Name: rs6054257
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.

rs6054257

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:85729 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.204662 (54172/264690, TOPMED)
G=0.197870 (27724/140112, GnomAD)
G=0.44646 (12616/28258, 14KJPN) (+ 17 more)
G=0.19677 (3717/18890, ALFA)
G=0.44290 (7423/16760, 8.3KJPN)
G=0.2409 (1543/6404, 1000G_30x)
G=0.2466 (1235/5008, 1000G)
G=0.1953 (875/4480, Estonian)
G=0.2029 (782/3854, ALSPAC)
G=0.2131 (790/3708, TWINSUK)
G=0.4635 (1358/2930, KOREAN)
G=0.4765 (873/1832, Korea1K)
G=0.203 (203/998, GoNL)
G=0.212 (127/600, NorthernSweden)
G=0.196 (97/496, SGDP_PRJ)
G=0.227 (74/326, HapMap)
G=0.273 (59/216, Qatari)
A=0.458 (98/214, Vietnamese)
G=0.26 (13/50, Siberian)
G=0.23 (9/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DEFB125 : 2KB Upstream 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	G=0.19677	A=0.80323
European	Sub	14286	G=0.19733	A=0.80267
African	Sub	2946	G=0.1636	A=0.8364
African Others	Sub	114	G=0.149	A=0.851
African American	Sub	2832	G=0.1642	A=0.8358
Asian	Sub	112	G=0.473	A=0.527
East Asian	Sub	86	G=0.45	A=0.55
Other Asian	Sub	26	G=0.54	A=0.46
Latin American 1	Sub	146	G=0.185	A=0.815
Latin American 2	Sub	610	G=0.300	A=0.700
South Asian	Sub	98	G=0.22	A=0.78
Other	Sub	692	G=0.189	A=0.811

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=0.204662	A=0.795338
gnomAD - Genomes	Global	Study-wide	140112	G=0.197870	A=0.802130
gnomAD - Genomes	European	Sub	75876	G=0.20277	A=0.79723
gnomAD - Genomes	African	Sub	41996	G=0.15573	A=0.84427
gnomAD - Genomes	American	Sub	13638	G=0.25106	A=0.74894
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.1652	A=0.8348
gnomAD - Genomes	East Asian	Sub	3124	G=0.4289	A=0.5711
gnomAD - Genomes	Other	Sub	2154	G=0.2256	A=0.7744
14KJPN	JAPANESE	Study-wide	28258	G=0.44646	A=0.55354
Allele Frequency Aggregator	Total	Global	18890	G=0.19677	A=0.80323
Allele Frequency Aggregator	European	Sub	14286	G=0.19733	A=0.80267
Allele Frequency Aggregator	African	Sub	2946	G=0.1636	A=0.8364
Allele Frequency Aggregator	Other	Sub	692	G=0.189	A=0.811
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.300	A=0.700
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.185	A=0.815
Allele Frequency Aggregator	Asian	Sub	112	G=0.473	A=0.527
Allele Frequency Aggregator	South Asian	Sub	98	G=0.22	A=0.78
8.3KJPN	JAPANESE	Study-wide	16760	G=0.44290	A=0.55710
1000Genomes_30x	Global	Study-wide	6404	G=0.2409	A=0.7591
1000Genomes_30x	African	Sub	1786	G=0.1473	A=0.8527
1000Genomes_30x	Europe	Sub	1266	G=0.1991	A=0.8009
1000Genomes_30x	South Asian	Sub	1202	G=0.2271	A=0.7729
1000Genomes_30x	East Asian	Sub	1170	G=0.4385	A=0.5615
1000Genomes_30x	American	Sub	980	G=0.247	A=0.753
1000Genomes	Global	Study-wide	5008	G=0.2466	A=0.7534
1000Genomes	African	Sub	1322	G=0.1467	A=0.8533
1000Genomes	East Asian	Sub	1008	G=0.4365	A=0.5635
1000Genomes	Europe	Sub	1006	G=0.1988	A=0.8012
1000Genomes	South Asian	Sub	978	G=0.234	A=0.766
1000Genomes	American	Sub	694	G=0.248	A=0.752
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.1953	A=0.8047
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.2029	A=0.7971
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.2131	A=0.7869
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.4635	A=0.5365
Korean Genome Project	KOREAN	Study-wide	1832	G=0.4765	A=0.5235
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.203	A=0.797
Northern Sweden	ACPOP	Study-wide	600	G=0.212	A=0.788
SGDP_PRJ	Global	Study-wide	496	G=0.196	A=0.804
HapMap	Global	Study-wide	326	G=0.227	A=0.773
HapMap	African	Sub	118	G=0.110	A=0.890
HapMap	American	Sub	118	G=0.203	A=0.797
HapMap	Asian	Sub	90	G=0.41	A=0.59
Qatari	Global	Study-wide	216	G=0.273	A=0.727
A Vietnamese Genetic Variation Database	Global	Study-wide	214	G=0.542	A=0.458
Siberian	Global	Study-wide	50	G=0.26	A=0.74
The Danish reference pan genome	Danish	Study-wide	40	G=0.23	A=0.78

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.85729G>A
GRCh37.p13 chr 20	NC_000020.10:g.66370G>A

Gene: DEFB125, defensin beta 125 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
DEFB125 transcript	NM_153325.4:c.	N/A	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	G=	A
GRCh38.p14 chr 20	NC_000020.11:g.85729=	NC_000020.11:g.85729G>A
GRCh37.p13 chr 20	NC_000020.10:g.66370=	NC_000020.10:g.66370G>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#.

75 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8367660	Apr 21, 2003 (114)
2	SC_SNP	ss11108551	Jul 11, 2003 (117)
3	WI_SSAHASNP	ss12488835	Jul 11, 2003 (117)
4	CSHL-HAPMAP	ss20125552	Feb 27, 2004 (120)
5	SSAHASNP	ss21768915	Apr 05, 2004 (121)
6	ABI	ss41417635	Mar 13, 2006 (126)
7	HGSV	ss83430118	Dec 16, 2007 (130)
8	HGSV	ss84231557	Dec 16, 2007 (130)
9	BCMHGSC_JDW	ss91611611	Mar 24, 2008 (129)
10	HUMANGENOME_JCVI	ss96180628	Feb 06, 2009 (130)
11	1000GENOMES	ss111581030	Jan 25, 2009 (130)
12	1000GENOMES	ss115345920	Jan 25, 2009 (130)
13	ILLUMINA-UK	ss117452054	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss167637399	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss168828483	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss171804844	Jul 04, 2010 (132)
17	BUSHMAN	ss203804012	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss208599144	Jul 04, 2010 (132)
19	1000GENOMES	ss228210647	Jul 14, 2010 (132)
20	1000GENOMES	ss237729940	Jul 15, 2010 (132)
21	1000GENOMES	ss243923461	Jul 15, 2010 (132)
22	BL	ss255419683	May 09, 2011 (134)
23	GMI	ss283268941	May 04, 2012 (137)
24	GMI	ss287408431	Apr 25, 2013 (138)
25	PJP	ss292559575	May 09, 2011 (134)
26	TISHKOFF	ss566082465	Apr 25, 2013 (138)
27	SSMP	ss661953386	Apr 25, 2013 (138)
28	EVA-GONL	ss994456712	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1082009530	Aug 21, 2014 (142)
30	1000GENOMES	ss1363765817	Aug 21, 2014 (142)
31	DDI	ss1428970659	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1579402588	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1638249132	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1681243165	Apr 01, 2015 (144)
35	EVA_DECODE	ss1698510266	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1809383611	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1937965351	Feb 12, 2016 (147)
38	GENOMED	ss1969071123	Jul 19, 2016 (147)
39	JJLAB	ss2029757241	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2158311814	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2240713187	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2629376453	Nov 08, 2017 (151)
43	GRF	ss2703983089	Nov 08, 2017 (151)
44	GNOMAD	ss2964602144	Nov 08, 2017 (151)
45	SWEGEN	ss3017743792	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3028710409	Nov 08, 2017 (151)
47	CSHL	ss3352380170	Nov 08, 2017 (151)
48	URBANLAB	ss3650952960	Oct 12, 2018 (152)
49	EGCUT_WGS	ss3684456414	Jul 13, 2019 (153)
50	EVA_DECODE	ss3706405148	Jul 13, 2019 (153)
51	ACPOP	ss3743178858	Jul 13, 2019 (153)
52	EVA	ss3758326061	Jul 13, 2019 (153)
53	PACBIO	ss3788576762	Jul 13, 2019 (153)
54	PACBIO	ss3793480306	Jul 13, 2019 (153)
55	PACBIO	ss3798367454	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3821498999	Jul 13, 2019 (153)
57	EVA	ss3835544935	Apr 27, 2020 (154)
58	EVA	ss3841395539	Apr 27, 2020 (154)
59	EVA	ss3846902803	Apr 27, 2020 (154)
60	SGDP_PRJ	ss3888570274	Apr 27, 2020 (154)
61	KRGDB	ss3938746984	Apr 27, 2020 (154)
62	KOGIC	ss3981678614	Apr 27, 2020 (154)
63	TOPMED	ss5079734164	Apr 27, 2021 (155)
64	TOMMO_GENOMICS	ss5228505546	Apr 27, 2021 (155)
65	1000G_HIGH_COVERAGE	ss5307820332	Oct 13, 2022 (156)
66	EVA	ss5435782980	Oct 13, 2022 (156)
67	HUGCELL_USP	ss5500245738	Oct 13, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5613776649	Oct 13, 2022 (156)
69	SANFORD_IMAGENETICS	ss5662711327	Oct 13, 2022 (156)
70	TOMMO_GENOMICS	ss5787397220	Oct 13, 2022 (156)
71	YY_MCH	ss5817748618	Oct 13, 2022 (156)
72	EVA	ss5845337198	Oct 13, 2022 (156)
73	EVA	ss5853034203	Oct 13, 2022 (156)
74	EVA	ss5922371404	Oct 13, 2022 (156)
75	EVA	ss5957606950	Oct 13, 2022 (156)
76	1000Genomes	NC_000020.10 - 66370	Oct 12, 2018 (152)
77	1000Genomes_30x	NC_000020.11 - 85729	Oct 13, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 66370	Oct 12, 2018 (152)
79	Genetic variation in the Estonian population	NC_000020.10 - 66370	Oct 12, 2018 (152)
80	The Danish reference pan genome	NC_000020.10 - 66370	Apr 27, 2020 (154)
81	gnomAD - Genomes	NC_000020.11 - 85729	Apr 27, 2021 (155)
82	Genome of the Netherlands Release 5	NC_000020.10 - 66370	Apr 27, 2020 (154)
83	HapMap	NC_000020.11 - 85729	Apr 27, 2020 (154)
84	KOREAN population from KRGDB	NC_000020.10 - 66370	Apr 27, 2020 (154)
85	Korean Genome Project	NC_000020.11 - 85729	Apr 27, 2020 (154)
86	Northern Sweden	NC_000020.10 - 66370	Jul 13, 2019 (153)
87	Qatari	NC_000020.10 - 66370	Apr 27, 2020 (154)
88	SGDP_PRJ	NC_000020.10 - 66370	Apr 27, 2020 (154)
89	Siberian	NC_000020.10 - 66370	Apr 27, 2020 (154)
90	8.3KJPN	NC_000020.10 - 66370	Apr 27, 2021 (155)
91	14KJPN	NC_000020.11 - 85729	Oct 13, 2022 (156)
92	TopMed	NC_000020.11 - 85729	Apr 27, 2021 (155)
93	UK 10K study - Twins	NC_000020.10 - 66370	Oct 12, 2018 (152)
94	A Vietnamese Genetic Variation Database	NC_000020.10 - 66370	Jul 13, 2019 (153)
95	ALFA	NC_000020.11 - 85729	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)
rs6516170	Aug 26, 2003 (117)
rs17563752	Dec 02, 2004 (124)
rs61417577	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss83430118, ss84231557, ss91611611, ss111581030, ss115345920, ss117452054, ss167637399, ss168828483, ss171804844, ss203804012, ss208599144, ss255419683, ss283268941, ss287408431, ss292559575, ss1698510266	NC_000020.9:14369:G:A	NC_000020.11:85728:G:A	(self)
77195169, 42725419, 30194662, 5567527, 19037538, 45924378, 16463723, 20007273, 40587254, 10828168, 86474853, 42725419, 9432357, ss228210647, ss237729940, ss243923461, ss566082465, ss661953386, ss994456712, ss1082009530, ss1363765817, ss1428970659, ss1579402588, ss1638249132, ss1681243165, ss1809383611, ss1937965351, ss1969071123, ss2029757241, ss2158311814, ss2629376453, ss2703983089, ss2964602144, ss3017743792, ss3352380170, ss3684456414, ss3743178858, ss3758326061, ss3788576762, ss3793480306, ss3798367454, ss3835544935, ss3841395539, ss3888570274, ss3938746984, ss5228505546, ss5435782980, ss5662711327, ss5845337198, ss5957606950	NC_000020.10:66369:G:A	NC_000020.11:85728:G:A	(self)
101302584, 544379925, 2047574, 38056615, 121234324, 354843109, 9335816517, ss2240713187, ss3028710409, ss3650952960, ss3706405148, ss3821498999, ss3846902803, ss3981678614, ss5079734164, ss5307820332, ss5500245738, ss5613776649, ss5787397220, ss5817748618, ss5853034203, ss5922371404	NC_000020.11:85728:G:A	NC_000020.11:85728:G:A	(self)
ss8367660, ss11108551, ss12488835, ss20125552, ss21768915, ss41417635, ss96180628	NT_011387.8:6369:G:A	NC_000020.11:85728:G: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 rs6054257

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

rs6054257