Sub	2898	T=0.5483	A=0.4517
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.734	A=0.266
Allele Frequency Aggregator	Other	Sub	504	T=0.700	A=0.300
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.699	A=0.301
Allele Frequency Aggregator	Asian	Sub	112	T=0.580	A=0.420
Allele Frequency Aggregator	South Asian	Sub	98	T=0.78	A=0.22
8.3KJPN	JAPANESE	Study-wide	16754	T=0.71619	A=0.28381
1000Genomes_30x	Global	Study-wide	6404	T=0.6438	A=0.3562
1000Genomes_30x	African	Sub	1786	T=0.5090	A=0.4910
1000Genomes_30x	Europe	Sub	1266	T=0.7101	A=0.2899
1000Genomes_30x	South Asian	Sub	1202	T=0.6755	A=0.3245
1000Genomes_30x	East Asian	Sub	1170	T=0.6658	A=0.3342
1000Genomes_30x	American	Sub	980	T=0.739	A=0.261
1000Genomes	Global	Study-wide	5008	T=0.6494	A=0.3506
1000Genomes	African	Sub	1322	T=0.5182	A=0.4818
1000Genomes	East Asian	Sub	1008	T=0.6667	A=0.3333
1000Genomes	Europe	Sub	1006	T=0.7127	A=0.2873
1000Genomes	South Asian	Sub	978	T=0.683	A=0.317
1000Genomes	American	Sub	694	T=0.735	A=0.265
Genetic variation in the Estonian population	Estonian	Study-wide	4478	T=0.6903	A=0.3097
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.7151	A=0.2849
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.7193	A=0.2807
KOREAN population from KRGDB	KOREAN	Study-wide	2928	T=0.7309	A=0.2691
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.715	A=0.285
Northern Sweden	ACPOP	Study-wide	600	T=0.725	A=0.275
SGDP_PRJ	Global	Study-wide	290	T=0.369	A=0.631
Qatari	Global	Study-wide	216	T=0.741	A=0.259
The Danish reference pan genome	Danish	Study-wide	40	T=0.60	A=0.40
Siberian	Global	Study-wide	36	T=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.16618692T>A
GRCh37.p13 chr 20	NC_000020.10:g.16599337T>A

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	T=	A
GRCh38.p14 chr 20	NC_000020.11:g.16618692=	NC_000020.11:g.16618692T>A
GRCh37.p13 chr 20	NC_000020.10:g.16599337=	NC_000020.10:g.16599337T>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#.

57 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8354289	Apr 21, 2003 (114)
2	HGSV	ss80802196	Dec 14, 2007 (130)
3	HGSV	ss83740315	Dec 14, 2007 (130)
4	HGSV	ss85698041	Dec 14, 2007 (130)
5	IGMI-SNU	ss115463946	Feb 04, 2009 (130)
6	COMPLETE_GENOMICS	ss169208888	Jul 04, 2010 (132)
7	BUSHMAN	ss203845215	Jul 04, 2010 (132)
8	BCM-HGSC-SUB	ss208732643	Jul 04, 2010 (132)
9	1000GENOMES	ss212004471	Jul 14, 2010 (132)
10	BL	ss255510832	May 09, 2011 (134)
11	GMI	ss283318039	May 04, 2012 (137)
12	GMI	ss287430946	Apr 25, 2013 (138)
13	PJP	ss292621255	May 09, 2011 (134)
14	1000GENOMES	ss465751247	Sep 17, 2011 (135)
15	TISHKOFF	ss566164594	Apr 25, 2013 (138)
16	EVA-GONL	ss994588525	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1082110161	Aug 21, 2014 (142)
18	1000GENOMES	ss1364241899	Aug 21, 2014 (142)
19	DDI	ss1429011053	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1579457066	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1638509875	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1681503908	Apr 01, 2015 (144)
23	HAMMER_LAB	ss1809442679	Sep 08, 2015 (146)
24	WEILL_CORNELL_DGM	ss1938096695	Feb 12, 2016 (147)
25	GENOMED	ss1969103131	Jul 19, 2016 (147)
26	JJLAB	ss2029830393	Sep 14, 2016 (149)
27	USC_VALOUEV	ss2158384135	Dec 20, 2016 (150)
28	SYSTEMSBIOZJU	ss2629411345	Nov 08, 2017 (151)
29	GRF	ss2704058448	Nov 08, 2017 (151)
30	GNOMAD	ss2965930957	Nov 08, 2017 (151)
31	SWEGEN	ss3017940110	Nov 08, 2017 (151)
32	BIOINF_KMB_FNS_UNIBA	ss3028748873	Nov 08, 2017 (151)
33	CSHL	ss3352441609	Nov 08, 2017 (151)
34	EGCUT_WGS	ss3684660980	Jul 13, 2019 (153)
35	EVA_DECODE	ss3706647709	Jul 13, 2019 (153)
36	ACPOP	ss3743289569	Jul 13, 2019 (153)
37	EVA	ss3758478973	Jul 13, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3821650217	Jul 13, 2019 (153)
39	EVA	ss3835611982	Apr 27, 2020 (154)
40	EVA	ss3841431953	Apr 27, 2020 (154)
41	EVA	ss3846939893	Apr 27, 2020 (154)
42	SGDP_PRJ	ss3888825124	Apr 27, 2020 (154)
43	KRGDB	ss3939023053	Apr 27, 2020 (154)
44	TOPMED	ss5083830318	Apr 27, 2021 (155)
45	TOMMO_GENOMICS	ss5229038469	Apr 27, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5308238978	Oct 13, 2022 (156)
47	EVA	ss5436547285	Oct 13, 2022 (156)
48	HUGCELL_USP	ss5500626200	Oct 13, 2022 (156)
49	EVA	ss5512170503	Oct 13, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5614401110	Oct 13, 2022 (156)
51	SANFORD_IMAGENETICS	ss5662953979	Oct 13, 2022 (156)
52	TOMMO_GENOMICS	ss5788080905	Oct 13, 2022 (156)
53	YY_MCH	ss5817855441	Oct 13, 2022 (156)
54	EVA	ss5845507811	Oct 13, 2022 (156)
55	EVA	ss5853088720	Oct 13, 2022 (156)
56	EVA	ss5922854638	Oct 13, 2022 (156)
57	EVA	ss5957862328	Oct 13, 2022 (156)
58	1000Genomes	NC_000020.10 - 16599337	Oct 12, 2018 (152)
59	1000Genomes_30x	NC_000020.11 - 16618692	Oct 13, 2022 (156)
60	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 16599337	Oct 12, 2018 (152)
61	Genetic variation in the Estonian population	NC_000020.10 - 16599337	Oct 12, 2018 (152)
62	The Danish reference pan genome	NC_000020.10 - 16599337	Apr 27, 2020 (154)
63	gnomAD - Genomes	NC_000020.11 - 16618692	Apr 27, 2021 (155)
64	Genome of the Netherlands Release 5	NC_000020.10 - 16599337	Apr 27, 2020 (154)
65	KOREAN population from KRGDB	NC_000020.10 - 16599337	Apr 27, 2020 (154)
66	Northern Sweden	NC_000020.10 - 16599337	Jul 13, 2019 (153)
67	Qatari	NC_000020.10 - 16599337	Apr 27, 2020 (154)
68	SGDP_PRJ	NC_000020.10 - 16599337	Apr 27, 2020 (154)
69	Siberian	NC_000020.10 - 16599337	Apr 27, 2020 (154)
70	8.3KJPN	NC_000020.10 - 16599337	Apr 27, 2021 (155)
71	14KJPN	NC_000020.11 - 16618692	Oct 13, 2022 (156)
72	TopMed	NC_000020.11 - 16618692	Apr 27, 2021 (155)
73	UK 10K study - Twins	NC_000020.10 - 16599337	Oct 12, 2018 (152)
74	ALFA	NC_000020.11 - 16618692	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)
rs57803049	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80802196, ss83740315, ss85698041, ss169208888, ss203845215, ss208732643, ss212004471, ss255510832, ss283318039, ss287430946, ss292621255	NC_000020.9:16547336:T:A	NC_000020.11:16618691:T:A	(self)
77687796, 43012037, 30399228, 5622005, 19165853, 46200447, 16574434, 20138617, 40842104, 10900489, 87007776, 43012037, ss465751247, ss566164594, ss994588525, ss1082110161, ss1364241899, ss1429011053, ss1579457066, ss1638509875, ss1681503908, ss1809442679, ss1938096695, ss1969103131, ss2029830393, ss2158384135, ss2629411345, ss2704058448, ss2965930957, ss3017940110, ss3352441609, ss3684660980, ss3743289569, ss3758478973, ss3835611982, ss3841431953, ss3888825124, ss3939023053, ss5229038469, ss5436547285, ss5512170503, ss5662953979, ss5845507811, ss5957862328	NC_000020.10:16599336:T:A	NC_000020.11:16618691:T:A	(self)
101927045, 547756518, 121918009, 358939263, 5183772800, ss3028748873, ss3706647709, ss3821650217, ss3846939893, ss5083830318, ss5308238978, ss5500626200, ss5614401110, ss5788080905, ss5817855441, ss5853088720, ss5922854638	NC_000020.11:16618691:T:A	NC_000020.11:16618691:T:A	(self)
ss8354289, ss115463946	NT_011387.8:16539336:T:A	NC_000020.11:16618691:T:A	(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 rs6044171

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

rs6044171