Name: rs529
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.

rs529

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:39547491 (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: C=0.298243 (78942/264690, TOPMED)
C=0.302668 (42388/140048, GnomAD)
C=0.13292 (3756/28258, 14KJPN) (+ 16 more)
C=0.30233 (5711/18890, ALFA)
C=0.13407 (2247/16760, 8.3KJPN)
C=0.2578 (1651/6404, 1000G_30x)
C=0.2534 (1269/5008, 1000G)
C=0.2493 (1117/4480, Estonian)
C=0.3176 (1224/3854, ALSPAC)
C=0.3339 (1238/3708, TWINSUK)
C=0.1338 (392/2930, KOREAN)
C=0.2772 (519/1872, HapMap)
C=0.305 (304/998, GoNL)
C=0.297 (178/600, NorthernSweden)
C=0.182 (97/532, SGDP_PRJ)
C=0.389 (84/216, Qatari)
C=0.167 (36/216, Vietnamese)
C=0.19 (10/54, Siberian)
C=0.42 (17/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: UGDH-AS1 : Intron Variant
SMIM14 : 3 Prime UTR 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	18890	C=0.30233	G=0.69767
European	Sub	14286	C=0.30673	G=0.69327
African	Sub	2946	C=0.3126	G=0.6874
African Others	Sub	114	C=0.333	G=0.667
African American	Sub	2832	C=0.3118	G=0.6882
Asian	Sub	112	C=0.143	G=0.857
East Asian	Sub	86	C=0.13	G=0.87
Other Asian	Sub	26	C=0.19	G=0.81
Latin American 1	Sub	146	C=0.349	G=0.651
Latin American 2	Sub	610	C=0.169	G=0.831
South Asian	Sub	98	C=0.26	G=0.74
Other	Sub	692	C=0.308	G=0.692

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=0.298243	G=0.701757
gnomAD - Genomes	Global	Study-wide	140048	C=0.302668	G=0.697332
gnomAD - Genomes	European	Sub	75872	C=0.31714	G=0.68286
gnomAD - Genomes	African	Sub	41952	C=0.29822	G=0.70178
gnomAD - Genomes	American	Sub	13622	C=0.25092	G=0.74908
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.3748	G=0.6252
gnomAD - Genomes	East Asian	Sub	3134	C=0.1487	G=0.8513
gnomAD - Genomes	Other	Sub	2146	C=0.3197	G=0.6803
14KJPN	JAPANESE	Study-wide	28258	C=0.13292	G=0.86708
Allele Frequency Aggregator	Total	Global	18890	C=0.30233	G=0.69767
Allele Frequency Aggregator	European	Sub	14286	C=0.30673	G=0.69327
Allele Frequency Aggregator	African	Sub	2946	C=0.3126	G=0.6874
Allele Frequency Aggregator	Other	Sub	692	C=0.308	G=0.692
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.169	G=0.831
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.349	G=0.651
Allele Frequency Aggregator	Asian	Sub	112	C=0.143	G=0.857
Allele Frequency Aggregator	South Asian	Sub	98	C=0.26	G=0.74
8.3KJPN	JAPANESE	Study-wide	16760	C=0.13407	G=0.86593
1000Genomes_30x	Global	Study-wide	6404	C=0.2578	G=0.7422
1000Genomes_30x	African	Sub	1786	C=0.2934	G=0.7066
1000Genomes_30x	Europe	Sub	1266	C=0.3270	G=0.6730
1000Genomes_30x	South Asian	Sub	1202	C=0.2687	G=0.7313
1000Genomes_30x	East Asian	Sub	1170	C=0.1641	G=0.8359
1000Genomes_30x	American	Sub	980	C=0.202	G=0.798
1000Genomes	Global	Study-wide	5008	C=0.2534	G=0.7466
1000Genomes	African	Sub	1322	C=0.2867	G=0.7133
1000Genomes	East Asian	Sub	1008	C=0.1677	G=0.8323
1000Genomes	Europe	Sub	1006	C=0.3171	G=0.6829
1000Genomes	South Asian	Sub	978	C=0.260	G=0.740
1000Genomes	American	Sub	694	C=0.213	G=0.787
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.2493	G=0.7507
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.3176	G=0.6824
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.3339	G=0.6661
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.1338	G=0.8662
HapMap	Global	Study-wide	1872	C=0.2772	G=0.7228
HapMap	American	Sub	762	C=0.262	G=0.738
HapMap	African	Sub	682	C=0.318	G=0.682
HapMap	Asian	Sub	254	C=0.181	G=0.819
HapMap	Europe	Sub	174	C=0.322	G=0.678
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.305	G=0.695
Northern Sweden	ACPOP	Study-wide	600	C=0.297	G=0.703
SGDP_PRJ	Global	Study-wide	532	C=0.182	G=0.818
Qatari	Global	Study-wide	216	C=0.389	G=0.611
A Vietnamese Genetic Variation Database	Global	Study-wide	216	C=0.167	G=0.833
Siberian	Global	Study-wide	54	C=0.19	G=0.81
The Danish reference pan genome	Danish	Study-wide	40	C=0.42	G=0.57

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 4	NC_000004.12:g.39547491C>G
GRCh37.p13 chr 4	NC_000004.11:g.39549111C>G

Gene: SMIM14, small integral membrane protein 14 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SMIM14 transcript variant 2	NM_174921.3:c.*4635=	N/A	3 Prime UTR Variant
SMIM14 transcript variant 3	NM_001317897.2:c.*4635=	N/A	3 Prime UTR Variant
SMIM14 transcript variant 1	NM_001317896.2:c.*4635=	N/A	3 Prime UTR Variant
SMIM14 transcript variant X1	XM_047449743.1:c.*4635=	N/A	3 Prime UTR Variant
SMIM14 transcript variant X2	XM_047449744.1:c.*4635=	N/A	3 Prime UTR Variant
SMIM14 transcript variant X3	XM_047449745.1:c.*4635=	N/A	3 Prime UTR Variant
SMIM14 transcript variant X4	XM_047449746.1:c.*4635=	N/A	3 Prime UTR Variant

Gene: UGDH-AS1, UGDH antisense RNA 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
UGDH-AS1 transcript	NR_047679.1:n.	N/A	Intron 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 4	NC_000004.12:g.39547491=	NC_000004.12:g.39547491C>G
GRCh37.p13 chr 4	NC_000004.11:g.39549111=	NC_000004.11:g.39549111C>G
SMIM14 transcript variant 2	NM_174921.3:c.*4635=	NM_174921.3:c.*4635G>C
SMIM14 transcript variant 2	NM_174921.2:c.*4635=	NM_174921.2:c.*4635G>C
SMIM14 transcript variant 1	NM_001317896.2:c.*4635=	NM_001317896.2:c.*4635G>C
SMIM14 transcript variant 1	NM_001317896.1:c.*4635=	NM_001317896.1:c.*4635G>C
SMIM14 transcript variant 3	NM_001317897.2:c.*4635=	NM_001317897.2:c.*4635G>C
SMIM14 transcript variant 3	NM_001317897.1:c.*4635=	NM_001317897.1:c.*4635G>C
SMIM14 transcript variant X1	XM_047449743.1:c.*4635=	XM_047449743.1:c.*4635G>C
SMIM14 transcript variant X2	XM_047449744.1:c.*4635=	XM_047449744.1:c.*4635G>C
SMIM14 transcript variant X4	XM_047449746.1:c.*4635=	XM_047449746.1:c.*4635G>C
SMIM14 transcript variant X3	XM_047449745.1:c.*4635=	XM_047449745.1:c.*4635G>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, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	DEBNICK	ss533	Sep 19, 2000 (36)
2	CGAP-GAI	ss10037	Sep 19, 2000 (52)
3	LEE	ss1520047	Oct 04, 2000 (86)
4	LEE	ss4393420	May 29, 2002 (106)
5	LEE	ss4411925	May 29, 2002 (106)
6	BCM_SSAHASNP	ss10158731	Jul 11, 2003 (116)
7	WI_SSAHASNP	ss11666922	Jul 11, 2003 (116)
8	CGAP-GAI	ss16242906	Feb 27, 2004 (120)
9	CSHL-HAPMAP	ss17804893	Feb 27, 2004 (120)
10	SSAHASNP	ss22075472	Apr 05, 2004 (121)
11	PERLEGEN	ss23719270	Sep 20, 2004 (123)
12	ABI	ss42132816	Mar 13, 2006 (126)
13	AFFY	ss76664326	Dec 07, 2007 (129)
14	BCMHGSC_JDW	ss92540704	Mar 24, 2008 (129)
15	HUMANGENOME_JCVI	ss98815797	Feb 04, 2009 (130)
16	KRIBB_YJKIM	ss104807682	Feb 04, 2009 (130)
17	BGI	ss105821285	Feb 04, 2009 (130)
18	1000GENOMES	ss112123959	Jan 25, 2009 (130)
19	1000GENOMES	ss113037769	Jan 25, 2009 (130)
20	ILLUMINA-UK	ss116960874	Feb 14, 2009 (130)
21	ENSEMBL	ss134733249	Dec 01, 2009 (131)
22	ENSEMBL	ss139551011	Dec 01, 2009 (131)
23	GMI	ss157126690	Dec 01, 2009 (131)
24	COMPLETE_GENOMICS	ss163363367	Jul 04, 2010 (132)
25	BUSHMAN	ss198391387	Jul 04, 2010 (132)
26	BCM-HGSC-SUB	ss206443605	Jul 04, 2010 (132)
27	1000GENOMES	ss220870724	Jul 14, 2010 (132)
28	1000GENOMES	ss232352591	Jul 14, 2010 (132)
29	1000GENOMES	ss239654562	Jul 15, 2010 (132)
30	BL	ss253056659	May 09, 2011 (134)
31	GMI	ss277664455	May 04, 2012 (137)
32	GMI	ss284885189	Apr 25, 2013 (138)
33	PJP	ss293329381	May 09, 2011 (134)
34	TISHKOFF	ss557450669	Apr 25, 2013 (138)
35	SSMP	ss651233311	Apr 25, 2013 (138)
36	EVA-GONL	ss980002634	Aug 21, 2014 (142)
37	JMKIDD_LAB	ss1071455414	Aug 21, 2014 (142)
38	1000GENOMES	ss1309303975	Aug 21, 2014 (142)
39	DDI	ss1429846526	Apr 01, 2015 (144)
40	EVA_GENOME_DK	ss1580511902	Apr 01, 2015 (144)
41	EVA_DECODE	ss1589497346	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1609873185	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1652867218	Apr 01, 2015 (144)
44	EVA_SVP	ss1712666644	Apr 01, 2015 (144)
45	HAMMER_LAB	ss1801305851	Sep 08, 2015 (146)
46	WEILL_CORNELL_DGM	ss1923234389	Feb 12, 2016 (147)
47	GENOMED	ss1969714902	Jul 19, 2016 (147)
48	JJLAB	ss2022201418	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2150312991	Dec 20, 2016 (150)
50	HUMAN_LONGEVITY	ss2262194574	Dec 20, 2016 (150)
51	SYSTEMSBIOZJU	ss2625601526	Nov 08, 2017 (151)
52	GRF	ss2705766805	Nov 08, 2017 (151)
53	GNOMAD	ss2808047069	Nov 08, 2017 (151)
54	SWEGEN	ss2994492110	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3024870965	Nov 08, 2017 (151)
56	CSHL	ss3345652657	Nov 08, 2017 (151)
57	URBANLAB	ss3647702085	Oct 12, 2018 (152)
58	EGCUT_WGS	ss3662412691	Jul 13, 2019 (153)
59	EVA_DECODE	ss3711840510	Jul 13, 2019 (153)
60	ACPOP	ss3731056109	Jul 13, 2019 (153)
61	EVA	ss3761673520	Jul 13, 2019 (153)
62	PACBIO	ss3784681582	Jul 13, 2019 (153)
63	PACBIO	ss3790144298	Jul 13, 2019 (153)
64	PACBIO	ss3795019459	Jul 13, 2019 (153)
65	KHV_HUMAN_GENOMES	ss3804805534	Jul 13, 2019 (153)
66	EVA	ss3828485951	Apr 26, 2020 (154)
67	EVA	ss3837679450	Apr 26, 2020 (154)
68	EVA	ss3843114497	Apr 26, 2020 (154)
69	SGDP_PRJ	ss3858684698	Apr 26, 2020 (154)
70	KRGDB	ss3904860943	Apr 26, 2020 (154)
71	TOPMED	ss4610194234	Apr 26, 2021 (155)
72	TOMMO_GENOMICS	ss5165163608	Apr 26, 2021 (155)
73	1000G_HIGH_COVERAGE	ss5258808208	Oct 13, 2022 (156)
74	HUGCELL_USP	ss5457633608	Oct 13, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5539650401	Oct 13, 2022 (156)
76	SANFORD_IMAGENETICS	ss5634795103	Oct 13, 2022 (156)
77	TOMMO_GENOMICS	ss5699074997	Oct 13, 2022 (156)
78	YY_MCH	ss5804956879	Oct 13, 2022 (156)
79	EVA	ss5843849439	Oct 13, 2022 (156)
80	EVA	ss5854178809	Oct 13, 2022 (156)
81	EVA	ss5863024159	Oct 13, 2022 (156)
82	EVA	ss5963188120	Oct 13, 2022 (156)
83	EVA	ss5981221762	Oct 13, 2022 (156)
84	1000Genomes	NC_000004.11 - 39549111	Oct 12, 2018 (152)
85	1000Genomes_30x	NC_000004.12 - 39547491	Oct 13, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 39549111	Oct 12, 2018 (152)
87	Genetic variation in the Estonian population	NC_000004.11 - 39549111	Oct 12, 2018 (152)
88	The Danish reference pan genome	NC_000004.11 - 39549111	Apr 26, 2020 (154)
89	gnomAD - Genomes	NC_000004.12 - 39547491	Apr 26, 2021 (155)
90	Genome of the Netherlands Release 5	NC_000004.11 - 39549111	Apr 26, 2020 (154)
91	HapMap	NC_000004.12 - 39547491	Apr 26, 2020 (154)
92	KOREAN population from KRGDB	NC_000004.11 - 39549111	Apr 26, 2020 (154)
93	Northern Sweden	NC_000004.11 - 39549111	Jul 13, 2019 (153)
94	Qatari	NC_000004.11 - 39549111	Apr 26, 2020 (154)
95	SGDP_PRJ	NC_000004.11 - 39549111	Apr 26, 2020 (154)
96	Siberian	NC_000004.11 - 39549111	Apr 26, 2020 (154)
97	8.3KJPN	NC_000004.11 - 39549111	Apr 26, 2021 (155)
98	14KJPN	NC_000004.12 - 39547491	Oct 13, 2022 (156)
99	TopMed	NC_000004.12 - 39547491	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000004.11 - 39549111	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000004.11 - 39549111	Jul 13, 2019 (153)
102	ALFA	NC_000004.12 - 39547491	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)
rs3172639	Jul 03, 2002 (106)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss76664326, ss92540704, ss112123959, ss113037769, ss116960874, ss163363367, ss198391387, ss206443605, ss253056659, ss277664455, ss284885189, ss293329381, ss1589497346, ss1712666644	NC_000004.10:39225505:C:G	NC_000004.12:39547490:C:G	(self)
20684008, 11524919, 8150939, 6676841, 5078135, 12038337, 4340974, 5276319, 10701678, 2829345, 23132915, 11524919, 2530012, ss220870724, ss232352591, ss239654562, ss557450669, ss651233311, ss980002634, ss1071455414, ss1309303975, ss1429846526, ss1580511902, ss1609873185, ss1652867218, ss1801305851, ss1923234389, ss1969714902, ss2022201418, ss2150312991, ss2625601526, ss2705766805, ss2808047069, ss2994492110, ss3345652657, ss3662412691, ss3731056109, ss3761673520, ss3784681582, ss3790144298, ss3795019459, ss3828485951, ss3837679450, ss3858684698, ss3904860943, ss5165163608, ss5634795103, ss5843849439, ss5963188120, ss5981221762	NC_000004.11:39549110:C:G	NC_000004.12:39547490:C:G	(self)
27176336, 146436220, 2598014, 32912101, 447571790, 2241362655, ss2262194574, ss3024870965, ss3647702085, ss3711840510, ss3804805534, ss3843114497, ss4610194234, ss5258808208, ss5457633608, ss5539650401, ss5699074997, ss5804956879, ss5854178809, ss5863024159	NC_000004.12:39547490:C:G	NC_000004.12:39547490:C:G	(self)
ss10158731, ss11666922	NT_016297.14:6697753:C:G	NC_000004.12:39547490:C:G	(self)
ss17804893, ss22075472	NT_016297.15:6697753:C:G	NC_000004.12:39547490:C:G	(self)
ss533, ss10037, ss1520047, ss4393420, ss4411925, ss16242906, ss23719270, ss42132816, ss98815797, ss104807682, ss105821285, ss134733249, ss139551011, ss157126690	NT_016297.16:6708472:C:G	NC_000004.12:39547490:C:G	(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 rs529

PMID	Title	Author	Year	Journal
31874497	[Effect of opioid-related gene polymorphisms on patients with high-dose opioid-tolerant cancer pain].	Xie GL et al.	2019	Zhonghua yi xue za zhi

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

rs529