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dbSNP Short Genetic Variations

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.

rs1036332

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:199043349 (GRCh38.p13) 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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.294903 (78058/264690, TOPMED)
A=0.295312 (41300/139852, GnomAD)
A=0.28112 (20871/74242, ALFA) (+ 15 more)
A=0.18150 (3042/16760, 8.3KJPN)
A=0.2762 (1383/5008, 1000G)
A=0.2987 (1338/4480, Estonian)
A=0.2545 (981/3854, ALSPAC)
A=0.2748 (1019/3708, TWINSUK)
A=0.2041 (598/2930, KOREAN)
A=0.2442 (509/2084, HGDP_Stanford)
A=0.2627 (497/1892, HapMap)
A=0.261 (260/998, GoNL)
A=0.262 (157/600, NorthernSweden)
A=0.178 (92/516, SGDP_PRJ)
A=0.407 (88/216, Qatari)
A=0.143 (30/210, Vietnamese)
A=0.19 (10/54, Siberian)
A=0.28 (11/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
LINC01221 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
Help

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.p13 chr 1 NC_000001.11:g.199043349A>C
GRCh38.p13 chr 1 NC_000001.11:g.199043349A>G
GRCh38.p13 chr 1 NC_000001.11:g.199043349A>T
GRCh37.p13 chr 1 NC_000001.10:g.199012478A>C
GRCh37.p13 chr 1 NC_000001.10:g.199012478A>G
GRCh37.p13 chr 1 NC_000001.10:g.199012478A>T
Gene: LINC01221, long intergenic non-protein coding RNA 1221 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LINC01221 transcript NR_126351.1:n. N/A Intron Variant
Help

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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 74242 A=0.28112 C=0.71888
European Sub 57970 A=0.27221 C=0.72779
African Sub 5202 A=0.3554 C=0.6446
African Others Sub 182 A=0.401 C=0.599
African American Sub 5020 A=0.3538 C=0.6462
Asian Sub 238 A=0.210 C=0.790
East Asian Sub 164 A=0.177 C=0.823
Other Asian Sub 74 A=0.28 C=0.72
Latin American 1 Sub 396 A=0.308 C=0.692
Latin American 2 Sub 3390 A=0.3053 C=0.6947
South Asian Sub 4966 A=0.2934 C=0.7066
Other Sub 2080 A=0.2779 C=0.7221


Help

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 A=0.294903 C=0.705097
gnomAD - Genomes Global Study-wide 139852 A=0.295312 C=0.704688
gnomAD - Genomes European Sub 75746 A=0.27101 C=0.72899
gnomAD - Genomes African Sub 41906 A=0.35167 C=0.64833
gnomAD - Genomes American Sub 13612 A=0.28835 C=0.71165
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.2778 C=0.7222
gnomAD - Genomes East Asian Sub 3120 A=0.1904 C=0.8096
gnomAD - Genomes Other Sub 2146 A=0.2763 C=0.7237
8.3KJPN JAPANESE Study-wide 16760 A=0.18150 C=0.81850
1000Genomes Global Study-wide 5008 A=0.2762 C=0.7238
1000Genomes African Sub 1322 A=0.3684 C=0.6316
1000Genomes East Asian Sub 1008 A=0.1687 C=0.8313
1000Genomes Europe Sub 1006 A=0.2644 C=0.7356
1000Genomes South Asian Sub 978 A=0.274 C=0.726
1000Genomes American Sub 694 A=0.277 C=0.723
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.2987 C=0.7013
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.2545 C=0.7455
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.2748 C=0.7252
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.2041 C=0.7959, G=0.0000, T=0.0000
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 A=0.2442 C=0.7558
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=0.172 C=0.828
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 A=0.254 C=0.746
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=0.280 C=0.720
HGDP-CEPH-db Supplement 1 Europe Sub 320 A=0.259 C=0.741
HGDP-CEPH-db Supplement 1 Africa Sub 242 A=0.421 C=0.579
HGDP-CEPH-db Supplement 1 America Sub 216 A=0.167 C=0.833
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=0.06 C=0.94
HapMap Global Study-wide 1892 A=0.2627 C=0.7373
HapMap American Sub 770 A=0.255 C=0.745
HapMap African Sub 692 A=0.308 C=0.692
HapMap Asian Sub 254 A=0.154 C=0.846
HapMap Europe Sub 176 A=0.278 C=0.722
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.261 C=0.739
Northern Sweden ACPOP Study-wide 600 A=0.262 C=0.738
SGDP_PRJ Global Study-wide 516 A=0.178 C=0.822
Qatari Global Study-wide 216 A=0.407 C=0.593
A Vietnamese Genetic Variation Database Global Study-wide 210 A=0.143 C=0.857
Siberian Global Study-wide 54 A=0.19 C=0.81
The Danish reference pan genome Danish Study-wide 40 A=0.28 C=0.72
Help

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 A= C G T
GRCh38.p13 chr 1 NC_000001.11:g.199043349= NC_000001.11:g.199043349A>C NC_000001.11:g.199043349A>G NC_000001.11:g.199043349A>T
GRCh37.p13 chr 1 NC_000001.10:g.199012478= NC_000001.10:g.199012478A>C NC_000001.10:g.199012478A>G NC_000001.10:g.199012478A>T
Help

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#.

92 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1502377 Oct 05, 2000 (86)
2 WI_SSAHASNP ss6793970 Feb 20, 2003 (111)
3 SSAHASNP ss20525873 Apr 05, 2004 (121)
4 PERLEGEN ss23208080 Sep 20, 2004 (123)
5 ABI ss43935518 Mar 14, 2006 (126)
6 AFFY ss65923560 Dec 02, 2006 (127)
7 ILLUMINA ss66569695 Dec 02, 2006 (127)
8 ILLUMINA ss66881263 Dec 02, 2006 (127)
9 ILLUMINA ss66972605 Dec 02, 2006 (127)
10 ILLUMINA ss70364660 May 18, 2007 (127)
11 ILLUMINA ss70476967 May 23, 2008 (130)
12 ILLUMINA ss70999980 May 18, 2007 (127)
13 ILLUMINA ss74949862 Dec 07, 2007 (129)
14 AFFY ss76801754 Dec 07, 2007 (129)
15 HGSV ss78553108 Dec 07, 2007 (129)
16 KRIBB_YJKIM ss83669572 Dec 14, 2007 (130)
17 BCMHGSC_JDW ss87929771 Mar 23, 2008 (129)
18 HUMANGENOME_JCVI ss97996185 Feb 03, 2009 (130)
19 BGI ss106623247 Feb 03, 2009 (130)
20 1000GENOMES ss108850080 Jan 23, 2009 (130)
21 ILLUMINA-UK ss119168263 Feb 15, 2009 (130)
22 ILLUMINA ss121299707 Dec 01, 2009 (131)
23 ENSEMBL ss138133646 Dec 01, 2009 (131)
24 ENSEMBL ss139105207 Dec 01, 2009 (131)
25 ILLUMINA ss152715680 Dec 01, 2009 (131)
26 GMI ss156137263 Dec 01, 2009 (131)
27 ILLUMINA ss159121559 Dec 01, 2009 (131)
28 COMPLETE_GENOMICS ss164872616 Jul 04, 2010 (132)
29 COMPLETE_GENOMICS ss165662416 Jul 04, 2010 (132)
30 COMPLETE_GENOMICS ss167416323 Jul 04, 2010 (132)
31 ILLUMINA ss169366665 Jul 04, 2010 (132)
32 ILLUMINA ss170010087 Jul 04, 2010 (132)
33 BUSHMAN ss199460725 Jul 04, 2010 (132)
34 1000GENOMES ss210711573 Jul 14, 2010 (132)
35 1000GENOMES ss218817577 Jul 14, 2010 (132)
36 1000GENOMES ss230853136 Jul 14, 2010 (132)
37 1000GENOMES ss238474688 Jul 15, 2010 (132)
38 BL ss253736526 May 09, 2011 (134)
39 GMI ss276169211 May 04, 2012 (137)
40 GMI ss284206515 Apr 25, 2013 (138)
41 PJP ss290709277 May 09, 2011 (134)
42 ILLUMINA ss536600659 Sep 08, 2015 (146)
43 TISHKOFF ss555029048 Apr 25, 2013 (138)
44 SSMP ss648616462 Apr 25, 2013 (138)
45 ILLUMINA ss825334391 Apr 01, 2015 (144)
46 ILLUMINA ss832634284 Jul 12, 2019 (153)
47 EVA-GONL ss976012089 Aug 21, 2014 (142)
48 JMKIDD_LAB ss1068506696 Aug 21, 2014 (142)
49 1000GENOMES ss1294160388 Aug 21, 2014 (142)
50 DDI ss1426074596 Apr 01, 2015 (144)
51 EVA_GENOME_DK ss1574596385 Apr 01, 2015 (144)
52 EVA_DECODE ss1585406924 Apr 01, 2015 (144)
53 EVA_UK10K_ALSPAC ss1601873944 Apr 01, 2015 (144)
54 EVA_UK10K_TWINSUK ss1644867977 Apr 01, 2015 (144)
55 EVA_SVP ss1712394589 Apr 01, 2015 (144)
56 HAMMER_LAB ss1795547752 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1919242090 Feb 12, 2016 (147)
58 GENOMED ss1966942359 Jul 19, 2016 (147)
59 JJLAB ss2020139789 Sep 14, 2016 (149)
60 USC_VALOUEV ss2148166406 Dec 20, 2016 (150)
61 HUMAN_LONGEVITY ss2169094909 Dec 20, 2016 (150)
62 TOPMED ss2331678913 Dec 20, 2016 (150)
63 SYSTEMSBIOZJU ss2624577393 Nov 08, 2017 (151)
64 GRF ss2698156271 Nov 08, 2017 (151)
65 GNOMAD ss2764835514 Nov 08, 2017 (151)
66 SWEGEN ss2988247104 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3023829544 Nov 08, 2017 (151)
68 TOPMED ss3100228349 Nov 08, 2017 (151)
69 CSHL ss3343853922 Nov 08, 2017 (151)
70 ILLUMINA ss3626278100 Oct 11, 2018 (152)
71 ILLUMINA ss3637805918 Oct 11, 2018 (152)
72 ILLUMINA ss3638918581 Oct 11, 2018 (152)
73 ILLUMINA ss3639457937 Oct 11, 2018 (152)
74 ILLUMINA ss3642813219 Oct 11, 2018 (152)
75 URBANLAB ss3646859843 Oct 11, 2018 (152)
76 EGCUT_WGS ss3656207012 Jul 12, 2019 (153)
77 EVA_DECODE ss3688383758 Jul 12, 2019 (153)
78 ACPOP ss3727752536 Jul 12, 2019 (153)
79 EVA ss3747182818 Jul 12, 2019 (153)
80 PACBIO ss3783654005 Jul 12, 2019 (153)
81 PACBIO ss3789271624 Jul 12, 2019 (153)
82 PACBIO ss3794143812 Jul 12, 2019 (153)
83 KHV_HUMAN_GENOMES ss3800190502 Jul 12, 2019 (153)
84 EVA ss3826580571 Apr 25, 2020 (154)
85 EVA ss3836689432 Apr 25, 2020 (154)
86 EVA ss3842100398 Apr 25, 2020 (154)
87 HGDP ss3847359034 Apr 25, 2020 (154)
88 SGDP_PRJ ss3850644666 Apr 25, 2020 (154)
89 KRGDB ss3895926309 Apr 25, 2020 (154)
90 EVA ss4016954804 Apr 25, 2021 (155)
91 TOPMED ss4479293771 Apr 25, 2021 (155)
92 TOMMO_GENOMICS ss5147873737 Apr 25, 2021 (155)
93 1000Genomes NC_000001.10 - 199012478 Oct 11, 2018 (152)
94 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 199012478 Oct 11, 2018 (152)
95 Genetic variation in the Estonian population NC_000001.10 - 199012478 Oct 11, 2018 (152)
96 The Danish reference pan genome NC_000001.10 - 199012478 Apr 25, 2020 (154)
97 gnomAD - Genomes NC_000001.11 - 199043349 Apr 25, 2021 (155)
98 Genome of the Netherlands Release 5 NC_000001.10 - 199012478 Apr 25, 2020 (154)
99 HGDP-CEPH-db Supplement 1 NC_000001.9 - 197279101 Apr 25, 2020 (154)
100 HapMap NC_000001.11 - 199043349 Apr 25, 2020 (154)
101 KOREAN population from KRGDB NC_000001.10 - 199012478 Apr 25, 2020 (154)
102 Northern Sweden NC_000001.10 - 199012478 Jul 12, 2019 (153)
103 Qatari NC_000001.10 - 199012478 Apr 25, 2020 (154)
104 SGDP_PRJ NC_000001.10 - 199012478 Apr 25, 2020 (154)
105 Siberian NC_000001.10 - 199012478 Apr 25, 2020 (154)
106 8.3KJPN NC_000001.10 - 199012478 Apr 25, 2021 (155)
107 TopMed NC_000001.11 - 199043349 Apr 25, 2021 (155)
108 UK 10K study - Twins NC_000001.10 - 199012478 Oct 11, 2018 (152)
109 A Vietnamese Genetic Variation Database NC_000001.10 - 199012478 Jul 12, 2019 (153)
110 ALFA NC_000001.11 - 199043349 Apr 25, 2021 (155)
Help

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)
rs56859656 May 23, 2008 (130)
rs386512446 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78553108, ss3638918581, ss3639457937 NC_000001.8:195744134:A:C NC_000001.11:199043348:A:C (self)
36926, ss76801754, ss87929771, ss108850080, ss119168263, ss164872616, ss165662416, ss167416323, ss199460725, ss210711573, ss253736526, ss276169211, ss284206515, ss290709277, ss825334391, ss1585406924, ss1712394589, ss3642813219, ss3847359034 NC_000001.9:197279100:A:C NC_000001.11:199043348:A:C (self)
4997391, 2745895, 1945260, 1834225, 1198961, 3103703, 1037401, 1284020, 2661646, 682760, 5843044, 2745895, 593679, ss218817577, ss230853136, ss238474688, ss536600659, ss555029048, ss648616462, ss832634284, ss976012089, ss1068506696, ss1294160388, ss1426074596, ss1574596385, ss1601873944, ss1644867977, ss1795547752, ss1919242090, ss1966942359, ss2020139789, ss2148166406, ss2331678913, ss2624577393, ss2698156271, ss2764835514, ss2988247104, ss3343853922, ss3626278100, ss3637805918, ss3656207012, ss3727752536, ss3747182818, ss3783654005, ss3789271624, ss3794143812, ss3826580571, ss3836689432, ss3850644666, ss3895926309, ss4016954804, ss5147873737 NC_000001.10:199012477:A:C NC_000001.11:199043348:A:C (self)
36046352, 240899, 26954719, 42900106, 10148194748, ss2169094909, ss3023829544, ss3100228349, ss3646859843, ss3688383758, ss3800190502, ss3842100398, ss4479293771 NC_000001.11:199043348:A:C NC_000001.11:199043348:A:C (self)
ss1502377, ss6793970, ss23208080, ss43935518, ss65923560, ss66569695, ss66881263, ss66972605, ss70364660, ss70476967, ss70999980, ss74949862, ss83669572, ss97996185, ss106623247, ss121299707, ss138133646, ss139105207, ss152715680, ss156137263, ss159121559, ss169366665, ss170010087 NT_004487.19:50501119:A:C NC_000001.11:199043348:A:C (self)
ss20525873 NT_004671.15:10367461:A:C NC_000001.11:199043348:A:C (self)
3103703, ss3895926309 NC_000001.10:199012477:A:G NC_000001.11:199043348:A:G (self)
3103703, ss3895926309 NC_000001.10:199012477:A:T NC_000001.11:199043348:A:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1036332

Help

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.

Software version is: 2.0.1.post596+ae089ad