Name: rs1575013
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.

rs1575013

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:113088855 (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=0.295882 (78317/264690, TOPMED)
A=0.21783 (13547/62192, ALFA)
A=0.05181 (1464/28258, 14KJPN) (+ 17 more)
A=0.05257 (881/16758, 8.3KJPN)
A=0.3028 (1939/6404, 1000G_30x)
A=0.2963 (1484/5008, 1000G)
A=0.2067 (926/4480, Estonian)
A=0.2270 (875/3854, ALSPAC)
A=0.2066 (766/3708, TWINSUK)
A=0.0753 (220/2922, KOREAN)
A=0.2380 (496/2084, HGDP_Stanford)
A=0.3613 (675/1868, HapMap)
A=0.215 (215/998, GoNL)
A=0.193 (116/600, NorthernSweden)
A=0.375 (81/216, Qatari)
A=0.056 (12/216, Vietnamese)
G=0.413 (81/196, SGDP_PRJ)
A=0.30 (12/40, GENOME_DK)
G=0.40 (8/20, Siberian)
A=0.2 (2/8, Ancient Sardinia)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GPR85 : 2KB Upstream Variant
Publications: 1 citation
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	62192	G=0.78217	A=0.21783, C=0.00000
European	Sub	52528	G=0.79689	A=0.20311, C=0.00000
African	Sub	2394	G=0.6529	A=0.3471, C=0.0000
African Others	Sub	80	G=0.53	A=0.47, C=0.00
African American	Sub	2314	G=0.6573	A=0.3427, C=0.0000
Asian	Sub	172	G=0.977	A=0.023, C=0.000
East Asian	Sub	134	G=0.970	A=0.030, C=0.000
Other Asian	Sub	38	G=1.00	A=0.00, C=0.00
Latin American 1	Sub	184	G=0.891	A=0.109, C=0.000
Latin American 2	Sub	1084	G=0.9179	A=0.0821, C=0.0000
South Asian	Sub	4878	G=0.6433	A=0.3567, C=0.0000
Other	Sub	952	G=0.796	A=0.204, 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=0.704118	A=0.295882
Allele Frequency Aggregator	Total	Global	62192	G=0.78217	A=0.21783, C=0.00000
Allele Frequency Aggregator	European	Sub	52528	G=0.79689	A=0.20311, C=0.00000
Allele Frequency Aggregator	South Asian	Sub	4878	G=0.6433	A=0.3567, C=0.0000
Allele Frequency Aggregator	African	Sub	2394	G=0.6529	A=0.3471, C=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	1084	G=0.9179	A=0.0821, C=0.0000
Allele Frequency Aggregator	Other	Sub	952	G=0.796	A=0.204, C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	184	G=0.891	A=0.109, C=0.000
Allele Frequency Aggregator	Asian	Sub	172	G=0.977	A=0.023, C=0.000
14KJPN	JAPANESE	Study-wide	28258	G=0.94819	A=0.05181
8.3KJPN	JAPANESE	Study-wide	16758	G=0.94743	A=0.05257
1000Genomes_30x	Global	Study-wide	6404	G=0.6972	A=0.3028
1000Genomes_30x	African	Sub	1786	G=0.4485	A=0.5515
1000Genomes_30x	Europe	Sub	1266	G=0.7828	A=0.2172
1000Genomes_30x	South Asian	Sub	1202	G=0.6389	A=0.3611
1000Genomes_30x	East Asian	Sub	1170	G=0.9444	A=0.0556
1000Genomes_30x	American	Sub	980	G=0.816	A=0.184
1000Genomes	Global	Study-wide	5008	G=0.7037	A=0.2963
1000Genomes	African	Sub	1322	G=0.4508	A=0.5492
1000Genomes	East Asian	Sub	1008	G=0.9425	A=0.0575
1000Genomes	Europe	Sub	1006	G=0.7823	A=0.2177
1000Genomes	South Asian	Sub	978	G=0.636	A=0.364
1000Genomes	American	Sub	694	G=0.820	A=0.180
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7933	A=0.2067
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7730	A=0.2270
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7934	A=0.2066
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9247	A=0.0753
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	G=0.7620	A=0.2380
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	G=0.921	A=0.079
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	G=0.655	A=0.345
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	G=0.666	A=0.334
HGDP-CEPH-db Supplement 1	Europe	Sub	320	G=0.787	A=0.212
HGDP-CEPH-db Supplement 1	Africa	Sub	242	G=0.479	A=0.521
HGDP-CEPH-db Supplement 1	America	Sub	216	G=0.991	A=0.009
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	G=0.96	A=0.04
HapMap	Global	Study-wide	1868	G=0.6387	A=0.3613
HapMap	American	Sub	760	G=0.736	A=0.264
HapMap	African	Sub	688	G=0.424	A=0.576
HapMap	Asian	Sub	246	G=0.915	A=0.085
HapMap	Europe	Sub	174	G=0.672	A=0.328
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.785	A=0.215
Northern Sweden	ACPOP	Study-wide	600	G=0.807	A=0.193
Qatari	Global	Study-wide	216	G=0.625	A=0.375
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.944	A=0.056
SGDP_PRJ	Global	Study-wide	196	G=0.413	A=0.587
The Danish reference pan genome	Danish	Study-wide	40	G=0.70	A=0.30
Siberian	Global	Study-wide	20	G=0.40	A=0.60
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	8	G=0.8	A=0.2

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 7	NC_000007.14:g.113088855G>A
GRCh38.p14 chr 7	NC_000007.14:g.113088855G>C
GRCh37.p13 chr 7	NC_000007.13:g.112728910G>A
GRCh37.p13 chr 7	NC_000007.13:g.112728910G>C

Gene: GPR85, G protein-coupled receptor 85 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
GPR85 transcript variant 1	NM_001146265.2:c.	N/A	Upstream Transcript Variant
GPR85 transcript variant 2	NM_018970.7:c.	N/A	Upstream Transcript Variant
GPR85 transcript variant 3	NM_001146266.2:c.	N/A	N/A
GPR85 transcript variant 4	NM_001146267.2:c.	N/A	N/A
GPR85 transcript variant X2	XM_005250451.3:c.	N/A	N/A
GPR85 transcript variant X1	XM_017012352.3:c.	N/A	N/A

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 7	NC_000007.14:g.113088855=	NC_000007.14:g.113088855G>A	NC_000007.14:g.113088855G>C
GRCh37.p13 chr 7	NC_000007.13:g.112728910=	NC_000007.13:g.112728910G>A	NC_000007.13:g.112728910G>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#.

83 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2089197	Oct 24, 2000 (88)
2	SC_JCM	ss3454367	Sep 28, 2001 (100)
3	SC_JCM	ss3802940	Sep 28, 2001 (100)
4	WI_SSAHASNP	ss11858228	Jul 11, 2003 (116)
5	WUGSC_SSAHASNP	ss14583422	Dec 05, 2003 (120)
6	PERLEGEN	ss23440812	Sep 20, 2004 (123)
7	ILLUMINA	ss67138056	Dec 03, 2006 (127)
8	ILLUMINA	ss67478498	Dec 03, 2006 (127)
9	ILLUMINA	ss68159696	Dec 12, 2006 (127)
10	ILLUMINA	ss70634985	May 25, 2008 (130)
11	ILLUMINA	ss71185426	May 16, 2007 (127)
12	ILLUMINA	ss75488925	Dec 07, 2007 (129)
13	KRIBB_YJKIM	ss83845218	Dec 15, 2007 (130)
14	HGSV	ss85167495	Dec 15, 2007 (130)
15	1000GENOMES	ss112456275	Jan 25, 2009 (130)
16	1000GENOMES	ss114285794	Jan 25, 2009 (130)
17	ILLUMINA-UK	ss116257585	Feb 14, 2009 (130)
18	ILLUMINA	ss153526825	Dec 01, 2009 (131)
19	ILLUMINA	ss159287329	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss162631084	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss165174355	Jul 04, 2010 (132)
22	ILLUMINA	ss172590965	Jul 04, 2010 (132)
23	BUSHMAN	ss198112141	Jul 04, 2010 (132)
24	1000GENOMES	ss223275064	Jul 14, 2010 (132)
25	1000GENOMES	ss234126618	Jul 15, 2010 (132)
26	ILLUMINA	ss244280271	Jul 04, 2010 (132)
27	TISHKOFF	ss560240789	Apr 25, 2013 (138)
28	SSMP	ss654645480	Apr 25, 2013 (138)
29	ILLUMINA	ss832799452	Jul 13, 2019 (153)
30	EVA-GONL	ss984685052	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1074899395	Aug 21, 2014 (142)
32	1000GENOMES	ss1326711552	Aug 21, 2014 (142)
33	DDI	ss1431249248	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1582360588	Apr 01, 2015 (144)
35	EVA_DECODE	ss1594267560	Apr 01, 2015 (144)
36	EVA_UK10K_ALSPAC	ss1618989255	Apr 01, 2015 (144)
37	EVA_UK10K_TWINSUK	ss1661983288	Apr 01, 2015 (144)
38	EVA_SVP	ss1712980709	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1805174666	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1927947807	Feb 12, 2016 (147)
41	GENOMED	ss1970791406	Jul 19, 2016 (147)
42	JJLAB	ss2024657451	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2152881745	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2296951515	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2626819280	Nov 08, 2017 (151)
46	GRF	ss2708596762	Nov 08, 2017 (151)
47	GNOMAD	ss2857868187	Nov 08, 2017 (151)
48	SWEGEN	ss3001864782	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3026120255	Nov 08, 2017 (151)
50	CSHL	ss3347797481	Nov 08, 2017 (151)
51	ILLUMINA	ss3638718500	Oct 12, 2018 (152)
52	ILLUMINA	ss3639360708	Oct 12, 2018 (152)
53	ILLUMINA	ss3639974753	Oct 12, 2018 (152)
54	ILLUMINA	ss3643652774	Oct 12, 2018 (152)
55	ILLUMINA	ss3644018684	Oct 12, 2018 (152)
56	EGCUT_WGS	ss3669612202	Jul 13, 2019 (153)
57	EVA_DECODE	ss3720485826	Jul 13, 2019 (153)
58	ACPOP	ss3734981319	Jul 13, 2019 (153)
59	EVA	ss3767034509	Jul 13, 2019 (153)
60	PACBIO	ss3785930808	Jul 13, 2019 (153)
61	PACBIO	ss3791214158	Jul 13, 2019 (153)
62	PACBIO	ss3796094249	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3810206892	Jul 13, 2019 (153)
64	EVA	ss3830768247	Apr 26, 2020 (154)
65	EVA	ss3838883282	Apr 26, 2020 (154)
66	EVA	ss3844339193	Apr 26, 2020 (154)
67	HGDP	ss3847887956	Apr 26, 2020 (154)
68	SGDP_PRJ	ss3868181106	Apr 26, 2020 (154)
69	KRGDB	ss3915502906	Apr 26, 2020 (154)
70	EVA	ss3985316194	Apr 25, 2021 (155)
71	TOPMED	ss4759860707	Apr 25, 2021 (155)
72	TOMMO_GENOMICS	ss5185105095	Apr 25, 2021 (155)
73	1000G_HIGH_COVERAGE	ss5274368393	Oct 13, 2022 (156)
74	HUGCELL_USP	ss5471293084	Oct 13, 2022 (156)
75	EVA	ss5509093789	Oct 13, 2022 (156)
76	1000G_HIGH_COVERAGE	ss5563321534	Oct 13, 2022 (156)
77	SANFORD_IMAGENETICS	ss5643777589	Oct 13, 2022 (156)
78	TOMMO_GENOMICS	ss5725958610	Oct 13, 2022 (156)
79	YY_MCH	ss5809006016	Oct 13, 2022 (156)
80	EVA	ss5823384192	Oct 13, 2022 (156)
81	EVA	ss5856055957	Oct 13, 2022 (156)
82	EVA	ss5860457682	Oct 13, 2022 (156)
83	EVA	ss5972963427	Oct 13, 2022 (156)
84	1000Genomes	NC_000007.13 - 112728910	Oct 12, 2018 (152)
85	1000Genomes_30x	NC_000007.14 - 113088855	Oct 13, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 112728910	Oct 12, 2018 (152)
87	Genetic variation in the Estonian population	NC_000007.13 - 112728910	Oct 12, 2018 (152)
88	The Danish reference pan genome	NC_000007.13 - 112728910	Apr 26, 2020 (154)
89	gnomAD - Genomes Submission ignored due to conflicting rows: Row 273438342 (NC_000007.14:113088854:G:A 41004/139896) Row 273438343 (NC_000007.14:113088854:G:C 3/139956)	-	Apr 25, 2021 (155)
90	gnomAD - Genomes Submission ignored due to conflicting rows: Row 273438342 (NC_000007.14:113088854:G:A 41004/139896) Row 273438343 (NC_000007.14:113088854:G:C 3/139956)	-	Apr 25, 2021 (155)
91	Genome of the Netherlands Release 5	NC_000007.13 - 112728910	Apr 26, 2020 (154)
92	HGDP-CEPH-db Supplement 1	NC_000007.12 - 112516146	Apr 26, 2020 (154)
93	HapMap	NC_000007.14 - 113088855	Apr 26, 2020 (154)
94	KOREAN population from KRGDB	NC_000007.13 - 112728910	Apr 26, 2020 (154)
95	Northern Sweden	NC_000007.13 - 112728910	Jul 13, 2019 (153)
96	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000007.13 - 112728910	Apr 25, 2021 (155)
97	Qatari	NC_000007.13 - 112728910	Apr 26, 2020 (154)
98	SGDP_PRJ	NC_000007.13 - 112728910	Apr 26, 2020 (154)
99	Siberian	NC_000007.13 - 112728910	Apr 26, 2020 (154)
100	8.3KJPN	NC_000007.13 - 112728910	Apr 25, 2021 (155)
101	14KJPN	NC_000007.14 - 113088855	Oct 13, 2022 (156)
102	TopMed	NC_000007.14 - 113088855	Apr 25, 2021 (155)
103	UK 10K study - Twins	NC_000007.13 - 112728910	Oct 12, 2018 (152)
104	A Vietnamese Genetic Variation Database	NC_000007.13 - 112728910	Jul 13, 2019 (153)
105	ALFA	NC_000007.14 - 113088855	Apr 25, 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)
rs10377873	Feb 27, 2004 (120)
rs59875624	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss85167495, ss3639360708, ss3639974753, ss3644018684	NC_000007.11:112322860:G:A	NC_000007.14:113088854:G:A	(self)
565848, ss112456275, ss114285794, ss116257585, ss162631084, ss165174355, ss198112141, ss1594267560, ss1712980709, ss3643652774, ss3847887956	NC_000007.12:112516145:G:A	NC_000007.14:113088854:G:A	(self)
38739065, 21550791, 15350450, 8525527, 9618488, 22680300, 8266184, 542121, 9989737, 20198086, 5398099, 43074402, 21550791, 4802583, ss223275064, ss234126618, ss560240789, ss654645480, ss832799452, ss984685052, ss1074899395, ss1326711552, ss1431249248, ss1582360588, ss1618989255, ss1661983288, ss1805174666, ss1927947807, ss1970791406, ss2024657451, ss2152881745, ss2626819280, ss2708596762, ss2857868187, ss3001864782, ss3347797481, ss3638718500, ss3669612202, ss3734981319, ss3767034509, ss3785930808, ss3791214158, ss3796094249, ss3830768247, ss3838883282, ss3868181106, ss3915502906, ss3985316194, ss5185105095, ss5509093789, ss5643777589, ss5823384192, ss5972963427	NC_000007.13:112728909:G:A	NC_000007.14:113088854:G:A	(self)
50847469, 3472036, 59795714, 597238266, 4212630657, ss2296951515, ss3026120255, ss3720485826, ss3810206892, ss3844339193, ss4759860707, ss5274368393, ss5471293084, ss5563321534, ss5725958610, ss5809006016, ss5856055957, ss5860457682	NC_000007.14:113088854:G:A	NC_000007.14:113088854:G:A	(self)
ss11858228	NT_007933.12:37911627:G:A	NC_000007.14:113088854:G:A	(self)
ss14583422	NT_007933.13:37911627:G:A	NC_000007.14:113088854:G:A	(self)
ss2089197, ss3454367, ss3802940, ss23440812, ss67138056, ss67478498, ss68159696, ss70634985, ss71185426, ss75488925, ss83845218, ss153526825, ss159287329, ss172590965, ss244280271	NT_007933.15:50761752:G:A	NC_000007.14:113088854:G:A	(self)
4212630657	NC_000007.14:113088854:G:C	NC_000007.14:113088854:G:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

1 citation for rs1575013

PMID	Title	Author	Year	Journal
18413613	The evolutionarily conserved G protein-coupled receptor SREB2/GPR85 influences brain size, behavior, and vulnerability to schizophrenia.	Matsumoto M et al.	2008	Proceedings of the National Academy of Sciences of the United States of America

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

rs1575013