Name: rs12142017
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.

rs12142017

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:155007865 (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=0.074782 (19794/264690, TOPMED)
C=0.066247 (9273/139976, GnomAD)
C=0.07054 (2790/39554, ALFA) (+ 14 more)
C=0.06374 (1801/28256, 14KJPN)
C=0.06539 (1096/16760, 8.3KJPN)
C=0.0753 (482/6404, 1000G_30x)
C=0.0735 (368/5008, 1000G)
C=0.0491 (220/4480, Estonian)
C=0.0752 (290/3854, ALSPAC)
C=0.0798 (296/3708, TWINSUK)
C=0.0795 (232/2920, KOREAN)
C=0.0857 (157/1832, Korea1K)
C=0.067 (67/998, GoNL)
C=0.083 (50/600, NorthernSweden)
C=0.148 (32/216, Qatari)
T=0.471 (65/138, SGDP_PRJ)
T=0.4 (3/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ZBTB7B : 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	39554	T=0.92946	C=0.07054
European	Sub	34646	T=0.92954	C=0.07046
African	Sub	2946	T=0.9474	C=0.0526
African Others	Sub	114	T=0.965	C=0.035
African American	Sub	2832	T=0.9467	C=0.0533
Asian	Sub	156	T=0.872	C=0.128
East Asian	Sub	130	T=0.885	C=0.115
Other Asian	Sub	26	T=0.81	C=0.19
Latin American 1	Sub	146	T=0.897	C=0.103
Latin American 2	Sub	610	T=0.874	C=0.126
South Asian	Sub	98	T=0.91	C=0.09
Other	Sub	952	T=0.923	C=0.077

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=0.925218	C=0.074782
gnomAD - Genomes	Global	Study-wide	139976	T=0.933753	C=0.066247
gnomAD - Genomes	European	Sub	75830	T=0.93194	C=0.06806
gnomAD - Genomes	African	Sub	41910	T=0.95249	C=0.04751
gnomAD - Genomes	American	Sub	13642	T=0.88931	C=0.11069
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.9436	C=0.0564
gnomAD - Genomes	East Asian	Sub	3130	T=0.9192	C=0.0808
gnomAD - Genomes	Other	Sub	2146	T=0.9203	C=0.0797
Allele Frequency Aggregator	Total	Global	39554	T=0.92946	C=0.07054
Allele Frequency Aggregator	European	Sub	34646	T=0.92954	C=0.07046
Allele Frequency Aggregator	African	Sub	2946	T=0.9474	C=0.0526
Allele Frequency Aggregator	Other	Sub	952	T=0.923	C=0.077
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.874	C=0.126
Allele Frequency Aggregator	Asian	Sub	156	T=0.872	C=0.128
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.897	C=0.103
Allele Frequency Aggregator	South Asian	Sub	98	T=0.91	C=0.09
14KJPN	JAPANESE	Study-wide	28256	T=0.93626	C=0.06374
8.3KJPN	JAPANESE	Study-wide	16760	T=0.93461	C=0.06539
1000Genomes_30x	Global	Study-wide	6404	T=0.9247	C=0.0753
1000Genomes_30x	African	Sub	1786	T=0.9608	C=0.0392
1000Genomes_30x	Europe	Sub	1266	T=0.9352	C=0.0648
1000Genomes_30x	South Asian	Sub	1202	T=0.9343	C=0.0657
1000Genomes_30x	East Asian	Sub	1170	T=0.9000	C=0.1000
1000Genomes_30x	American	Sub	980	T=0.863	C=0.137
1000Genomes	Global	Study-wide	5008	T=0.9265	C=0.0735
1000Genomes	African	Sub	1322	T=0.9569	C=0.0431
1000Genomes	East Asian	Sub	1008	T=0.9028	C=0.0972
1000Genomes	Europe	Sub	1006	T=0.9394	C=0.0606
1000Genomes	South Asian	Sub	978	T=0.937	C=0.063
1000Genomes	American	Sub	694	T=0.870	C=0.130
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9509	C=0.0491
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9248	C=0.0752
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9202	C=0.0798
KOREAN population from KRGDB	KOREAN	Study-wide	2920	T=0.9205	C=0.0795
Korean Genome Project	KOREAN	Study-wide	1832	T=0.9143	C=0.0857
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.933	C=0.067
Northern Sweden	ACPOP	Study-wide	600	T=0.917	C=0.083
Qatari	Global	Study-wide	216	T=0.852	C=0.148
SGDP_PRJ	Global	Study-wide	138	T=0.471	C=0.529
Siberian	Global	Study-wide	8	T=0.4	C=0.6

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.155007865T>C
GRCh37.p13 chr 1	NC_000001.10:g.154980341T>C

Gene: ZBTB7B, zinc finger and BTB domain containing 7B (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ZBTB7B transcript variant 3	NM_001252406.3:c.-144-239… NM_001252406.3:c.-144-2393T>C	N/A	Intron Variant
ZBTB7B transcript variant 5	NM_001256455.2:c.-7+4922T… NM_001256455.2:c.-7+4922T>C	N/A	Intron Variant
ZBTB7B transcript variant 4	NM_001377451.1:c.-144-239… NM_001377451.1:c.-144-2393T>C	N/A	Intron Variant
ZBTB7B transcript variant 2	NM_001377452.1:c.-86+4922… NM_001377452.1:c.-86+4922T>C	N/A	Intron Variant
ZBTB7B transcript variant 1	NM_001377453.1:c.-7+4922T… NM_001377453.1:c.-7+4922T>C	N/A	Intron Variant
ZBTB7B transcript variant 6	NM_001377454.1:c.-146-239… NM_001377454.1:c.-146-2393T>C	N/A	Intron Variant
ZBTB7B transcript variant 7	NM_001377455.1:c.-7+4922T… NM_001377455.1:c.-7+4922T>C	N/A	Intron Variant
ZBTB7B transcript variant X7	XM_006711359.3:c.-146-239… XM_006711359.3:c.-146-2393T>C	N/A	Intron Variant
ZBTB7B transcript variant X2	XM_047421851.1:c.110-2393… XM_047421851.1:c.110-2393T>C	N/A	Intron Variant
ZBTB7B transcript variant X10	XM_047421865.1:c.-86+4922… XM_047421865.1:c.-86+4922T>C	N/A	Intron Variant
ZBTB7B transcript variant X13	XM_047421871.1:c.-56+4922… XM_047421871.1:c.-56+4922T>C	N/A	Intron Variant
ZBTB7B transcript variant X11	XM_006711356.4:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X9	XM_011509599.3:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X1	XM_017001399.2:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X3	XM_047421852.1:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X4	XM_047421853.1:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X5	XM_047421854.1:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X6	XM_047421858.1:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X8	XM_047421863.1:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X12	XM_047421868.1:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X14	XM_047421876.1:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X15	XM_047421883.1:c.	N/A	Genic Upstream Transcript Variant
ZBTB7B transcript variant X16	XM_047421894.1:c.	N/A	Genic Upstream Transcript 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 1	NC_000001.11:g.155007865=	NC_000001.11:g.155007865T>C
GRCh37.p13 chr 1	NC_000001.10:g.154980341=	NC_000001.10:g.154980341T>C
ZBTB7B transcript variant 3	NM_001252406.2:c.-144-2393=	NM_001252406.2:c.-144-2393T>C
ZBTB7B transcript variant 3	NM_001252406.3:c.-144-2393=	NM_001252406.3:c.-144-2393T>C
ZBTB7B transcript variant 5	NM_001256455.1:c.-7+4922=	NM_001256455.1:c.-7+4922T>C
ZBTB7B transcript variant 5	NM_001256455.2:c.-7+4922=	NM_001256455.2:c.-7+4922T>C
ZBTB7B transcript variant 4	NM_001377451.1:c.-144-2393=	NM_001377451.1:c.-144-2393T>C
ZBTB7B transcript variant 2	NM_001377452.1:c.-86+4922=	NM_001377452.1:c.-86+4922T>C
ZBTB7B transcript variant 1	NM_001377453.1:c.-7+4922=	NM_001377453.1:c.-7+4922T>C
ZBTB7B transcript variant 6	NM_001377454.1:c.-146-2393=	NM_001377454.1:c.-146-2393T>C
ZBTB7B transcript variant 7	NM_001377455.1:c.-7+4922=	NM_001377455.1:c.-7+4922T>C
ZBTB7B transcript variant X7	XM_006711359.3:c.-146-2393=	XM_006711359.3:c.-146-2393T>C
ZBTB7B transcript variant X2	XM_047421851.1:c.110-2393=	XM_047421851.1:c.110-2393T>C
ZBTB7B transcript variant X10	XM_047421865.1:c.-86+4922=	XM_047421865.1:c.-86+4922T>C
ZBTB7B transcript variant X13	XM_047421871.1:c.-56+4922=	XM_047421871.1:c.-56+4922T>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#.

54 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18290850	Feb 28, 2004 (120)
2	BGI	ss102785886	Dec 01, 2009 (131)
3	BUSHMAN	ss199089933	Jul 04, 2010 (132)
4	1000GENOMES	ss210463454	Jul 14, 2010 (132)
5	1000GENOMES	ss230732978	Jul 14, 2010 (132)
6	GMI	ss276052162	May 04, 2012 (137)
7	ILLUMINA	ss482107601	May 04, 2012 (137)
8	ILLUMINA	ss483350389	May 04, 2012 (137)
9	TISHKOFF	ss554697781	Apr 25, 2013 (138)
10	SSMP	ss648415691	Apr 25, 2013 (138)
11	ILLUMINA	ss782118311	Aug 21, 2014 (142)
12	EVA-GONL	ss975685311	Aug 21, 2014 (142)
13	JMKIDD_LAB	ss1068271510	Aug 21, 2014 (142)
14	1000GENOMES	ss1292936699	Aug 21, 2014 (142)
15	DDI	ss1425979788	Apr 01, 2015 (144)
16	EVA_DECODE	ss1585066915	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1601220094	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1644214127	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1795096136	Sep 08, 2015 (146)
20	WEILL_CORNELL_DGM	ss1918919351	Feb 12, 2016 (147)
21	GENOMED	ss1966868108	Jul 19, 2016 (147)
22	JJLAB	ss2019975132	Sep 14, 2016 (149)
23	USC_VALOUEV	ss2147999828	Dec 20, 2016 (150)
24	HUMAN_LONGEVITY	ss2166565242	Dec 20, 2016 (150)
25	ILLUMINA	ss2632576560	Nov 08, 2017 (151)
26	GRF	ss2697972717	Nov 08, 2017 (151)
27	ILLUMINA	ss2710682916	Nov 08, 2017 (151)
28	GNOMAD	ss2761348703	Nov 08, 2017 (151)
29	SWEGEN	ss2987756490	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3023744776	Nov 08, 2017 (151)
31	CSHL	ss3343711801	Nov 08, 2017 (151)
32	ILLUMINA	ss3641616886	Oct 11, 2018 (152)
33	EGCUT_WGS	ss3655696897	Jul 12, 2019 (153)
34	EVA_DECODE	ss3687788168	Jul 12, 2019 (153)
35	ACPOP	ss3727487925	Jul 12, 2019 (153)
36	EVA	ss3746811588	Jul 12, 2019 (153)
37	KHV_HUMAN_GENOMES	ss3799812907	Jul 12, 2019 (153)
38	EVA	ss3826425540	Apr 25, 2020 (154)
39	SGDP_PRJ	ss3850012079	Apr 25, 2020 (154)
40	KRGDB	ss3895219699	Apr 25, 2020 (154)
41	KOGIC	ss3945657679	Apr 25, 2020 (154)
42	TOPMED	ss4468404964	Apr 25, 2021 (155)
43	TOMMO_GENOMICS	ss5146496647	Apr 25, 2021 (155)
44	1000G_HIGH_COVERAGE	ss5244302633	Oct 12, 2022 (156)
45	EVA	ss5322068291	Oct 12, 2022 (156)
46	HUGCELL_USP	ss5444895138	Oct 12, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5517635771	Oct 12, 2022 (156)
48	SANFORD_IMAGENETICS	ss5626596794	Oct 12, 2022 (156)
49	TOMMO_GENOMICS	ss5673696655	Oct 12, 2022 (156)
50	YY_MCH	ss5801262481	Oct 12, 2022 (156)
51	EVA	ss5832669182	Oct 12, 2022 (156)
52	EVA	ss5849109885	Oct 12, 2022 (156)
53	EVA	ss5910256928	Oct 12, 2022 (156)
54	EVA	ss5938390864	Oct 12, 2022 (156)
55	1000Genomes	NC_000001.10 - 154980341	Oct 11, 2018 (152)
56	1000Genomes_30x	NC_000001.11 - 155007865	Oct 12, 2022 (156)
57	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 154980341	Oct 11, 2018 (152)
58	Genetic variation in the Estonian population	NC_000001.10 - 154980341	Oct 11, 2018 (152)
59	gnomAD - Genomes	NC_000001.11 - 155007865	Apr 25, 2021 (155)
60	Genome of the Netherlands Release 5	NC_000001.10 - 154980341	Apr 25, 2020 (154)
61	KOREAN population from KRGDB	NC_000001.10 - 154980341	Apr 25, 2020 (154)
62	Korean Genome Project	NC_000001.11 - 155007865	Apr 25, 2020 (154)
63	Northern Sweden	NC_000001.10 - 154980341	Jul 12, 2019 (153)
64	Qatari	NC_000001.10 - 154980341	Apr 25, 2020 (154)
65	SGDP_PRJ	NC_000001.10 - 154980341	Apr 25, 2020 (154)
66	Siberian	NC_000001.10 - 154980341	Apr 25, 2020 (154)
67	8.3KJPN	NC_000001.10 - 154980341	Apr 25, 2021 (155)
68	14KJPN	NC_000001.11 - 155007865	Oct 12, 2022 (156)
69	TopMed	NC_000001.11 - 155007865	Apr 25, 2021 (155)
70	UK 10K study - Twins	NC_000001.10 - 154980341	Oct 11, 2018 (152)
71	ALFA	NC_000001.11 - 155007865	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss199089933, ss210463454, ss276052162, ss482107601, ss1585066915	NC_000001.9:153246964:T:C	NC_000001.11:155007864:T:C	(self)
3729120, 2027950, 1435145, 880820, 2397093, 772790, 961281, 2029059, 516182, 4465954, 2027950, ss230732978, ss483350389, ss554697781, ss648415691, ss782118311, ss975685311, ss1068271510, ss1292936699, ss1425979788, ss1601220094, ss1644214127, ss1795096136, ss1918919351, ss1966868108, ss2019975132, ss2147999828, ss2632576560, ss2697972717, ss2710682916, ss2761348703, ss2987756490, ss3343711801, ss3641616886, ss3655696897, ss3727487925, ss3746811588, ss3826425540, ss3850012079, ss3895219699, ss5146496647, ss5322068291, ss5626596794, ss5832669182, ss5938390864	NC_000001.10:154980340:T:C	NC_000001.11:155007864:T:C	(self)
5161706, 27135276, 2035680, 7533759, 32011299, 12900101495, ss2166565242, ss3023744776, ss3687788168, ss3799812907, ss3945657679, ss4468404964, ss5244302633, ss5444895138, ss5517635771, ss5673696655, ss5801262481, ss5849109885, ss5910256928	NC_000001.11:155007864:T:C	NC_000001.11:155007864:T:C	(self)
ss102785886	NT_004487.19:6468982:T:C	NC_000001.11:155007864:T:C	(self)
ss18290850	NT_079484.1:1430172:T:C	NC_000001.11:155007864: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 rs12142017

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

rs12142017