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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.

rs73993544

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:219210071 (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
A=0.01318 (374/28374, ALFA)
A=0.10253 (2897/28256, 14KJPN)
A=0.10346 (1734/16760, 8.3KJPN) (+ 16 more)
A=0.03568 (464/13006, GO-ESP)
A=0.0486 (311/6404, 1000G_30x)
A=0.0487 (244/5008, 1000G)
A=0.0400 (179/4480, Estonian)
A=0.0106 (41/3854, ALSPAC)
A=0.0100 (37/3708, TWINSUK)
A=0.1403 (411/2930, KOREAN)
A=0.1436 (263/1832, Korea1K)
A=0.006 (6/998, GoNL)
A=0.017 (10/600, NorthernSweden)
A=0.002 (1/534, MGP)
A=0.051 (11/216, Qatari)
A=0.051 (11/216, Vietnamese)
T=0.48 (27/56, SGDP_PRJ)
T=0.50 (6/12, Siberian)
A=0.50 (6/12, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ABCB6 : Intron Variant
ZFAND2B : 500B Downstream 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 28374 T=0.98650 A=0.01318, C=0.00032
European Sub 21334 T=0.98627 A=0.01345, C=0.00028
African Sub 3098 T=0.9881 A=0.0119, C=0.0000
African Others Sub 108 T=1.000 A=0.000, C=0.000
African American Sub 2990 T=0.9876 A=0.0124, C=0.0000
Asian Sub 144 T=0.972 A=0.028, C=0.000
East Asian Sub 98 T=0.97 A=0.03, C=0.00
Other Asian Sub 46 T=0.98 A=0.02, C=0.00
Latin American 1 Sub 136 T=1.000 A=0.000, C=0.000
Latin American 2 Sub 604 T=1.000 A=0.000, C=0.000
South Asian Sub 90 T=1.00 A=0.00, C=0.00
Other Sub 2968 T=0.9835 A=0.0155, C=0.0010


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
Allele Frequency Aggregator Total Global 28374 T=0.98650 A=0.01318, C=0.00032
Allele Frequency Aggregator European Sub 21334 T=0.98627 A=0.01345, C=0.00028
Allele Frequency Aggregator African Sub 3098 T=0.9881 A=0.0119, C=0.0000
Allele Frequency Aggregator Other Sub 2968 T=0.9835 A=0.0155, C=0.0010
Allele Frequency Aggregator Latin American 2 Sub 604 T=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 144 T=0.972 A=0.028, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 136 T=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 90 T=1.00 A=0.00, C=0.00
14KJPN JAPANESE Study-wide 28256 T=0.89747 A=0.10253
8.3KJPN JAPANESE Study-wide 16760 T=0.89654 A=0.10346
GO Exome Sequencing Project Global Study-wide 13006 T=0.96432 A=0.03568
GO Exome Sequencing Project European American Sub 8600 T=0.9890 A=0.0110
GO Exome Sequencing Project African American Sub 4406 T=0.9163 A=0.0837
1000Genomes_30x Global Study-wide 6404 T=0.9514 A=0.0486
1000Genomes_30x African Sub 1786 T=0.9115 A=0.0885
1000Genomes_30x Europe Sub 1266 T=0.9826 A=0.0174
1000Genomes_30x South Asian Sub 1202 T=0.9850 A=0.0150
1000Genomes_30x East Asian Sub 1170 T=0.9128 A=0.0872
1000Genomes_30x American Sub 980 T=0.989 A=0.011
1000Genomes Global Study-wide 5008 T=0.9513 A=0.0487
1000Genomes African Sub 1322 T=0.9130 A=0.0870
1000Genomes East Asian Sub 1008 T=0.9097 A=0.0903
1000Genomes Europe Sub 1006 T=0.9821 A=0.0179
1000Genomes South Asian Sub 978 T=0.987 A=0.013
1000Genomes American Sub 694 T=0.990 A=0.010
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9600 A=0.0400
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9894 A=0.0106
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9900 A=0.0100
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.8597 A=0.1403
Korean Genome Project KOREAN Study-wide 1832 T=0.8564 A=0.1436
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.994 A=0.006
Northern Sweden ACPOP Study-wide 600 T=0.983 A=0.017
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.998 A=0.002
Qatari Global Study-wide 216 T=0.949 A=0.051
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.949 A=0.051
SGDP_PRJ Global Study-wide 56 T=0.48 A=0.52
Siberian Global Study-wide 12 T=0.50 A=0.50
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.p14 chr 2 NC_000002.12:g.219210071T>A
GRCh38.p14 chr 2 NC_000002.12:g.219210071T>C
GRCh37.p13 chr 2 NC_000002.11:g.220074793T>A
GRCh37.p13 chr 2 NC_000002.11:g.220074793T>C
LAN blood group RefSeqGene (LRG_824) NG_032110.1:g.13920A>T
LAN blood group RefSeqGene (LRG_824) NG_032110.1:g.13920A>G
Gene: ABCB6, ATP binding cassette subfamily B member 6 (Langereis blood group) (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ABCB6 transcript variant 2 NM_001349828.2:c.2283-25A…

NM_001349828.2:c.2283-25A>T

N/A Intron Variant
ABCB6 transcript variant 1 NM_005689.4:c.2421-25A>T N/A Intron Variant
Gene: ZFAND2B, zinc finger AN1-type containing 2B (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
ZFAND2B transcript variant 2 NM_001270998.2:c. N/A Downstream Transcript Variant
ZFAND2B transcript variant 3 NM_001270999.2:c. N/A Downstream Transcript Variant
ZFAND2B transcript variant 1 NM_138802.3:c. N/A Downstream Transcript Variant
ZFAND2B transcript variant X1 XM_006712285.2:c. N/A Downstream Transcript Variant
ZFAND2B transcript variant X2 XM_006712286.4:c. N/A Downstream Transcript Variant
ZFAND2B transcript variant X3 XM_017003368.2:c. N/A Downstream Transcript 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.

Allele: A (allele ID: 1231054 )
ClinVar Accession Disease Names Clinical Significance
RCV001641603.2 not provided Benign
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 T= A C
GRCh38.p14 chr 2 NC_000002.12:g.219210071= NC_000002.12:g.219210071T>A NC_000002.12:g.219210071T>C
GRCh37.p13 chr 2 NC_000002.11:g.220074793= NC_000002.11:g.220074793T>A NC_000002.11:g.220074793T>C
LAN blood group RefSeqGene (LRG_824) NG_032110.1:g.13920= NG_032110.1:g.13920A>T NG_032110.1:g.13920A>G
ABCB6 transcript variant 2 NM_001349828.2:c.2283-25= NM_001349828.2:c.2283-25A>T NM_001349828.2:c.2283-25A>G
ABCB6 transcript NM_005689.2:c.2421-25= NM_005689.2:c.2421-25A>T NM_005689.2:c.2421-25A>G
ABCB6 transcript variant 1 NM_005689.4:c.2421-25= NM_005689.4:c.2421-25A>T NM_005689.4:c.2421-25A>G
ABCB6 transcript variant X1 XM_005246215.1:c.2283-25= XM_005246215.1:c.2283-25A>T XM_005246215.1:c.2283-25A>G
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#.

73 SubSNP, 26 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA-UK ss118084317 Feb 14, 2009 (130)
2 ILLUMINA ss152536304 Dec 01, 2009 (131)
3 GMI ss154729686 Dec 01, 2009 (131)
4 ILLUMINA ss159100352 Dec 01, 2009 (131)
5 ILLUMINA ss159102617 Dec 01, 2009 (131)
6 ILLUMINA ss159845995 Dec 01, 2009 (131)
7 ILLUMINA ss168870679 Jul 04, 2010 (132)
8 BUSHMAN ss201760914 Jul 04, 2010 (132)
9 1000GENOMES ss219822475 Jul 14, 2010 (132)
10 1000GENOMES ss239050236 Jul 15, 2010 (132)
11 GMI ss276903973 May 04, 2012 (137)
12 ILLUMINA ss479154414 Sep 08, 2015 (146)
13 1000GENOMES ss489853056 May 04, 2012 (137)
14 ILLUMINA ss535383102 Sep 08, 2015 (146)
15 TISHKOFF ss556231152 Apr 25, 2013 (138)
16 SSMP ss649896689 Apr 25, 2013 (138)
17 NHLBI-ESP ss712488632 Apr 25, 2013 (138)
18 ILLUMINA ss832615413 Jul 13, 2019 (153)
19 EVA-GONL ss977977966 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1069954234 Aug 21, 2014 (142)
21 1000GENOMES ss1301715447 Aug 21, 2014 (142)
22 DDI ss1428916098 Apr 01, 2015 (144)
23 EVA_DECODE ss1587433639 Apr 01, 2015 (144)
24 EVA_UK10K_ALSPAC ss1605831095 Apr 01, 2015 (144)
25 EVA_UK10K_TWINSUK ss1648825128 Apr 01, 2015 (144)
26 EVA_EXAC ss1686742791 Apr 01, 2015 (144)
27 EVA_EXAC ss1686742792 Apr 01, 2015 (144)
28 EVA_MGP ss1710997327 Apr 01, 2015 (144)
29 HAMMER_LAB ss1798386179 Sep 08, 2015 (146)
30 WEILL_CORNELL_DGM ss1921223448 Feb 12, 2016 (147)
31 JJLAB ss2021159559 Sep 14, 2016 (149)
32 USC_VALOUEV ss2149221962 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2239298327 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2625079125 Nov 08, 2017 (151)
35 GRF ss2703871416 Nov 08, 2017 (151)
36 GNOMAD ss2733343836 Nov 08, 2017 (151)
37 GNOMAD ss2746883368 Nov 08, 2017 (151)
38 GNOMAD ss2786531072 Nov 08, 2017 (151)
39 SWEGEN ss2991386114 Nov 08, 2017 (151)
40 ILLUMINA ss3628290526 Oct 11, 2018 (152)
41 ILLUMINA ss3636502780 Oct 11, 2018 (152)
42 ILLUMINA ss3638319809 Oct 11, 2018 (152)
43 EGCUT_WGS ss3659281434 Jul 13, 2019 (153)
44 EVA_DECODE ss3706057063 Jul 13, 2019 (153)
45 EVA_DECODE ss3706057064 Jul 13, 2019 (153)
46 ACPOP ss3729387004 Jul 13, 2019 (153)
47 EVA ss3758104963 Jul 13, 2019 (153)
48 KHV_HUMAN_GENOMES ss3802468891 Jul 13, 2019 (153)
49 EVA ss3823857104 Apr 25, 2020 (154)
50 EVA ss3825619569 Apr 25, 2020 (154)
51 EVA ss3827514714 Apr 25, 2020 (154)
52 SGDP_PRJ ss3854630538 Apr 25, 2020 (154)
53 KRGDB ss3900354070 Apr 25, 2020 (154)
54 KOGIC ss3950120503 Apr 25, 2020 (154)
55 FSA-LAB ss3984202994 Apr 26, 2021 (155)
56 FSA-LAB ss3984202995 Apr 26, 2021 (155)
57 EVA ss3986215686 Apr 26, 2021 (155)
58 TOPMED ss4545265937 Apr 26, 2021 (155)
59 TOPMED ss4545265938 Apr 26, 2021 (155)
60 TOMMO_GENOMICS ss5156576527 Apr 26, 2021 (155)
61 1000G_HIGH_COVERAGE ss5252094116 Oct 12, 2022 (156)
62 EVA ss5336150830 Oct 12, 2022 (156)
63 HUGCELL_USP ss5451699136 Oct 12, 2022 (156)
64 EVA ss5506802204 Oct 12, 2022 (156)
65 1000G_HIGH_COVERAGE ss5529473190 Oct 12, 2022 (156)
66 SANFORD_IMAGENETICS ss5630987239 Oct 12, 2022 (156)
67 TOMMO_GENOMICS ss5687484750 Oct 12, 2022 (156)
68 YY_MCH ss5803235848 Oct 12, 2022 (156)
69 EVA ss5821615519 Oct 12, 2022 (156)
70 EVA ss5848535556 Oct 12, 2022 (156)
71 EVA ss5852958283 Oct 12, 2022 (156)
72 EVA ss5934777871 Oct 12, 2022 (156)
73 EVA ss5957244669 Oct 12, 2022 (156)
74 1000Genomes NC_000002.11 - 220074793 Oct 11, 2018 (152)
75 1000Genomes_30x NC_000002.12 - 219210071 Oct 12, 2022 (156)
76 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 220074793 Oct 11, 2018 (152)
77 Genetic variation in the Estonian population NC_000002.11 - 220074793 Oct 11, 2018 (152)
78 ExAC

Submission ignored due to conflicting rows:
Row 6647868 (NC_000002.11:220074792:T:T 117695/121146, NC_000002.11:220074792:T:A 3451/121146)
Row 6647869 (NC_000002.11:220074792:T:T 121132/121146, NC_000002.11:220074792:T:C 14/121146)

- Oct 11, 2018 (152)
79 ExAC

Submission ignored due to conflicting rows:
Row 6647868 (NC_000002.11:220074792:T:T 117695/121146, NC_000002.11:220074792:T:A 3451/121146)
Row 6647869 (NC_000002.11:220074792:T:T 121132/121146, NC_000002.11:220074792:T:C 14/121146)

- Oct 11, 2018 (152)
80 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 91444033 (NC_000002.12:219210070:T:A 5416/140028)
Row 91444034 (NC_000002.12:219210070:T:C 12/140034)

- Apr 26, 2021 (155)
81 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 91444033 (NC_000002.12:219210070:T:A 5416/140028)
Row 91444034 (NC_000002.12:219210070:T:C 12/140034)

- Apr 26, 2021 (155)
82 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 2411014 (NC_000002.11:220074792:T:T 244549/251252, NC_000002.11:220074792:T:A 6703/251252)
Row 2411015 (NC_000002.11:220074792:T:T 251223/251252, NC_000002.11:220074792:T:C 29/251252)

- Jul 13, 2019 (153)
83 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 2411014 (NC_000002.11:220074792:T:T 244549/251252, NC_000002.11:220074792:T:A 6703/251252)
Row 2411015 (NC_000002.11:220074792:T:T 251223/251252, NC_000002.11:220074792:T:C 29/251252)

- Jul 13, 2019 (153)
84 GO Exome Sequencing Project NC_000002.11 - 220074793 Oct 11, 2018 (152)
85 Genome of the Netherlands Release 5 NC_000002.11 - 220074793 Apr 25, 2020 (154)
86 KOREAN population from KRGDB NC_000002.11 - 220074793 Apr 25, 2020 (154)
87 Korean Genome Project NC_000002.12 - 219210071 Apr 25, 2020 (154)
88 Medical Genome Project healthy controls from Spanish population NC_000002.11 - 220074793 Apr 25, 2020 (154)
89 Northern Sweden NC_000002.11 - 220074793 Jul 13, 2019 (153)
90 Qatari NC_000002.11 - 220074793 Apr 25, 2020 (154)
91 SGDP_PRJ NC_000002.11 - 220074793 Apr 25, 2020 (154)
92 Siberian NC_000002.11 - 220074793 Apr 25, 2020 (154)
93 8.3KJPN NC_000002.11 - 220074793 Apr 26, 2021 (155)
94 14KJPN NC_000002.12 - 219210071 Oct 12, 2022 (156)
95 TopMed

Submission ignored due to conflicting rows:
Row 349088816 (NC_000002.12:219210070:T:A 10138/264690)
Row 349088817 (NC_000002.12:219210070:T:C 24/264690)

- Apr 26, 2021 (155)
96 TopMed

Submission ignored due to conflicting rows:
Row 349088816 (NC_000002.12:219210070:T:A 10138/264690)
Row 349088817 (NC_000002.12:219210070:T:C 24/264690)

- Apr 26, 2021 (155)
97 UK 10K study - Twins NC_000002.11 - 220074793 Oct 11, 2018 (152)
98 A Vietnamese Genetic Variation Database NC_000002.11 - 220074793 Jul 13, 2019 (153)
99 ALFA NC_000002.12 - 219210071 Apr 26, 2021 (155)
100 ClinVar RCV001641603.2 Oct 12, 2022 (156)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss118084317, ss159845995, ss201760914, ss276903973, ss1587433639 NC_000002.10:219783036:T:A NC_000002.12:219210070:T:A (self)
12823243, 7093114, 5019682, 315507, 3109766, 7531464, 113866, 2671869, 3265378, 6647518, 1738316, 14545834, 7093114, 1541313, ss219822475, ss239050236, ss479154414, ss489853056, ss535383102, ss556231152, ss649896689, ss712488632, ss832615413, ss977977966, ss1069954234, ss1301715447, ss1428916098, ss1605831095, ss1648825128, ss1686742791, ss1710997327, ss1798386179, ss1921223448, ss2021159559, ss2149221962, ss2625079125, ss2703871416, ss2733343836, ss2746883368, ss2786531072, ss2991386114, ss3628290526, ss3636502780, ss3638319809, ss3659281434, ss3729387004, ss3758104963, ss3823857104, ss3825619569, ss3827514714, ss3854630538, ss3900354070, ss3984202994, ss3984202995, ss3986215686, ss5156576527, ss5336150830, ss5506802204, ss5630987239, ss5821615519, ss5848535556, ss5957244669 NC_000002.11:220074792:T:A NC_000002.12:219210070:T:A (self)
RCV001641603.2, 16999125, 6498504, 21321854, 97137879, ss2239298327, ss3706057063, ss3802468891, ss3950120503, ss4545265937, ss5252094116, ss5451699136, ss5529473190, ss5687484750, ss5803235848, ss5852958283, ss5934777871 NC_000002.12:219210070:T:A NC_000002.12:219210070:T:A (self)
ss152536304, ss154729686, ss159100352, ss159102617, ss168870679 NT_005403.17:70284210:T:A NC_000002.12:219210070:T:A (self)
ss1686742792, ss2733343836 NC_000002.11:220074792:T:C NC_000002.12:219210070:T:C (self)
97137879, ss2239298327, ss3706057064, ss4545265938 NC_000002.12:219210070:T:C NC_000002.12:219210070:T:C (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 rs73993544

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.post761+d5e8e07