Name: rs10975056
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.

rs10975056

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:5337682 (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=0.407839 (107951/264690, TOPMED)
A=0.421175 (58823/139664, GnomAD)
A=0.16220 (4583/28256, 14KJPN) (+ 16 more)
A=0.42657 (8058/18890, ALFA)
A=0.16480 (2762/16760, 8.3KJPN)
A=0.3598 (2304/6404, 1000G_30x)
A=0.3598 (1802/5008, 1000G)
A=0.4242 (1635/3854, ALSPAC)
A=0.4377 (1623/3708, TWINSUK)
A=0.1771 (519/2930, KOREAN)
A=0.3384 (628/1856, HapMap)
A=0.1861 (341/1832, Korea1K)
A=0.426 (425/998, GoNL)
A=0.477 (286/600, NorthernSweden)
T=0.352 (107/304, SGDP_PRJ)
A=0.324 (70/216, Qatari)
A=0.276 (59/214, Vietnamese)
A=0.40 (16/40, GENOME_DK)
T=0.23 (9/40, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RLN2 : Intron Variant
RLN1 : 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	18890	T=0.57343	A=0.42657
European	Sub	14286	T=0.56265	A=0.43735
African	Sub	2946	T=0.5838	A=0.4162
African Others	Sub	114	T=0.579	A=0.421
African American	Sub	2832	T=0.5840	A=0.4160
Asian	Sub	112	T=0.777	A=0.223
East Asian	Sub	86	T=0.76	A=0.24
Other Asian	Sub	26	T=0.85	A=0.15
Latin American 1	Sub	146	T=0.658	A=0.342
Latin American 2	Sub	610	T=0.705	A=0.295
South Asian	Sub	98	T=0.53	A=0.47
Other	Sub	692	T=0.591	A=0.409

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=0.592161	A=0.407839
gnomAD - Genomes	Global	Study-wide	139664	T=0.578825	A=0.421175
gnomAD - Genomes	European	Sub	75730	T=0.56440	A=0.43560
gnomAD - Genomes	African	Sub	41770	T=0.58580	A=0.41420
gnomAD - Genomes	American	Sub	13588	T=0.61135	A=0.38865
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.5018	A=0.4982
gnomAD - Genomes	East Asian	Sub	3114	T=0.7768	A=0.2232
gnomAD - Genomes	Other	Sub	2140	T=0.5780	A=0.4220
14KJPN	JAPANESE	Study-wide	28256	T=0.83780	A=0.16220
Allele Frequency Aggregator	Total	Global	18890	T=0.57343	A=0.42657
Allele Frequency Aggregator	European	Sub	14286	T=0.56265	A=0.43735
Allele Frequency Aggregator	African	Sub	2946	T=0.5838	A=0.4162
Allele Frequency Aggregator	Other	Sub	692	T=0.591	A=0.409
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.705	A=0.295
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.658	A=0.342
Allele Frequency Aggregator	Asian	Sub	112	T=0.777	A=0.223
Allele Frequency Aggregator	South Asian	Sub	98	T=0.53	A=0.47
8.3KJPN	JAPANESE	Study-wide	16760	T=0.83520	A=0.16480
1000Genomes_30x	Global	Study-wide	6404	T=0.6402	A=0.3598
1000Genomes_30x	African	Sub	1786	T=0.6131	A=0.3869
1000Genomes_30x	Europe	Sub	1266	T=0.5964	A=0.4036
1000Genomes_30x	South Asian	Sub	1202	T=0.6381	A=0.3619
1000Genomes_30x	East Asian	Sub	1170	T=0.7667	A=0.2333
1000Genomes_30x	American	Sub	980	T=0.598	A=0.402
1000Genomes	Global	Study-wide	5008	T=0.6402	A=0.3598
1000Genomes	African	Sub	1322	T=0.6082	A=0.3918
1000Genomes	East Asian	Sub	1008	T=0.7679	A=0.2321
1000Genomes	Europe	Sub	1006	T=0.5974	A=0.4026
1000Genomes	South Asian	Sub	978	T=0.629	A=0.371
1000Genomes	American	Sub	694	T=0.594	A=0.406
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5758	A=0.4242
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5623	A=0.4377
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.8229	A=0.1771
HapMap	Global	Study-wide	1856	T=0.6616	A=0.3384
HapMap	American	Sub	752	T=0.648	A=0.352
HapMap	African	Sub	678	T=0.649	A=0.351
HapMap	Asian	Sub	252	T=0.774	A=0.226
HapMap	Europe	Sub	174	T=0.609	A=0.391
Korean Genome Project	KOREAN	Study-wide	1832	T=0.8139	A=0.1861
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.574	A=0.426
Northern Sweden	ACPOP	Study-wide	600	T=0.523	A=0.477
SGDP_PRJ	Global	Study-wide	304	T=0.352	A=0.648
Qatari	Global	Study-wide	216	T=0.676	A=0.324
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.724	A=0.276
The Danish reference pan genome	Danish	Study-wide	40	T=0.60	A=0.40
Siberian	Global	Study-wide	40	T=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 9	NC_000009.12:g.5337682T>A
GRCh37.p13 chr 9	NC_000009.11:g.5337682T>A

Gene: RLN1, relaxin 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RLN1 transcript	NM_006911.4:c.211+1854A>T	N/A	Intron Variant
RLN1 transcript variant X1	XM_047423703.1:c.312+1580… XM_047423703.1:c.312+1580A>T	N/A	Intron Variant
RLN1 transcript variant X2	XM_047423704.1:c.-48+1580… XM_047423704.1:c.-48+1580A>T	N/A	Intron Variant
RLN1 transcript variant X3	XM_047423705.1:c.-48+1681… XM_047423705.1:c.-48+1681A>T	N/A	Intron Variant
RLN1 transcript variant X4	XM_047423706.1:c.-47-2085… XM_047423706.1:c.-47-2085A>T	N/A	Intron Variant

Gene: RLN2, relaxin 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RLN2 transcript variant 3	NM_001329191.2:c.	N/A	Genic Upstream Transcript Variant
RLN2 transcript variant 2	NM_005059.4:c.	N/A	Genic Upstream Transcript Variant
RLN2 transcript variant 1	NM_134441.3:c.	N/A	Genic Upstream Transcript Variant
RLN2 transcript variant X1	XM_047423707.1:c.-338+158… XM_047423707.1:c.-338+1580A>T	N/A	Intron Variant
RLN2 transcript variant X3	XM_047423709.1:c.-2641+15… XM_047423709.1:c.-2641+1580A>T	N/A	Intron Variant
RLN2 transcript variant X2	XM_047423708.1:c.	N/A	Genic 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=	A
GRCh38.p14 chr 9	NC_000009.12:g.5337682=	NC_000009.12:g.5337682T>A
GRCh37.p13 chr 9	NC_000009.11:g.5337682=	NC_000009.11:g.5337682T>A
RLN1 transcript	NM_006911.3:c.211+1854=	NM_006911.3:c.211+1854A>T
RLN1 transcript	NM_006911.4:c.211+1854=	NM_006911.4:c.211+1854A>T
RLN1 transcript variant X1	XM_005251541.1:c.312+1580=	XM_005251541.1:c.312+1580A>T
RLN1 transcript variant X1	XM_047423703.1:c.312+1580=	XM_047423703.1:c.312+1580A>T
RLN1 transcript variant X2	XM_047423704.1:c.-48+1580=	XM_047423704.1:c.-48+1580A>T
RLN1 transcript variant X3	XM_047423705.1:c.-48+1681=	XM_047423705.1:c.-48+1681A>T
RLN1 transcript variant X4	XM_047423706.1:c.-47-2085=	XM_047423706.1:c.-47-2085A>T
RLN2 transcript variant X1	XM_047423707.1:c.-338+1580=	XM_047423707.1:c.-338+1580A>T
RLN2 transcript variant X3	XM_047423709.1:c.-2641+1580=	XM_047423709.1:c.-2641+1580A>T

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#.

70 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss15852130	Feb 27, 2004 (120)
2	SC_SNP	ss19028120	Feb 27, 2004 (120)
3	SSAHASNP	ss22797801	Apr 05, 2004 (121)
4	AFFY	ss76707389	Dec 06, 2007 (129)
5	HGSV	ss78362832	Dec 06, 2007 (129)
6	BCMHGSC_JDW	ss94000997	Mar 25, 2008 (129)
7	HUMANGENOME_JCVI	ss97702637	Feb 04, 2009 (130)
8	KRIBB_YJKIM	ss105019820	Feb 04, 2009 (130)
9	1000GENOMES	ss108546486	Jan 23, 2009 (130)
10	ENSEMBL	ss134124201	Dec 01, 2009 (131)
11	ENSEMBL	ss143910455	Dec 01, 2009 (131)
12	ILLUMINA	ss159156650	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss166068508	Jul 04, 2010 (132)
14	BUSHMAN	ss200027116	Jul 04, 2010 (132)
15	BCM-HGSC-SUB	ss206768849	Jul 04, 2010 (132)
16	1000GENOMES	ss224092832	Jul 14, 2010 (132)
17	1000GENOMES	ss234704587	Jul 15, 2010 (132)
18	1000GENOMES	ss241502761	Jul 15, 2010 (132)
19	BL	ss254010300	May 09, 2011 (134)
20	GMI	ss280082738	May 04, 2012 (137)
21	PJP	ss294317987	May 09, 2011 (134)
22	TISHKOFF	ss561202832	Apr 25, 2013 (138)
23	SSMP	ss655631254	Apr 25, 2013 (138)
24	ILLUMINA	ss832669256	Jul 13, 2019 (153)
25	EVA-GONL	ss986254827	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1076067454	Aug 21, 2014 (142)
27	1000GENOMES	ss1332682724	Aug 21, 2014 (142)
28	EVA_GENOME_DK	ss1582964025	Apr 01, 2015 (144)
29	EVA_DECODE	ss1595879498	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1622139048	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1665133081	Apr 01, 2015 (144)
32	EVA_SVP	ss1713086587	Apr 01, 2015 (144)
33	HAMMER_LAB	ss1805854976	Sep 08, 2015 (146)
34	WEILL_CORNELL_DGM	ss1929534480	Feb 12, 2016 (147)
35	GENOMED	ss1971141594	Jul 19, 2016 (147)
36	JJLAB	ss2025474561	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2153704444	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2627213333	Nov 08, 2017 (151)
39	GRF	ss2709500741	Nov 08, 2017 (151)
40	GNOMAD	ss2874819842	Nov 08, 2017 (151)
41	SWEGEN	ss3004301547	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3026525577	Nov 08, 2017 (151)
43	CSHL	ss3348498090	Nov 08, 2017 (151)
44	URBANLAB	ss3649058874	Oct 12, 2018 (152)
45	EVA_DECODE	ss3723374681	Jul 13, 2019 (153)
46	ACPOP	ss3736263464	Jul 13, 2019 (153)
47	EVA	ss3768848395	Jul 13, 2019 (153)
48	PACBIO	ss3786332697	Jul 13, 2019 (153)
49	PACBIO	ss3791560322	Jul 13, 2019 (153)
50	PACBIO	ss3796441947	Jul 13, 2019 (153)
51	KHV_HUMAN_GENOMES	ss3812008611	Jul 13, 2019 (153)
52	EVA	ss3831509991	Apr 26, 2020 (154)
53	EVA	ss3839267763	Apr 26, 2020 (154)
54	EVA	ss3844729576	Apr 26, 2020 (154)
55	SGDP_PRJ	ss3871411203	Apr 26, 2020 (154)
56	KRGDB	ss3919042044	Apr 26, 2020 (154)
57	KOGIC	ss3965205712	Apr 26, 2020 (154)
58	TOPMED	ss4810641625	Apr 26, 2021 (155)
59	TOMMO_GENOMICS	ss5191844894	Apr 26, 2021 (155)
60	1000G_HIGH_COVERAGE	ss5279610908	Oct 16, 2022 (156)
61	EVA	ss5385698669	Oct 16, 2022 (156)
62	HUGCELL_USP	ss5475913734	Oct 16, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5571273720	Oct 16, 2022 (156)
64	SANFORD_IMAGENETICS	ss5646799013	Oct 16, 2022 (156)
65	TOMMO_GENOMICS	ss5734827703	Oct 16, 2022 (156)
66	YY_MCH	ss5810297741	Oct 16, 2022 (156)
67	EVA	ss5828778539	Oct 16, 2022 (156)
68	EVA	ss5856648291	Oct 16, 2022 (156)
69	EVA	ss5915310945	Oct 16, 2022 (156)
70	EVA	ss5976065129	Oct 16, 2022 (156)
71	1000Genomes	NC_000009.11 - 5337682	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000009.12 - 5337682	Oct 16, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 5337682	Oct 12, 2018 (152)
74	The Danish reference pan genome	NC_000009.11 - 5337682	Apr 26, 2020 (154)
75	gnomAD - Genomes	NC_000009.12 - 5337682	Apr 26, 2021 (155)
76	Genome of the Netherlands Release 5	NC_000009.11 - 5337682	Apr 26, 2020 (154)
77	HapMap	NC_000009.12 - 5337682	Apr 26, 2020 (154)
78	KOREAN population from KRGDB	NC_000009.11 - 5337682	Apr 26, 2020 (154)
79	Korean Genome Project	NC_000009.12 - 5337682	Apr 26, 2020 (154)
80	Northern Sweden	NC_000009.11 - 5337682	Jul 13, 2019 (153)
81	Qatari	NC_000009.11 - 5337682	Apr 26, 2020 (154)
82	SGDP_PRJ	NC_000009.11 - 5337682	Apr 26, 2020 (154)
83	Siberian	NC_000009.11 - 5337682	Apr 26, 2020 (154)
84	8.3KJPN	NC_000009.11 - 5337682	Apr 26, 2021 (155)
85	14KJPN	NC_000009.12 - 5337682	Oct 16, 2022 (156)
86	TopMed	NC_000009.12 - 5337682	Apr 26, 2021 (155)
87	UK 10K study - Twins	NC_000009.11 - 5337682	Oct 12, 2018 (152)
88	A Vietnamese Genetic Variation Database	NC_000009.11 - 5337682	Jul 13, 2019 (153)
89	ALFA	NC_000009.12 - 5337682	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78362832	NC_000009.9:5327681:T:A	NC_000009.12:5337681:T:A	(self)
ss76707389, ss94000997, ss108546486, ss166068508, ss200027116, ss206768849, ss254010300, ss280082738, ss294317987, ss1595879498, ss1713086587	NC_000009.10:5327681:T:A	NC_000009.12:5337681:T:A	(self)
44904883, 24987845, 9128962, 11143876, 26219438, 9548329, 11576410, 23428183, 6220798, 49814201, 24987845, 5547738, ss224092832, ss234704587, ss241502761, ss561202832, ss655631254, ss832669256, ss986254827, ss1076067454, ss1332682724, ss1582964025, ss1622139048, ss1665133081, ss1805854976, ss1929534480, ss1971141594, ss2025474561, ss2153704444, ss2627213333, ss2709500741, ss2874819842, ss3004301547, ss3348498090, ss3736263464, ss3768848395, ss3786332697, ss3791560322, ss3796441947, ss3831509991, ss3839267763, ss3871411203, ss3919042044, ss5191844894, ss5385698669, ss5646799013, ss5828778539, ss5976065129	NC_000009.11:5337681:T:A	NC_000009.12:5337681:T:A	(self)
58799655, 316540876, 3765320, 21583713, 68664807, 648019186, 13017058289, ss3026525577, ss3649058874, ss3723374681, ss3812008611, ss3844729576, ss3965205712, ss4810641625, ss5279610908, ss5475913734, ss5571273720, ss5734827703, ss5810297741, ss5856648291, ss5915310945	NC_000009.12:5337681:T:A	NC_000009.12:5337681:T:A	(self)
ss15852130, ss19028120, ss22797801	NT_008413.16:5327681:T:A	NC_000009.12:5337681:T:A	(self)
ss97702637, ss105019820, ss134124201, ss143910455, ss159156650	NT_008413.18:5327681:T:A	NC_000009.12:5337681: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 rs10975056

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

rs10975056