Name: rs12046362
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.

rs12046362

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:187342488 (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 / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.091254 (24154/264690, TOPMED)
C=0.084650 (16568/195724, ALFA)
C=0.079023 (11064/140010, GnomAD) (+ 19 more)
C=0.24632 (6960/28256, 14KJPN)
C=0.24606 (4124/16760, 8.3KJPN)
C=0.1309 (838/6404, 1000G_30x)
C=0.1360 (681/5008, 1000G)
C=0.1100 (493/4480, Estonian)
C=0.0929 (358/3854, ALSPAC)
C=0.0771 (286/3708, TWINSUK)
C=0.2892 (845/2922, KOREAN)
C=0.1425 (297/2084, HGDP_Stanford)
C=0.1075 (203/1888, HapMap)
C=0.2844 (521/1832, Korea1K)
C=0.086 (86/998, GoNL)
C=0.058 (35/600, NorthernSweden)
C=0.028 (6/216, Qatari)
T=0.404 (63/156, SGDP_PRJ)
C=0.05 (2/44, Ancient Sardinia)
C=0.07 (3/40, GENOME_DK)
T=0.5 (3/6, Siberian)
C=0.5 (3/6, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LINC01036 : 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	195724	T=0.915350	C=0.084650
European	Sub	168786	T=0.919549	C=0.080451
African	Sub	6902	T=0.9571	C=0.0429
African Others	Sub	264	T=0.970	C=0.030
African American	Sub	6638	T=0.9566	C=0.0434
Asian	Sub	702	T=0.718	C=0.282
East Asian	Sub	556	T=0.710	C=0.290
Other Asian	Sub	146	T=0.747	C=0.253
Latin American 1	Sub	840	T=0.901	C=0.099
Latin American 2	Sub	6890	T=0.8192	C=0.1808
South Asian	Sub	5004	T=0.8903	C=0.1097
Other	Sub	6600	T=0.9065	C=0.0935

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=0.908746	C=0.091254
Allele Frequency Aggregator	Total	Global	195724	T=0.915350	C=0.084650
Allele Frequency Aggregator	European	Sub	168786	T=0.919549	C=0.080451
Allele Frequency Aggregator	African	Sub	6902	T=0.9571	C=0.0429
Allele Frequency Aggregator	Latin American 2	Sub	6890	T=0.8192	C=0.1808
Allele Frequency Aggregator	Other	Sub	6600	T=0.9065	C=0.0935
Allele Frequency Aggregator	South Asian	Sub	5004	T=0.8903	C=0.1097
Allele Frequency Aggregator	Latin American 1	Sub	840	T=0.901	C=0.099
Allele Frequency Aggregator	Asian	Sub	702	T=0.718	C=0.282
gnomAD - Genomes	Global	Study-wide	140010	T=0.920977	C=0.079023
gnomAD - Genomes	European	Sub	75860	T=0.92261	C=0.07739
gnomAD - Genomes	African	Sub	41978	T=0.95695	C=0.04305
gnomAD - Genomes	American	Sub	13598	T=0.84579	C=0.15421
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.9675	C=0.0325
gnomAD - Genomes	East Asian	Sub	3108	T=0.6824	C=0.3176
gnomAD - Genomes	Other	Sub	2146	T=0.9096	C=0.0904
14KJPN	JAPANESE	Study-wide	28256	T=0.75368	C=0.24632
8.3KJPN	JAPANESE	Study-wide	16760	T=0.75394	C=0.24606
1000Genomes_30x	Global	Study-wide	6404	T=0.8691	C=0.1309
1000Genomes_30x	African	Sub	1786	T=0.9675	C=0.0325
1000Genomes_30x	Europe	Sub	1266	T=0.9305	C=0.0695
1000Genomes_30x	South Asian	Sub	1202	T=0.8694	C=0.1306
1000Genomes_30x	East Asian	Sub	1170	T=0.6923	C=0.3077
1000Genomes_30x	American	Sub	980	T=0.821	C=0.179
1000Genomes	Global	Study-wide	5008	T=0.8640	C=0.1360
1000Genomes	African	Sub	1322	T=0.9660	C=0.0340
1000Genomes	East Asian	Sub	1008	T=0.6905	C=0.3095
1000Genomes	Europe	Sub	1006	T=0.9334	C=0.0666
1000Genomes	South Asian	Sub	978	T=0.863	C=0.137
1000Genomes	American	Sub	694	T=0.823	C=0.177
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.8900	C=0.1100
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9071	C=0.0929
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9229	C=0.0771
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.7108	A=0.0000, C=0.2892
HGDP-CEPH-db Supplement 1	Global	Study-wide	2084	T=0.8575	C=0.1425
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	470	T=0.740	C=0.260
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	414	T=0.911	C=0.089
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	T=0.960	C=0.040
HGDP-CEPH-db Supplement 1	Europe	Sub	320	T=0.916	C=0.084
HGDP-CEPH-db Supplement 1	Africa	Sub	242	T=0.959	C=0.041
HGDP-CEPH-db Supplement 1	America	Sub	216	T=0.616	C=0.384
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	T=0.94	C=0.06
HapMap	Global	Study-wide	1888	T=0.8925	C=0.1075
HapMap	American	Sub	770	T=0.865	C=0.135
HapMap	African	Sub	692	T=0.970	C=0.030
HapMap	Asian	Sub	250	T=0.732	C=0.268
HapMap	Europe	Sub	176	T=0.938	C=0.062
Korean Genome Project	KOREAN	Study-wide	1832	T=0.7156	C=0.2844
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.914	C=0.086
Northern Sweden	ACPOP	Study-wide	600	T=0.942	C=0.058
Qatari	Global	Study-wide	216	T=0.972	C=0.028
SGDP_PRJ	Global	Study-wide	156	T=0.404	C=0.596
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	44	T=0.95	C=0.05
The Danish reference pan genome	Danish	Study-wide	40	T=0.93	C=0.07
Siberian	Global	Study-wide	6	T=0.5	C=0.5

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 1	NC_000001.11:g.187342488T>A
GRCh38.p14 chr 1	NC_000001.11:g.187342488T>C
GRCh37.p13 chr 1	NC_000001.10:g.187311620T>A
GRCh37.p13 chr 1	NC_000001.10:g.187311620T>C

Gene: LINC01036, long intergenic non-protein coding RNA 1036 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LINC01036 transcript	NR_126347.1: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	T=	A	C
GRCh38.p14 chr 1	NC_000001.11:g.187342488=	NC_000001.11:g.187342488T>A	NC_000001.11:g.187342488T>C
GRCh37.p13 chr 1	NC_000001.10:g.187311620=	NC_000001.10:g.187311620T>A	NC_000001.10:g.187311620T>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#.

87 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18117287	Feb 28, 2004 (120)
2	ILLUMINA	ss70553500	May 24, 2008 (130)
3	ILLUMINA	ss71089764	May 17, 2007 (127)
4	ILLUMINA	ss75115761	Dec 07, 2007 (129)
5	ILLUMINA	ss153120572	Dec 01, 2009 (131)
6	GMI	ss156033229	Dec 01, 2009 (131)
7	ILLUMINA	ss159201478	Dec 01, 2009 (131)
8	ILLUMINA	ss160028849	Dec 01, 2009 (131)
9	ILLUMINA	ss171812504	Jul 04, 2010 (132)
10	1000GENOMES	ss218772133	Jul 14, 2010 (132)
11	1000GENOMES	ss230820276	Jul 14, 2010 (132)
12	1000GENOMES	ss238448532	Jul 15, 2010 (132)
13	GMI	ss276136393	May 04, 2012 (137)
14	ILLUMINA	ss479659776	May 04, 2012 (137)
15	ILLUMINA	ss479665158	May 04, 2012 (137)
16	ILLUMINA	ss480181197	Sep 08, 2015 (146)
17	ILLUMINA	ss484628563	May 04, 2012 (137)
18	ILLUMINA	ss536749627	Sep 08, 2015 (146)
19	TISHKOFF	ss554956746	Apr 25, 2013 (138)
20	ILLUMINA	ss778773043	Sep 08, 2015 (146)
21	ILLUMINA	ss782761087	Sep 08, 2015 (146)
22	ILLUMINA	ss783727516	Sep 08, 2015 (146)
23	ILLUMINA	ss832013351	Sep 08, 2015 (146)
24	ILLUMINA	ss832713930	Jul 12, 2019 (153)
25	ILLUMINA	ss834232914	Sep 08, 2015 (146)
26	EVA-GONL	ss975919847	Aug 21, 2014 (142)
27	1000GENOMES	ss1293829450	Aug 21, 2014 (142)
28	EVA_GENOME_DK	ss1574539678	Apr 01, 2015 (144)
29	EVA_DECODE	ss1585312434	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1601698747	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1644692780	Apr 01, 2015 (144)
32	EVA_SVP	ss1712389303	Apr 01, 2015 (144)
33	ILLUMINA	ss1751887113	Sep 08, 2015 (146)
34	WEILL_CORNELL_DGM	ss1919154202	Feb 12, 2016 (147)
35	GENOMED	ss1966921057	Jul 19, 2016 (147)
36	JJLAB	ss2020093345	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2148121868	Dec 20, 2016 (150)
38	HUMAN_LONGEVITY	ss2168394225	Dec 20, 2016 (150)
39	ILLUMINA	ss2632604932	Nov 08, 2017 (151)
40	GRF	ss2698106279	Nov 08, 2017 (151)
41	GNOMAD	ss2763876903	Nov 08, 2017 (151)
42	SWEGEN	ss2988114444	Nov 08, 2017 (151)
43	BIOINF_KMB_FNS_UNIBA	ss3023805906	Nov 08, 2017 (151)
44	CSHL	ss3343815099	Nov 08, 2017 (151)
45	ILLUMINA	ss3626263307	Oct 11, 2018 (152)
46	ILLUMINA	ss3630636119	Oct 11, 2018 (152)
47	ILLUMINA	ss3632918502	Oct 11, 2018 (152)
48	ILLUMINA	ss3633614209	Oct 11, 2018 (152)
49	ILLUMINA	ss3634363138	Oct 11, 2018 (152)
50	ILLUMINA	ss3635307471	Oct 11, 2018 (152)
51	ILLUMINA	ss3636041889	Oct 11, 2018 (152)
52	ILLUMINA	ss3637057986	Oct 11, 2018 (152)
53	ILLUMINA	ss3637802096	Oct 11, 2018 (152)
54	ILLUMINA	ss3640070492	Oct 11, 2018 (152)
55	ILLUMINA	ss3642809872	Oct 11, 2018 (152)
56	EGCUT_WGS	ss3656067113	Jul 12, 2019 (153)
57	EVA_DECODE	ss3688220482	Jul 12, 2019 (153)
58	ACPOP	ss3727679440	Jul 12, 2019 (153)
59	ILLUMINA	ss3744664001	Jul 12, 2019 (153)
60	EVA	ss3747083938	Jul 12, 2019 (153)
61	ILLUMINA	ss3772165014	Jul 12, 2019 (153)
62	KHV_HUMAN_GENOMES	ss3800084991	Jul 12, 2019 (153)
63	EVA	ss3826539617	Apr 25, 2020 (154)
64	EVA	ss3836666485	Apr 25, 2020 (154)
65	EVA	ss3842076951	Apr 25, 2020 (154)
66	HGDP	ss3847356916	Apr 25, 2020 (154)
67	SGDP_PRJ	ss3850469871	Apr 25, 2020 (154)
68	KRGDB	ss3895737761	Apr 25, 2020 (154)
69	KOGIC	ss3946094401	Apr 25, 2020 (154)
70	EVA	ss3984839943	Apr 25, 2021 (155)
71	EVA	ss4016951236	Apr 25, 2021 (155)
72	TOPMED	ss4476285576	Apr 25, 2021 (155)
73	TOMMO_GENOMICS	ss5147499033	Apr 25, 2021 (155)
74	1000G_HIGH_COVERAGE	ss5245075188	Oct 12, 2022 (156)
75	EVA	ss5314667837	Oct 12, 2022 (156)
76	EVA	ss5323482915	Oct 12, 2022 (156)
77	HUGCELL_USP	ss5445581743	Oct 12, 2022 (156)
78	EVA	ss5506112089	Oct 12, 2022 (156)
79	1000G_HIGH_COVERAGE	ss5518798206	Oct 12, 2022 (156)
80	SANFORD_IMAGENETICS	ss5627036442	Oct 12, 2022 (156)
81	TOMMO_GENOMICS	ss5674990789	Oct 12, 2022 (156)
82	EVA	ss5799505838	Oct 12, 2022 (156)
83	YY_MCH	ss5801455389	Oct 12, 2022 (156)
84	EVA	ss5832974362	Oct 12, 2022 (156)
85	EVA	ss5849197691	Oct 12, 2022 (156)
86	EVA	ss5911149011	Oct 12, 2022 (156)
87	EVA	ss5938856337	Oct 12, 2022 (156)
88	1000Genomes	NC_000001.10 - 187311620	Oct 11, 2018 (152)
89	1000Genomes_30x	NC_000001.11 - 187342488	Oct 12, 2022 (156)
90	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 187311620	Oct 11, 2018 (152)
91	Genetic variation in the Estonian population	NC_000001.10 - 187311620	Oct 11, 2018 (152)
92	The Danish reference pan genome	NC_000001.10 - 187311620	Apr 25, 2020 (154)
93	gnomAD - Genomes	NC_000001.11 - 187342488	Apr 25, 2021 (155)
94	Genome of the Netherlands Release 5	NC_000001.10 - 187311620	Apr 25, 2020 (154)
95	HGDP-CEPH-db Supplement 1	NC_000001.9 - 185578243	Apr 25, 2020 (154)
96	HapMap	NC_000001.11 - 187342488	Apr 25, 2020 (154)
97	KOREAN population from KRGDB	NC_000001.10 - 187311620	Apr 25, 2020 (154)
98	Korean Genome Project	NC_000001.11 - 187342488	Apr 25, 2020 (154)
99	Northern Sweden	NC_000001.10 - 187311620	Jul 12, 2019 (153)
100	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000001.10 - 187311620	Apr 25, 2021 (155)
101	Qatari	NC_000001.10 - 187311620	Apr 25, 2020 (154)
102	SGDP_PRJ	NC_000001.10 - 187311620	Apr 25, 2020 (154)
103	Siberian	NC_000001.10 - 187311620	Apr 25, 2020 (154)
104	8.3KJPN	NC_000001.10 - 187311620	Apr 25, 2021 (155)
105	14KJPN	NC_000001.11 - 187342488	Oct 12, 2022 (156)
106	TopMed	NC_000001.11 - 187342488	Apr 25, 2021 (155)
107	UK 10K study - Twins	NC_000001.10 - 187311620	Oct 11, 2018 (152)
108	ALFA	NC_000001.11 - 187342488	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)
rs386522649	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
2915155, ss3895737761	NC_000001.10:187311619:T:A	NC_000001.11:187342487:T:A	(self)
34808, ss276136393, ss479659776, ss1585312434, ss1712389303, ss3642809872, ss3847356916	NC_000001.9:185578242:T:C	NC_000001.11:187342487:T:C	(self)
4653427, 2553189, 1805361, 1799162, 1109399, 2915155, 964305, 65870, 1196132, 2486851, 638222, 5468340, 2553189, ss218772133, ss230820276, ss238448532, ss479665158, ss480181197, ss484628563, ss536749627, ss554956746, ss778773043, ss782761087, ss783727516, ss832013351, ss832713930, ss834232914, ss975919847, ss1293829450, ss1574539678, ss1601698747, ss1644692780, ss1751887113, ss1919154202, ss1966921057, ss2020093345, ss2148121868, ss2632604932, ss2698106279, ss2763876903, ss2988114444, ss3343815099, ss3626263307, ss3630636119, ss3632918502, ss3633614209, ss3634363138, ss3635307471, ss3636041889, ss3637057986, ss3637802096, ss3640070492, ss3656067113, ss3727679440, ss3744664001, ss3747083938, ss3772165014, ss3826539617, ss3836666485, ss3850469871, ss3895737761, ss3984839943, ss4016951236, ss5147499033, ss5314667837, ss5323482915, ss5506112089, ss5627036442, ss5799505838, ss5832974362, ss5938856337	NC_000001.10:187311619:T:C	NC_000001.11:187342487:T:C	(self)
6324141, 33569197, 223717, 2472402, 8827893, 39891911, 14151084342, ss2168394225, ss3023805906, ss3688220482, ss3800084991, ss3842076951, ss3946094401, ss4476285576, ss5245075188, ss5445581743, ss5518798206, ss5674990789, ss5801455389, ss5849197691, ss5911149011	NC_000001.11:187342487:T:C	NC_000001.11:187342487:T:C	(self)
ss18117287	NT_004487.16:16359727:T:C	NC_000001.11:187342487:T:C	(self)
ss70553500, ss71089764, ss75115761, ss153120572, ss156033229, ss159201478, ss160028849, ss171812504	NT_004487.19:38800261:T:C	NC_000001.11:187342487:T:C	(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 rs12046362

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

rs12046362