Name: rs1048076
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.

rs1048076

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:46144635 (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=0.425823 (112711/264690, TOPMED)
C=0.431203 (60227/139672, GnomAD)
C=0.48574 (23737/48868, ALFA) (+ 18 more)
C=0.35820 (10122/28258, 14KJPN)
C=0.35984 (6031/16760, 8.3KJPN)
C=0.4428 (2836/6404, 1000G_30x)
C=0.4467 (2237/5008, 1000G)
C=0.4873 (2183/4480, Estonian)
T=0.4811 (1854/3854, ALSPAC)
T=0.4709 (1746/3708, TWINSUK)
C=0.4031 (1181/2930, KOREAN)
C=0.3814 (720/1888, HapMap)
C=0.3794 (695/1832, Korea1K)
T=0.459 (458/998, GoNL)
C=0.489 (306/626, Chileans)
C=0.477 (286/600, NorthernSweden)
T=0.299 (112/374, SGDP_PRJ)
T=0.403 (87/216, Qatari)
C=0.454 (98/216, Vietnamese)
C=0.47 (19/40, GENOME_DK)
T=0.39 (14/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ENPP4 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	48868	T=0.51426	C=0.48574	0.276459	0.247933	0.475608	30
European	Sub	35078	T=0.47580	C=0.52420	0.230344	0.27875	0.490906	3
African	Sub	5608	T=0.7614	C=0.2386	0.580599	0.057775	0.361626	0
African Others	Sub	192	T=0.865	C=0.135	0.739583	0.010417	0.25	0
African American	Sub	5416	T=0.7578	C=0.2422	0.574963	0.059453	0.365583	0
Asian	Sub	486	T=0.611	C=0.389	0.382716	0.160494	0.45679	0
East Asian	Sub	388	T=0.629	C=0.371	0.402062	0.14433	0.453608	0
Other Asian	Sub	98	T=0.54	C=0.46	0.306122	0.22449	0.469388	0
Latin American 1	Sub	660	T=0.579	C=0.421	0.318182	0.160606	0.521212	1
Latin American 2	Sub	2996	T=0.5140	C=0.4860	0.26235	0.234312	0.503338	0
South Asian	Sub	172	T=0.326	C=0.674	0.116279	0.465116	0.418605	0
Other	Sub	3868	T=0.4902	C=0.5098	0.251293	0.270941	0.477766	2

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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	T=0.574177	C=0.425823
gnomAD - Genomes	Global	Study-wide	139672	T=0.568797	C=0.431203
gnomAD - Genomes	European	Sub	75654	T=0.47539	C=0.52461
gnomAD - Genomes	African	Sub	41908	T=0.76324	C=0.23676
gnomAD - Genomes	American	Sub	13540	T=0.53708	C=0.46292
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	T=0.3969	C=0.6031
gnomAD - Genomes	East Asian	Sub	3112	T=0.5630	C=0.4370
gnomAD - Genomes	Other	Sub	2142	T=0.5387	C=0.4613
Allele Frequency Aggregator	Total	Global	48868	T=0.51426	C=0.48574
Allele Frequency Aggregator	European	Sub	35078	T=0.47580	C=0.52420
Allele Frequency Aggregator	African	Sub	5608	T=0.7614	C=0.2386
Allele Frequency Aggregator	Other	Sub	3868	T=0.4902	C=0.5098
Allele Frequency Aggregator	Latin American 2	Sub	2996	T=0.5140	C=0.4860
Allele Frequency Aggregator	Latin American 1	Sub	660	T=0.579	C=0.421
Allele Frequency Aggregator	Asian	Sub	486	T=0.611	C=0.389
Allele Frequency Aggregator	South Asian	Sub	172	T=0.326	C=0.674
14KJPN	JAPANESE	Study-wide	28258	T=0.64180	C=0.35820
8.3KJPN	JAPANESE	Study-wide	16760	T=0.64016	C=0.35984
1000Genomes_30x	Global	Study-wide	6404	T=0.5572	C=0.4428
1000Genomes_30x	African	Sub	1786	T=0.8080	C=0.1920
1000Genomes_30x	Europe	Sub	1266	T=0.4660	C=0.5340
1000Genomes_30x	South Asian	Sub	1202	T=0.3045	C=0.6955
1000Genomes_30x	East Asian	Sub	1170	T=0.5385	C=0.4615
1000Genomes_30x	American	Sub	980	T=0.550	C=0.450
1000Genomes	Global	Study-wide	5008	T=0.5533	C=0.4467
1000Genomes	African	Sub	1322	T=0.8079	C=0.1921
1000Genomes	East Asian	Sub	1008	T=0.5456	C=0.4544
1000Genomes	Europe	Sub	1006	T=0.4652	C=0.5348
1000Genomes	South Asian	Sub	978	T=0.308	C=0.692
1000Genomes	American	Sub	694	T=0.553	C=0.447
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5127	C=0.4873
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.4811	C=0.5189
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.4709	C=0.5291
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.5969	C=0.4031
HapMap	Global	Study-wide	1888	T=0.6186	C=0.3814
HapMap	American	Sub	766	T=0.493	C=0.507
HapMap	African	Sub	692	T=0.805	C=0.195
HapMap	Asian	Sub	254	T=0.602	C=0.398
HapMap	Europe	Sub	176	T=0.455	C=0.545
Korean Genome Project	KOREAN	Study-wide	1832	T=0.6206	C=0.3794
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.459	C=0.541
Chileans	Chilean	Study-wide	626	T=0.511	C=0.489
Northern Sweden	ACPOP	Study-wide	600	T=0.523	C=0.477
SGDP_PRJ	Global	Study-wide	374	T=0.299	C=0.701
Qatari	Global	Study-wide	216	T=0.403	C=0.597
A Vietnamese Genetic Variation Database	Global	Study-wide	216	T=0.546	C=0.454
The Danish reference pan genome	Danish	Study-wide	40	T=0.53	C=0.47
Siberian	Global	Study-wide	36	T=0.39	C=0.61

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 6	NC_000006.12:g.46144635T>C
GRCh37.p13 chr 6	NC_000006.11:g.46112372T>C

Gene: ENPP4, ectonucleotide pyrophosphatase/phosphodiesterase 4 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ENPP4 transcript	NM_014936.5:c.*995=	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	T=	C
GRCh38.p14 chr 6	NC_000006.12:g.46144635=	NC_000006.12:g.46144635T>C
GRCh37.p13 chr 6	NC_000006.11:g.46112372=	NC_000006.11:g.46112372T>C
ENPP4 transcript	NM_014936.5:c.*995=	NM_014936.5:c.*995T>C
ENPP4 transcript	NM_014936.4:c.*995=	NM_014936.4:c.*995T>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#.

85 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	LEE	ss4393642	May 29, 2002 (106)
2	LEE	ss4412409	May 29, 2002 (106)
3	YUSUKE	ss4963698	Aug 28, 2002 (108)
4	SC_SNP	ss13087103	Dec 05, 2003 (119)
5	PERLEGEN	ss24000533	Sep 20, 2004 (123)
6	SI_EXO	ss52067399	Oct 16, 2006 (127)
7	AFFY	ss66022718	Dec 01, 2006 (127)
8	AFFY	ss66357957	Dec 01, 2006 (127)
9	AFFY	ss76074517	Dec 06, 2007 (129)
10	KRIBB_YJKIM	ss81452865	Dec 14, 2007 (130)
11	HGSV	ss81579186	Dec 15, 2007 (130)
12	HUMANGENOME_JCVI	ss98495937	Feb 05, 2009 (130)
13	1000GENOMES	ss110056235	Jan 24, 2009 (130)
14	GMI	ss156885014	Dec 01, 2009 (131)
15	ILLUMINA	ss159897888	Dec 01, 2009 (131)
16	COMPLETE_GENOMICS	ss162313364	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss166610620	Jul 04, 2010 (132)
18	AFFY	ss172411794	Jul 04, 2010 (132)
19	BUSHMAN	ss201774464	Jul 04, 2010 (132)
20	BCM-HGSC-SUB	ss207440979	Jul 04, 2010 (132)
21	1000GENOMES	ss222373027	Jul 14, 2010 (132)
22	1000GENOMES	ss233457861	Jul 14, 2010 (132)
23	1000GENOMES	ss240517520	Jul 15, 2010 (132)
24	BL	ss254295535	May 09, 2011 (134)
25	GMI	ss278781570	May 04, 2012 (137)
26	PJP	ss293590771	May 09, 2011 (134)
27	ILLUMINA	ss479657411	Sep 08, 2015 (146)
28	TISHKOFF	ss559183742	Apr 25, 2013 (138)
29	SSMP	ss653124443	Apr 25, 2013 (138)
30	EVA-GONL	ss982894346	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1073588266	Aug 21, 2014 (142)
32	1000GENOMES	ss1319986699	Aug 21, 2014 (142)
33	DDI	ss1430710670	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1581658293	Apr 01, 2015 (144)
35	EVA_DECODE	ss1592430679	Apr 01, 2015 (144)
36	EVA_UK10K_ALSPAC	ss1615505104	Apr 01, 2015 (144)
37	EVA_UK10K_TWINSUK	ss1658499137	Apr 01, 2015 (144)
38	EVA_SVP	ss1712861079	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1804412829	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1926150816	Feb 12, 2016 (147)
41	GENOMED	ss1970388649	Jul 19, 2016 (147)
42	JJLAB	ss2023715264	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2151894202	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2283787228	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2626344226	Nov 08, 2017 (151)
46	GRF	ss2707493275	Nov 08, 2017 (151)
47	GNOMAD	ss2838595260	Nov 08, 2017 (151)
48	SWEGEN	ss2999007501	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3025648712	Nov 08, 2017 (151)
50	CSHL	ss3346946097	Nov 08, 2017 (151)
51	ILLUMINA	ss3636789719	Oct 12, 2018 (152)
52	OMUKHERJEE_ADBS	ss3646339246	Oct 12, 2018 (152)
53	URBANLAB	ss3648343353	Oct 12, 2018 (152)
54	EGCUT_WGS	ss3666900404	Jul 13, 2019 (153)
55	EVA_DECODE	ss3717141529	Jul 13, 2019 (153)
56	ACPOP	ss3733474300	Jul 13, 2019 (153)
57	EVA	ss3764979740	Jul 13, 2019 (153)
58	PACBIO	ss3785464207	Jul 13, 2019 (153)
59	PACBIO	ss3790816550	Jul 13, 2019 (153)
60	PACBIO	ss3795695210	Jul 13, 2019 (153)
61	KHV_HUMAN_GENOMES	ss3808125642	Jul 13, 2019 (153)
62	EVA	ss3825700287	Apr 26, 2020 (154)
63	EVA	ss3829905662	Apr 26, 2020 (154)
64	EVA	ss3838429798	Apr 26, 2020 (154)
65	EVA	ss3843874296	Apr 26, 2020 (154)
66	SGDP_PRJ	ss3864507890	Apr 26, 2020 (154)
67	KRGDB	ss3911316665	Apr 26, 2020 (154)
68	KOGIC	ss3958967260	Apr 26, 2020 (154)
69	FSA-LAB	ss3984338987	Apr 26, 2021 (155)
70	FSA-LAB	ss3984338988	Apr 26, 2021 (155)
71	EVA	ss3986036055	Apr 26, 2021 (155)
72	TOPMED	ss4701737027	Apr 26, 2021 (155)
73	TOMMO_GENOMICS	ss5177346571	Apr 26, 2021 (155)
74	1000G_HIGH_COVERAGE	ss5268320468	Oct 13, 2022 (156)
75	EVA	ss5365396157	Oct 13, 2022 (156)
76	HUGCELL_USP	ss5466005584	Oct 13, 2022 (156)
77	EVA	ss5508476532	Oct 13, 2022 (156)
78	1000G_HIGH_COVERAGE	ss5554151308	Oct 13, 2022 (156)
79	SANFORD_IMAGENETICS	ss5640329336	Oct 13, 2022 (156)
80	TOMMO_GENOMICS	ss5715348370	Oct 13, 2022 (156)
81	YY_MCH	ss5807437390	Oct 13, 2022 (156)
82	EVA	ss5842194541	Oct 13, 2022 (156)
83	EVA	ss5855343405	Oct 13, 2022 (156)
84	EVA	ss5883672702	Oct 13, 2022 (156)
85	EVA	ss5968827670	Oct 13, 2022 (156)
86	1000Genomes	NC_000006.11 - 46112372	Oct 12, 2018 (152)
87	1000Genomes_30x	NC_000006.12 - 46144635	Oct 13, 2022 (156)
88	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 46112372	Oct 12, 2018 (152)
89	Chileans	NC_000006.11 - 46112372	Apr 26, 2020 (154)
90	Genetic variation in the Estonian population	NC_000006.11 - 46112372	Oct 12, 2018 (152)
91	The Danish reference pan genome	NC_000006.11 - 46112372	Apr 26, 2020 (154)
92	gnomAD - Genomes	NC_000006.12 - 46144635	Apr 26, 2021 (155)
93	Genome of the Netherlands Release 5	NC_000006.11 - 46112372	Apr 26, 2020 (154)
94	HapMap	NC_000006.12 - 46144635	Apr 26, 2020 (154)
95	KOREAN population from KRGDB	NC_000006.11 - 46112372	Apr 26, 2020 (154)
96	Korean Genome Project	NC_000006.12 - 46144635	Apr 26, 2020 (154)
97	Northern Sweden	NC_000006.11 - 46112372	Jul 13, 2019 (153)
98	Qatari	NC_000006.11 - 46112372	Apr 26, 2020 (154)
99	SGDP_PRJ	NC_000006.11 - 46112372	Apr 26, 2020 (154)
100	Siberian	NC_000006.11 - 46112372	Apr 26, 2020 (154)
101	8.3KJPN	NC_000006.11 - 46112372	Apr 26, 2021 (155)
102	14KJPN	NC_000006.12 - 46144635	Oct 13, 2022 (156)
103	TopMed	NC_000006.12 - 46144635	Apr 26, 2021 (155)
104	UK 10K study - Twins	NC_000006.11 - 46112372	Oct 12, 2018 (152)
105	A Vietnamese Genetic Variation Database	NC_000006.11 - 46112372	Jul 13, 2019 (153)
106	ALFA	NC_000006.12 - 46144635	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)
rs3173228	Jul 03, 2002 (106)
rs3777631	Oct 09, 2002 (108)
rs56993520	Feb 26, 2009 (130)
rs59026127	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss81579186	NC_000006.9:46220330:T:C	NC_000006.12:46144634:T:C	(self)
ss66357957, ss76074517, ss110056235, ss159897888, ss162313364, ss166610620, ss172411794, ss201774464, ss207440979, ss254295535, ss278781570, ss293590771, ss1592430679, ss1712861079	NC_000006.10:46220330:T:C	NC_000006.12:46144634:T:C	(self)
31770321, 17718582, 377343, 12638652, 7823232, 7884741, 18494059, 6759165, 8192746, 16524870, 4410556, 35315878, 17718582, 3932760, ss222373027, ss233457861, ss240517520, ss479657411, ss559183742, ss653124443, ss982894346, ss1073588266, ss1319986699, ss1430710670, ss1581658293, ss1615505104, ss1658499137, ss1804412829, ss1926150816, ss1970388649, ss2023715264, ss2151894202, ss2626344226, ss2707493275, ss2838595260, ss2999007501, ss3346946097, ss3636789719, ss3646339246, ss3666900404, ss3733474300, ss3764979740, ss3785464207, ss3790816550, ss3795695210, ss3825700287, ss3829905662, ss3838429798, ss3864507890, ss3911316665, ss3984338987, ss3984338988, ss3986036055, ss5177346571, ss5365396157, ss5508476532, ss5640329336, ss5842194541, ss5968827670	NC_000006.11:46112371:T:C	NC_000006.12:46144634:T:C	(self)
41677243, 224154303, 3124448, 15345261, 49185474, 539114585, 2258703062, ss2283787228, ss3025648712, ss3648343353, ss3717141529, ss3808125642, ss3843874296, ss3958967260, ss4701737027, ss5268320468, ss5466005584, ss5554151308, ss5715348370, ss5807437390, ss5855343405, ss5883672702	NC_000006.12:46144634:T:C	NC_000006.12:46144634:T:C	(self)
ss13087103	NT_007592.13:36909479:T:C	NC_000006.12:46144634:T:C	(self)
ss52067399	NT_007592.14:36970602:T:C	NC_000006.12:46144634:T:C	(self)
ss4393642, ss4412409, ss4963698, ss24000533, ss66022718, ss81452865, ss98495937, ss156885014	NT_007592.15:46052371:T:C	NC_000006.12:46144634:T: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 rs1048076

PMID	Title	Author	Year	Journal
21674006	Genome-wide association study of schizophrenia in Japanese population.	Yamada K et al.	2011	PloS one

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

rs1048076