Name: rs870500
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.

rs870500

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:3469577 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.188420 (49873/264690, TOPMED)
C=0.190598 (26301/137992, GnomAD)
C=0.13773 (3892/28258, 14KJPN) (+ 14 more)
C=0.21949 (5029/22912, ALFA)
C=0.13675 (2292/16760, 8.3KJPN)
C=0.1696 (1086/6404, 1000G_30x)
C=0.1729 (866/5008, 1000G)
C=0.2296 (885/3854, ALSPAC)
C=0.2276 (844/3708, TWINSUK)
C=0.1420 (415/2922, KOREAN)
C=0.1528 (280/1832, Korea1K)
C=0.251 (250/998, GoNL)
C=0.275 (165/600, NorthernSweden)
T=0.403 (95/236, SGDP_PRJ)
C=0.329 (71/216, Qatari)
C=0.28 (11/40, GENOME_DK)
T=0.44 (8/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATRN : 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	22912	T=0.78051	C=0.21949
European	Sub	18508	T=0.75470	C=0.24530
African	Sub	2898	T=0.9369	C=0.0631
African Others	Sub	114	T=0.982	C=0.018
African American	Sub	2784	T=0.9350	C=0.0650
Asian	Sub	112	T=0.839	C=0.161
East Asian	Sub	86	T=0.83	C=0.17
Other Asian	Sub	26	T=0.88	C=0.12
Latin American 1	Sub	146	T=0.774	C=0.226
Latin American 2	Sub	610	T=0.774	C=0.226
South Asian	Sub	98	T=0.80	C=0.20
Other	Sub	540	T=0.820	C=0.180

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=0.811580	C=0.188420
gnomAD - Genomes	Global	Study-wide	137992	T=0.809402	C=0.190598
gnomAD - Genomes	European	Sub	75018	T=0.75442	C=0.24558
gnomAD - Genomes	African	Sub	40996	T=0.93609	C=0.06391
gnomAD - Genomes	American	Sub	13482	T=0.75842	C=0.24158
gnomAD - Genomes	Ashkenazi Jewish	Sub	3306	T=0.6585	C=0.3415
gnomAD - Genomes	East Asian	Sub	3084	T=0.8512	C=0.1488
gnomAD - Genomes	Other	Sub	2106	T=0.8039	C=0.1961
14KJPN	JAPANESE	Study-wide	28258	T=0.86227	C=0.13773
Allele Frequency Aggregator	Total	Global	22912	T=0.78051	C=0.21949
Allele Frequency Aggregator	European	Sub	18508	T=0.75470	C=0.24530
Allele Frequency Aggregator	African	Sub	2898	T=0.9369	C=0.0631
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.774	C=0.226
Allele Frequency Aggregator	Other	Sub	540	T=0.820	C=0.180
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.774	C=0.226
Allele Frequency Aggregator	Asian	Sub	112	T=0.839	C=0.161
Allele Frequency Aggregator	South Asian	Sub	98	T=0.80	C=0.20
8.3KJPN	JAPANESE	Study-wide	16760	T=0.86325	C=0.13675
1000Genomes_30x	Global	Study-wide	6404	T=0.8304	C=0.1696
1000Genomes_30x	African	Sub	1786	T=0.9675	C=0.0325
1000Genomes_30x	Europe	Sub	1266	T=0.7378	C=0.2622
1000Genomes_30x	South Asian	Sub	1202	T=0.7354	C=0.2646
1000Genomes_30x	East Asian	Sub	1170	T=0.8786	C=0.1214
1000Genomes_30x	American	Sub	980	T=0.759	C=0.241
1000Genomes	Global	Study-wide	5008	T=0.8271	C=0.1729
1000Genomes	African	Sub	1322	T=0.9667	C=0.0333
1000Genomes	East Asian	Sub	1008	T=0.8790	C=0.1210
1000Genomes	Europe	Sub	1006	T=0.7316	C=0.2684
1000Genomes	South Asian	Sub	978	T=0.738	C=0.262
1000Genomes	American	Sub	694	T=0.749	C=0.251
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.7704	C=0.2296
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.7724	C=0.2276
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.8580	C=0.1420
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8472	C=0.1528
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.749	C=0.251
Northern Sweden	ACPOP	Study-wide	600	T=0.725	C=0.275
SGDP_PRJ	Global	Study-wide	236	T=0.403	C=0.597
Qatari	Global	Study-wide	216	T=0.671	C=0.329
The Danish reference pan genome	Danish	Study-wide	40	T=0.72	C=0.28
Siberian	Global	Study-wide	18	T=0.44	C=0.56

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.3469577T>C
GRCh37.p13 chr 20	NC_000020.10:g.3450224T>C
ATRN RefSeqGene	NG_029406.1:g.3560T>C

Gene: ATRN, attractin (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ATRN transcript variant 4	NM_001207047.3:c.	N/A	Upstream Transcript Variant
ATRN transcript variant 5	NM_001323332.2:c.	N/A	Upstream Transcript Variant
ATRN transcript variant 1	NM_139321.3:c.	N/A	Upstream Transcript Variant
ATRN transcript variant 2	NM_139322.4: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	T=	C
GRCh38.p14 chr 20	NC_000020.11:g.3469577=	NC_000020.11:g.3469577T>C
GRCh37.p13 chr 20	NC_000020.10:g.3450224=	NC_000020.10:g.3450224T>C
ATRN RefSeqGene	NG_029406.1:g.3560=	NG_029406.1:g.3560T>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#.

58 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1293204	Oct 05, 2000 (86)
2	SC_SNP	ss8406358	Apr 21, 2003 (114)
3	ABI	ss41432585	Mar 13, 2006 (126)
4	HGSV	ss77654506	Dec 06, 2007 (129)
5	1000GENOMES	ss111627889	Jan 25, 2009 (130)
6	IGMI-SNU	ss115459067	Feb 06, 2009 (130)
7	GMI	ss156095947	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss171835390	Jul 04, 2010 (132)
9	1000GENOMES	ss237740810	Jul 15, 2010 (132)
10	1000GENOMES	ss243931955	Jul 15, 2010 (132)
11	GMI	ss283279281	May 04, 2012 (137)
12	ILLUMINA	ss481988509	May 04, 2012 (137)
13	ILLUMINA	ss484182582	May 04, 2012 (137)
14	TISHKOFF	ss566100920	Apr 25, 2013 (138)
15	ILLUMINA	ss781619436	Aug 21, 2014 (142)
16	EVA-GONL	ss994484430	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1082029910	Aug 21, 2014 (142)
18	1000GENOMES	ss1363865582	Aug 21, 2014 (142)
19	DDI	ss1428979108	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1579414045	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1638303514	Apr 01, 2015 (144)
22	EVA_UK10K_TWINSUK	ss1681297547	Apr 01, 2015 (144)
23	WEILL_CORNELL_DGM	ss1937993375	Feb 12, 2016 (147)
24	JJLAB	ss2029773560	Sep 14, 2016 (149)
25	USC_VALOUEV	ss2158327664	Dec 20, 2016 (150)
26	HUMAN_LONGEVITY	ss2240915434	Dec 20, 2016 (150)
27	SYSTEMSBIOZJU	ss2629384141	Nov 08, 2017 (151)
28	ILLUMINA	ss2633769328	Nov 08, 2017 (151)
29	GRF	ss2703999530	Nov 08, 2017 (151)
30	GNOMAD	ss2964879217	Nov 08, 2017 (151)
31	SWEGEN	ss3017786199	Nov 08, 2017 (151)
32	CSHL	ss3352393368	Nov 08, 2017 (151)
33	ILLUMINA	ss3642169555	Oct 12, 2018 (152)
34	EVA_DECODE	ss3706457426	Jul 13, 2019 (153)
35	ACPOP	ss3743202869	Jul 13, 2019 (153)
36	EVA	ss3758359155	Jul 13, 2019 (153)
37	PACBIO	ss3788585059	Jul 13, 2019 (153)
38	PACBIO	ss3793487433	Jul 13, 2019 (153)
39	PACBIO	ss3798374563	Jul 13, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3821530723	Jul 13, 2019 (153)
41	EVA	ss3835559831	Apr 27, 2020 (154)
42	EVA	ss3841403560	Apr 27, 2020 (154)
43	EVA	ss3846910975	Apr 27, 2020 (154)
44	SGDP_PRJ	ss3888624934	Apr 27, 2020 (154)
45	KRGDB	ss3938806818	Apr 27, 2020 (154)
46	KOGIC	ss3981730048	Apr 27, 2020 (154)
47	TOPMED	ss5080566966	Apr 27, 2021 (155)
48	TOMMO_GENOMICS	ss5228619362	Apr 27, 2021 (155)
49	1000G_HIGH_COVERAGE	ss5307909910	Oct 16, 2022 (156)
50	HUGCELL_USP	ss5500327313	Oct 16, 2022 (156)
51	1000G_HIGH_COVERAGE	ss5613905785	Oct 16, 2022 (156)
52	SANFORD_IMAGENETICS	ss5662762719	Oct 16, 2022 (156)
53	TOMMO_GENOMICS	ss5787545004	Oct 16, 2022 (156)
54	YY_MCH	ss5817771344	Oct 16, 2022 (156)
55	EVA	ss5845373373	Oct 16, 2022 (156)
56	EVA	ss5853045632	Oct 16, 2022 (156)
57	EVA	ss5922472894	Oct 16, 2022 (156)
58	EVA	ss5957660505	Oct 16, 2022 (156)
59	1000Genomes	NC_000020.10 - 3450224	Oct 12, 2018 (152)
60	1000Genomes_30x	NC_000020.11 - 3469577	Oct 16, 2022 (156)
61	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 3450224	Oct 12, 2018 (152)
62	The Danish reference pan genome	NC_000020.10 - 3450224	Apr 27, 2020 (154)
63	gnomAD - Genomes	NC_000020.11 - 3469577	Apr 27, 2021 (155)
64	Genome of the Netherlands Release 5	NC_000020.10 - 3450224	Apr 27, 2020 (154)
65	KOREAN population from KRGDB	NC_000020.10 - 3450224	Apr 27, 2020 (154)
66	Korean Genome Project	NC_000020.11 - 3469577	Apr 27, 2020 (154)
67	Northern Sweden	NC_000020.10 - 3450224	Jul 13, 2019 (153)
68	Qatari	NC_000020.10 - 3450224	Apr 27, 2020 (154)
69	SGDP_PRJ	NC_000020.10 - 3450224	Apr 27, 2020 (154)
70	Siberian	NC_000020.10 - 3450224	Apr 27, 2020 (154)
71	8.3KJPN	NC_000020.10 - 3450224	Apr 27, 2021 (155)
72	14KJPN	NC_000020.11 - 3469577	Oct 16, 2022 (156)
73	TopMed	NC_000020.11 - 3469577	Apr 27, 2021 (155)
74	UK 10K study - Twins	NC_000020.10 - 3450224	Oct 12, 2018 (152)
75	ALFA	NC_000020.11 - 3469577	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77654506, ss111627889, ss171835390, ss283279281, ss484182582	NC_000020.9:3398223:T:C	NC_000020.11:3469576:T:C	(self)
77297925, 42785452, 5578984, 19064060, 45984212, 16487734, 20035297, 40641914, 10844018, 86588669, 42785452, ss237740810, ss243931955, ss481988509, ss566100920, ss781619436, ss994484430, ss1082029910, ss1363865582, ss1428979108, ss1579414045, ss1638303514, ss1681297547, ss1937993375, ss2029773560, ss2158327664, ss2629384141, ss2633769328, ss2703999530, ss2964879217, ss3017786199, ss3352393368, ss3642169555, ss3743202869, ss3758359155, ss3788585059, ss3793487433, ss3798374563, ss3835559831, ss3841403560, ss3888624934, ss3938806818, ss5228619362, ss5662762719, ss5845373373, ss5957660505	NC_000020.10:3450223:T:C	NC_000020.11:3469576:T:C	(self)
101431720, 545078331, 38108049, 121382108, 355675911, 12290399634, ss2240915434, ss3706457426, ss3821530723, ss3846910975, ss3981730048, ss5080566966, ss5307909910, ss5500327313, ss5613905785, ss5787545004, ss5817771344, ss5853045632, ss5922472894	NC_000020.11:3469576:T:C	NC_000020.11:3469576:T:C	(self)
ss1293204, ss8406358, ss41432585, ss115459067, ss156095947	NT_011387.8:3390223:T:C	NC_000020.11:3469576:T: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 rs870500

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
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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

rs870500