Name: rs1128786
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.

rs1128786

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr9:113163983 (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: C>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.312853 (82809/264690, TOPMED)
G=0.318619 (44578/139910, GnomAD)
G=0.13501 (3815/28258, 14KJPN) (+ 18 more)
G=0.32415 (6505/20068, ALFA)
G=0.13717 (2299/16760, 8.3KJPN)
G=0.2862 (1833/6404, 1000G_30x)
G=0.2829 (1417/5008, 1000G)
G=0.3304 (1480/4480, Estonian)
G=0.3124 (1204/3854, ALSPAC)
G=0.3166 (1174/3708, TWINSUK)
G=0.1670 (488/2922, KOREAN)
G=0.1528 (280/1832, Korea1K)
G=0.322 (321/998, GoNL)
G=0.272 (163/600, NorthernSweden)
G=0.305 (163/534, MGP)
G=0.241 (79/328, HapMap)
C=0.384 (99/258, SGDP_PRJ)
G=0.384 (83/216, Qatari)
G=0.194 (42/216, Vietnamese)
G=0.45 (18/40, GENOME_DK)
C=0.45 (9/20, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FKBP15 : 3 Prime UTR Variant
SLC31A2 : 3 Prime UTR 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	20068	C=0.67585	G=0.32415
European	Sub	15436	C=0.66785	G=0.33215
African	Sub	2946	C=0.6942	G=0.3058
African Others	Sub	114	C=0.728	G=0.272
African American	Sub	2832	C=0.6928	G=0.3072
Asian	Sub	112	C=0.848	G=0.152
East Asian	Sub	86	C=0.85	G=0.15
Other Asian	Sub	26	C=0.85	G=0.15
Latin American 1	Sub	146	C=0.651	G=0.349
Latin American 2	Sub	610	C=0.762	G=0.238
South Asian	Sub	98	C=0.72	G=0.28
Other	Sub	720	C=0.671	G=0.329

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	C=0.687147	G=0.312853
gnomAD - Genomes	Global	Study-wide	139910	C=0.681381	G=0.318619
gnomAD - Genomes	European	Sub	75774	C=0.67535	G=0.32465
gnomAD - Genomes	African	Sub	41896	C=0.67921	G=0.32079
gnomAD - Genomes	American	Sub	13644	C=0.69085	G=0.30915
gnomAD - Genomes	Ashkenazi Jewish	Sub	3314	C=0.6476	G=0.3524
gnomAD - Genomes	East Asian	Sub	3132	C=0.8423	G=0.1577
gnomAD - Genomes	Other	Sub	2150	C=0.6940	G=0.3060
14KJPN	JAPANESE	Study-wide	28258	C=0.86499	G=0.13501
Allele Frequency Aggregator	Total	Global	20068	C=0.67585	G=0.32415
Allele Frequency Aggregator	European	Sub	15436	C=0.66785	G=0.33215
Allele Frequency Aggregator	African	Sub	2946	C=0.6942	G=0.3058
Allele Frequency Aggregator	Other	Sub	720	C=0.671	G=0.329
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.762	G=0.238
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.651	G=0.349
Allele Frequency Aggregator	Asian	Sub	112	C=0.848	G=0.152
Allele Frequency Aggregator	South Asian	Sub	98	C=0.72	G=0.28
8.3KJPN	JAPANESE	Study-wide	16760	C=0.86283	G=0.13717
1000Genomes_30x	Global	Study-wide	6404	C=0.7138	G=0.2862
1000Genomes_30x	African	Sub	1786	C=0.6697	G=0.3303
1000Genomes_30x	Europe	Sub	1266	C=0.6540	G=0.3460
1000Genomes_30x	South Asian	Sub	1202	C=0.7280	G=0.2720
1000Genomes_30x	East Asian	Sub	1170	C=0.8342	G=0.1658
1000Genomes_30x	American	Sub	980	C=0.710	G=0.290
1000Genomes	Global	Study-wide	5008	C=0.7171	G=0.2829
1000Genomes	African	Sub	1322	C=0.6657	G=0.3343
1000Genomes	East Asian	Sub	1008	C=0.8383	G=0.1617
1000Genomes	Europe	Sub	1006	C=0.6511	G=0.3489
1000Genomes	South Asian	Sub	978	C=0.738	G=0.262
1000Genomes	American	Sub	694	C=0.705	G=0.295
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.6696	G=0.3304
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.6876	G=0.3124
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.6834	G=0.3166
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.8330	G=0.1670
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8472	G=0.1528
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.678	G=0.322
Northern Sweden	ACPOP	Study-wide	600	C=0.728	G=0.272
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	C=0.695	G=0.305
HapMap	Global	Study-wide	328	C=0.759	G=0.241
HapMap	African	Sub	120	C=0.717	G=0.283
HapMap	American	Sub	120	C=0.717	G=0.283
HapMap	Asian	Sub	88	C=0.88	G=0.12
SGDP_PRJ	Global	Study-wide	258	C=0.384	G=0.616
Qatari	Global	Study-wide	216	C=0.616	G=0.384
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.806	G=0.194
The Danish reference pan genome	Danish	Study-wide	40	C=0.55	G=0.45
Siberian	Global	Study-wide	20	C=0.45	G=0.55

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.113163983C>G
GRCh37.p13 chr 9	NC_000009.11:g.115926263C>G

Gene: SLC31A2, solute carrier family 31 member 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC31A2 transcript	NM_001860.3:c.*1066=	N/A	3 Prime UTR Variant

Gene: FKBP15, FKBP prolyl isomerase family member 15 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FKBP15 transcript	NM_015258.2:c.*2095=	N/A	3 Prime UTR Variant
FKBP15 transcript variant X1	XM_006717018.3:c.*2095=	N/A	3 Prime UTR Variant
FKBP15 transcript variant X2	XM_006717019.2:c.*2095=	N/A	3 Prime UTR 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	C=	G
GRCh38.p14 chr 9	NC_000009.12:g.113163983=	NC_000009.12:g.113163983C>G
GRCh37.p13 chr 9	NC_000009.11:g.115926263=	NC_000009.11:g.115926263C>G
FKBP15 transcript variant X1	XM_006717018.3:c.*2095=	XM_006717018.3:c.*2095G>C
SLC31A2 transcript	NM_001860.3:c.*1066=	NM_001860.3:c.*1066C>G
SLC31A2 transcript	NM_001860.2:c.*1066=	NM_001860.2:c.*1066C>G
FKBP15 transcript	NM_015258.2:c.*2095=	NM_015258.2:c.*2095G>C
FKBP15 transcript variant X2	XM_006717019.2:c.*2095=	XM_006717019.2:c.*2095G>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#.

82 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	LEE	ss1516925	Oct 13, 2000 (86)
2	HGBASE	ss2421949	Nov 14, 2000 (92)
3	LEE	ss4409474	May 29, 2002 (106)
4	WI_SSAHASNP	ss12025327	Jul 11, 2003 (116)
5	CGAP-GAI	ss16226235	Feb 27, 2004 (120)
6	SC_SNP	ss16264107	Feb 27, 2004 (120)
7	PERLEGEN	ss23515441	Sep 20, 2004 (123)
8	ILLUMINA	ss65721675	Oct 16, 2006 (127)
9	HGSV	ss78892104	Dec 07, 2007 (129)
10	1000GENOMES	ss109016329	Jan 23, 2009 (130)
11	1000GENOMES	ss114965055	Jan 25, 2009 (130)
12	ILLUMINA-UK	ss115787718	Feb 14, 2009 (130)
13	ILLUMINA	ss120243066	Dec 01, 2009 (131)
14	ILLUMINA	ss159976947	Dec 01, 2009 (131)
15	BUSHMAN	ss200791605	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss206726290	Jul 04, 2010 (132)
17	1000GENOMES	ss224414944	Jul 14, 2010 (132)
18	1000GENOMES	ss234943758	Jul 15, 2010 (132)
19	1000GENOMES	ss241695800	Jul 15, 2010 (132)
20	BL	ss254495799	May 09, 2011 (134)
21	GMI	ss280373025	May 04, 2012 (137)
22	GMI	ss286080958	Apr 25, 2013 (138)
23	PJP	ss294357264	May 09, 2011 (134)
24	ILLUMINA	ss479973557	Sep 08, 2015 (146)
25	ILLUMINA	ss535391813	Sep 08, 2015 (146)
26	TISHKOFF	ss561587539	Apr 25, 2013 (138)
27	SSMP	ss656084103	Apr 25, 2013 (138)
28	EVA-GONL	ss986905165	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1076553734	Aug 21, 2014 (142)
30	1000GENOMES	ss1335165200	Aug 21, 2014 (142)
31	DDI	ss1431940171	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1583231032	Apr 01, 2015 (144)
33	EVA_DECODE	ss1596543497	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1623406255	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1666400288	Apr 01, 2015 (144)
36	EVA_MGP	ss1711233983	Apr 01, 2015 (144)
37	HAMMER_LAB	ss1806129578	Sep 08, 2015 (146)
38	WEILL_CORNELL_DGM	ss1930219866	Feb 12, 2016 (147)
39	GENOMED	ss1971291902	Jul 19, 2016 (147)
40	JJLAB	ss2025831130	Sep 14, 2016 (149)
41	USC_VALOUEV	ss2154059779	Dec 20, 2016 (150)
42	HUMAN_LONGEVITY	ss2313819695	Dec 20, 2016 (150)
43	GRF	ss2709939129	Nov 08, 2017 (151)
44	GNOMAD	ss2882383795	Nov 08, 2017 (151)
45	SWEGEN	ss3005474336	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3026698010	Nov 08, 2017 (151)
47	CSHL	ss3348826566	Nov 08, 2017 (151)
48	ILLUMINA	ss3630338271	Oct 12, 2018 (152)
49	ILLUMINA	ss3636977283	Oct 12, 2018 (152)
50	OMUKHERJEE_ADBS	ss3646396680	Oct 12, 2018 (152)
51	EGCUT_WGS	ss3673013406	Jul 13, 2019 (153)
52	EVA_DECODE	ss3724607738	Jul 13, 2019 (153)
53	ACPOP	ss3736814437	Jul 13, 2019 (153)
54	EVA	ss3769598732	Jul 13, 2019 (153)
55	PACBIO	ss3786503774	Jul 13, 2019 (153)
56	PACBIO	ss3791706144	Jul 13, 2019 (153)
57	PACBIO	ss3796587638	Jul 13, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3812766867	Jul 13, 2019 (153)
59	EVA	ss3825760725	Apr 26, 2020 (154)
60	EVA	ss3831824311	Apr 26, 2020 (154)
61	EVA	ss3839440777	Apr 26, 2020 (154)
62	EVA	ss3844905220	Apr 26, 2020 (154)
63	SGDP_PRJ	ss3872920624	Apr 26, 2020 (154)
64	KRGDB	ss3920777651	Apr 26, 2020 (154)
65	KOGIC	ss3966595030	Apr 26, 2020 (154)
66	FSA-LAB	ss3984426428	Apr 26, 2021 (155)
67	FSA-LAB	ss3984426429	Apr 26, 2021 (155)
68	EVA	ss3986047678	Apr 26, 2021 (155)
69	TOPMED	ss4833063001	Apr 26, 2021 (155)
70	TOMMO_GENOMICS	ss5194964338	Apr 26, 2021 (155)
71	1000G_HIGH_COVERAGE	ss5281927744	Oct 13, 2022 (156)
72	EVA	ss5389780475	Oct 13, 2022 (156)
73	HUGCELL_USP	ss5477819473	Oct 13, 2022 (156)
74	EVA	ss5509825868	Oct 13, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5574857257	Oct 13, 2022 (156)
76	SANFORD_IMAGENETICS	ss5648125100	Oct 13, 2022 (156)
77	TOMMO_GENOMICS	ss5739395131	Oct 13, 2022 (156)
78	YY_MCH	ss5810942388	Oct 13, 2022 (156)
79	EVA	ss5829649366	Oct 13, 2022 (156)
80	EVA	ss5856906069	Oct 13, 2022 (156)
81	EVA	ss5917731124	Oct 13, 2022 (156)
82	EVA	ss5977325395	Oct 13, 2022 (156)
83	1000Genomes	NC_000009.11 - 115926263	Oct 12, 2018 (152)
84	1000Genomes_30x	NC_000009.12 - 113163983	Oct 13, 2022 (156)
85	The Avon Longitudinal Study of Parents and Children	NC_000009.11 - 115926263	Oct 12, 2018 (152)
86	Genetic variation in the Estonian population	NC_000009.11 - 115926263	Oct 12, 2018 (152)
87	The Danish reference pan genome	NC_000009.11 - 115926263	Apr 26, 2020 (154)
88	gnomAD - Genomes	NC_000009.12 - 113163983	Apr 26, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000009.11 - 115926263	Apr 26, 2020 (154)
90	HapMap	NC_000009.12 - 113163983	Apr 26, 2020 (154)
91	KOREAN population from KRGDB	NC_000009.11 - 115926263	Apr 26, 2020 (154)
92	Korean Genome Project	NC_000009.12 - 113163983	Apr 26, 2020 (154)
93	Medical Genome Project healthy controls from Spanish population	NC_000009.11 - 115926263	Apr 26, 2020 (154)
94	Northern Sweden	NC_000009.11 - 115926263	Jul 13, 2019 (153)
95	Qatari	NC_000009.11 - 115926263	Apr 26, 2020 (154)
96	SGDP_PRJ	NC_000009.11 - 115926263	Apr 26, 2020 (154)
97	Siberian	NC_000009.11 - 115926263	Apr 26, 2020 (154)
98	8.3KJPN	NC_000009.11 - 115926263	Apr 26, 2021 (155)
99	14KJPN	NC_000009.12 - 113163983	Oct 13, 2022 (156)
100	TopMed	NC_000009.12 - 113163983	Apr 26, 2021 (155)
101	UK 10K study - Twins	NC_000009.11 - 115926263	Oct 12, 2018 (152)
102	A Vietnamese Genetic Variation Database	NC_000009.11 - 115926263	Jul 13, 2019 (153)
103	ALFA	NC_000009.12 - 113163983	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).

Associated ID	History Updated (Build)
rs1801609	Jan 18, 2001 (92)
rs3186059	Jul 03, 2002 (106)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78892104	NC_000009.9:113005816:C:G	NC_000009.12:113163982:C:G	(self)
ss109016329, ss114965055, ss115787718, ss200791605, ss206726290, ss254495799, ss280373025, ss286080958, ss294357264, ss1596543497	NC_000009.10:114966083:C:G	NC_000009.12:113163982:C:G	(self)
47473272, 26376462, 18751654, 9395969, 11772535, 27955045, 349743, 10099302, 12261796, 24937604, 6576133, 52933645, 26376462, 5859773, ss224414944, ss234943758, ss241695800, ss479973557, ss535391813, ss561587539, ss656084103, ss986905165, ss1076553734, ss1335165200, ss1431940171, ss1583231032, ss1623406255, ss1666400288, ss1711233983, ss1806129578, ss1930219866, ss1971291902, ss2025831130, ss2154059779, ss2709939129, ss2882383795, ss3005474336, ss3348826566, ss3630338271, ss3636977283, ss3646396680, ss3673013406, ss3736814437, ss3769598732, ss3786503774, ss3791706144, ss3796587638, ss3825760725, ss3831824311, ss3839440777, ss3872920624, ss3920777651, ss3984426428, ss3984426429, ss3986047678, ss5194964338, ss5389780475, ss5509825868, ss5648125100, ss5829649366, ss5977325395	NC_000009.11:115926262:C:G	NC_000009.12:113163982:C:G	(self)
62383192, 335530147, 3901842, 22973031, 73232235, 670440562, 1230843591, ss2313819695, ss3026698010, ss3724607738, ss3812766867, ss3844905220, ss3966595030, ss4833063001, ss5281927744, ss5477819473, ss5574857257, ss5739395131, ss5810942388, ss5856906069, ss5917731124	NC_000009.12:113163982:C:G	NC_000009.12:113163982:C:G	(self)
ss12025327	NT_008470.15:17748888:C:G	NC_000009.12:113163982:C:G	(self)
ss16264107	NT_008470.16:17583997:C:G	NC_000009.12:113163982:C:G	(self)
ss1516925, ss2421949, ss4409474, ss16226235, ss23515441, ss65721675, ss120243066, ss159976947	NT_008470.19:45090794:C:G	NC_000009.12:113163982:C:G	(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 rs1128786

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

rs1128786