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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.

rs78861870

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr2:219210323 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.038351 (10151/264690, TOPMED)
C=0.026697 (6712/251416, GnomAD_exome)
C=0.038788 (5440/140248, GnomAD) (+ 19 more)
C=0.028450 (3452/121336, ExAC)
C=0.02374 (1487/62626, ALFA)
C=0.10334 (1732/16760, 8.3KJPN)
C=0.03583 (466/13006, GO-ESP)
C=0.0489 (245/5008, 1000G)
C=0.0400 (179/4480, Estonian)
C=0.0106 (41/3854, ALSPAC)
C=0.0100 (37/3708, TWINSUK)
C=0.1400 (410/2928, KOREAN)
C=0.1436 (263/1832, Korea1K)
C=0.006 (6/998, GoNL)
C=0.054 (33/610, Vietnamese)
C=0.017 (10/600, NorthernSweden)
C=0.002 (1/534, MGP)
C=0.033 (10/304, FINRISK)
C=0.051 (11/216, Qatari)
T=0.48 (27/56, SGDP_PRJ)
T=0.50 (6/12, Siberian)
C=0.50 (6/12, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ABCB6 : 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 2 NC_000002.12:g.219210323T>C
GRCh37.p13 chr 2 NC_000002.11:g.220075045T>C
Langereis blood group RefSeqGene (LRG_824) NG_032110.1:g.13668A>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.2214-25A…

NM_001349828.2:c.2214-25A>G

N/A Intron Variant
ABCB6 transcript variant 1 NM_005689.4:c.2352-25A>G 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 (New)
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 62626 T=0.97626 C=0.02374
European Sub 46406 T=0.98479 C=0.01521
African Sub 7196 T=0.9198 C=0.0802
African Others Sub 244 T=0.914 C=0.086
African American Sub 6952 T=0.9200 C=0.0800
Asian Sub 502 T=0.890 C=0.110
East Asian Sub 404 T=0.894 C=0.106
Other Asian Sub 98 T=0.88 C=0.12
Latin American 1 Sub 298 T=0.960 C=0.040
Latin American 2 Sub 1450 T=0.9931 C=0.0069
South Asian Sub 170 T=0.976 C=0.024
Other Sub 6604 T=0.9814 C=0.0186


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 T=0.961649 C=0.038351
gnomAD - Exomes Global Study-wide 251416 T=0.973303 C=0.026697
gnomAD - Exomes European Sub 135362 T=0.983112 C=0.016888
gnomAD - Exomes Asian Sub 49006 T=0.95141 C=0.04859
gnomAD - Exomes American Sub 34592 T=0.99222 C=0.00778
gnomAD - Exomes African Sub 16246 T=0.91204 C=0.08796
gnomAD - Exomes Ashkenazi Jewish Sub 10076 T=0.97866 C=0.02134
gnomAD - Exomes Other Sub 6134 T=0.9785 C=0.0215
gnomAD - Genomes Global Study-wide 140248 T=0.961212 C=0.038788
gnomAD - Genomes European Sub 75950 T=0.98483 C=0.01517
gnomAD - Genomes African Sub 42032 T=0.91476 C=0.08524
gnomAD - Genomes American Sub 13662 T=0.98690 C=0.01310
gnomAD - Genomes Ashkenazi Jewish Sub 3322 T=0.9777 C=0.0223
gnomAD - Genomes East Asian Sub 3128 T=0.8798 C=0.1202
gnomAD - Genomes Other Sub 2154 T=0.9647 C=0.0353
ExAC Global Study-wide 121336 T=0.971550 C=0.028450
ExAC Europe Sub 73324 T=0.98288 C=0.01712
ExAC Asian Sub 25140 T=0.95326 C=0.04674
ExAC American Sub 11574 T=0.99335 C=0.00665
ExAC African Sub 10392 T=0.91080 C=0.08920
ExAC Other Sub 906 T=0.980 C=0.020
8.3KJPN JAPANESE Study-wide 16760 T=0.89666 C=0.10334
GO Exome Sequencing Project Global Study-wide 13006 T=0.96417 C=0.03583
GO Exome Sequencing Project European American Sub 8600 T=0.9890 C=0.0110
GO Exome Sequencing Project African American Sub 4406 T=0.9158 C=0.0842
1000Genomes Global Study-wide 5008 T=0.9511 C=0.0489
1000Genomes African Sub 1322 T=0.9123 C=0.0877
1000Genomes East Asian Sub 1008 T=0.9097 C=0.0903
1000Genomes Europe Sub 1006 T=0.9821 C=0.0179
1000Genomes South Asian Sub 978 T=0.987 C=0.013
1000Genomes American Sub 694 T=0.990 C=0.010
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9600 C=0.0400
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.9894 C=0.0106
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.9900 C=0.0100
KOREAN population from KRGDB KOREAN Study-wide 2928 T=0.8600 C=0.1400
Korean Genome Project KOREAN Study-wide 1832 T=0.8564 C=0.1436
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.994 C=0.006
A Vietnamese Genetic Variation Database Global Study-wide 610 T=0.946 C=0.054
Northern Sweden ACPOP Study-wide 600 T=0.983 C=0.017
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.998 C=0.002
FINRISK Finnish from FINRISK project Study-wide 304 T=0.967 C=0.033
Qatari Global Study-wide 216 T=0.949 C=0.051
SGDP_PRJ Global Study-wide 56 T=0.48 C=0.52
Siberian Global Study-wide 12 T=0.50 C=0.50
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= C
GRCh38.p13 chr 2 NC_000002.12:g.219210323= NC_000002.12:g.219210323T>C
GRCh37.p13 chr 2 NC_000002.11:g.220075045= NC_000002.11:g.220075045T>C
Langereis blood group RefSeqGene (LRG_824) NG_032110.1:g.13668= NG_032110.1:g.13668A>G
ABCB6 transcript variant 2 NM_001349828.2:c.2214-25= NM_001349828.2:c.2214-25A>G
ABCB6 transcript NM_005689.2:c.2352-25= NM_005689.2:c.2352-25A>G
ABCB6 transcript variant 1 NM_005689.4:c.2352-25= NM_005689.4:c.2352-25A>G
ABCB6 transcript variant X1 XM_005246215.1:c.2214-25= XM_005246215.1:c.2214-25A>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#.

70 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss152536309 Dec 01, 2009 (131)
2 ILLUMINA ss159102618 Dec 01, 2009 (131)
3 ILLUMINA ss159845996 Dec 01, 2009 (131)
4 ILLUMINA ss168870693 Jul 04, 2010 (132)
5 1000GENOMES ss219822477 Jul 14, 2010 (132)
6 1000GENOMES ss239050237 Jul 15, 2010 (132)
7 GMI ss276903975 May 04, 2012 (137)
8 ILLUMINA ss479154418 Sep 08, 2015 (146)
9 ILLUMINA ss480563170 May 04, 2012 (137)
10 ILLUMINA ss484016397 May 04, 2012 (137)
11 1000GENOMES ss489853058 May 04, 2012 (137)
12 CLINSEQ_SNP ss491800498 May 04, 2012 (137)
13 ILLUMINA ss533815159 Sep 08, 2015 (146)
14 TISHKOFF ss556231154 Apr 25, 2013 (138)
15 SSMP ss649896690 Apr 25, 2013 (138)
16 NHLBI-ESP ss712488637 Apr 25, 2013 (138)
17 ILLUMINA ss779765040 Aug 21, 2014 (142)
18 ILLUMINA ss781262024 Aug 21, 2014 (142)
19 ILLUMINA ss832615414 Aug 21, 2014 (142)
20 ILLUMINA ss833206103 Aug 21, 2014 (142)
21 ILLUMINA ss835240384 Aug 21, 2014 (142)
22 JMKIDD_LAB ss974445786 Aug 21, 2014 (142)
23 EVA-GONL ss977977968 Aug 21, 2014 (142)
24 JMKIDD_LAB ss1067445466 Aug 21, 2014 (142)
25 JMKIDD_LAB ss1069954236 Aug 21, 2014 (142)
26 1000GENOMES ss1301715456 Aug 21, 2014 (142)
27 DDI ss1428916099 Apr 01, 2015 (144)
28 BGI ss1558284888 Apr 01, 2015 (144)
29 EVA_FINRISK ss1584024007 Apr 01, 2015 (144)
30 EVA_DECODE ss1587433640 Apr 01, 2015 (144)
31 EVA_UK10K_ALSPAC ss1605831101 Apr 01, 2015 (144)
32 EVA_UK10K_TWINSUK ss1648825134 Apr 01, 2015 (144)
33 EVA_EXAC ss1686742828 Apr 01, 2015 (144)
34 EVA_MGP ss1710997330 Apr 01, 2015 (144)
35 HAMMER_LAB ss1798386185 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1921223450 Feb 12, 2016 (147)
37 JJLAB ss2021159560 Sep 14, 2016 (149)
38 USC_VALOUEV ss2149221963 Dec 20, 2016 (150)
39 HUMAN_LONGEVITY ss2239298347 Dec 20, 2016 (150)
40 TOPMED ss2405756851 Dec 20, 2016 (150)
41 SYSTEMSBIOZJU ss2625079126 Nov 08, 2017 (151)
42 ILLUMINA ss2633741866 Nov 08, 2017 (151)
43 GRF ss2703871417 Nov 08, 2017 (151)
44 GNOMAD ss2733343889 Nov 08, 2017 (151)
45 GNOMAD ss2746883386 Nov 08, 2017 (151)
46 GNOMAD ss2786531094 Nov 08, 2017 (151)
47 AFFY ss2985821491 Nov 08, 2017 (151)
48 SWEGEN ss2991386115 Nov 08, 2017 (151)
49 TOPMED ss3338865495 Nov 08, 2017 (151)
50 ILLUMINA ss3628290529 Oct 11, 2018 (152)
51 ILLUMINA ss3631701753 Oct 11, 2018 (152)
52 ILLUMINA ss3636502781 Oct 11, 2018 (152)
53 ILLUMINA ss3638319810 Oct 11, 2018 (152)
54 ILLUMINA ss3642156214 Oct 11, 2018 (152)
55 EGCUT_WGS ss3659281435 Jul 13, 2019 (153)
56 EVA_DECODE ss3706057066 Jul 13, 2019 (153)
57 ACPOP ss3729387005 Jul 13, 2019 (153)
58 EVA ss3758104966 Jul 13, 2019 (153)
59 KHV_HUMAN_GENOMES ss3802468894 Jul 13, 2019 (153)
60 EVA ss3823857110 Apr 25, 2020 (154)
61 EVA ss3825619571 Apr 25, 2020 (154)
62 EVA ss3827514715 Apr 25, 2020 (154)
63 SGDP_PRJ ss3854630542 Apr 25, 2020 (154)
64 KRGDB ss3900354076 Apr 25, 2020 (154)
65 KOGIC ss3950120509 Apr 25, 2020 (154)
66 FSA-LAB ss3984202996 Apr 26, 2021 (155)
67 FSA-LAB ss3984202997 Apr 26, 2021 (155)
68 EVA ss3986215688 Apr 26, 2021 (155)
69 TOPMED ss4545266011 Apr 26, 2021 (155)
70 TOMMO_GENOMICS ss5156576539 Apr 26, 2021 (155)
71 1000Genomes NC_000002.11 - 220075045 Oct 11, 2018 (152)
72 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 220075045 Oct 11, 2018 (152)
73 Genetic variation in the Estonian population NC_000002.11 - 220075045 Oct 11, 2018 (152)
74 ExAC NC_000002.11 - 220075045 Oct 11, 2018 (152)
75 FINRISK NC_000002.11 - 220075045 Apr 25, 2020 (154)
76 gnomAD - Genomes NC_000002.12 - 219210323 Apr 26, 2021 (155)
77 gnomAD - Exomes NC_000002.11 - 220075045 Jul 13, 2019 (153)
78 GO Exome Sequencing Project NC_000002.11 - 220075045 Oct 11, 2018 (152)
79 Genome of the Netherlands Release 5 NC_000002.11 - 220075045 Apr 25, 2020 (154)
80 KOREAN population from KRGDB NC_000002.11 - 220075045 Apr 25, 2020 (154)
81 Korean Genome Project NC_000002.12 - 219210323 Apr 25, 2020 (154)
82 Medical Genome Project healthy controls from Spanish population NC_000002.11 - 220075045 Apr 25, 2020 (154)
83 Northern Sweden NC_000002.11 - 220075045 Jul 13, 2019 (153)
84 Qatari NC_000002.11 - 220075045 Apr 25, 2020 (154)
85 SGDP_PRJ NC_000002.11 - 220075045 Apr 25, 2020 (154)
86 Siberian NC_000002.11 - 220075045 Apr 25, 2020 (154)
87 8.3KJPN NC_000002.11 - 220075045 Apr 26, 2021 (155)
88 TopMed NC_000002.12 - 219210323 Apr 26, 2021 (155)
89 UK 10K study - Twins NC_000002.11 - 220075045 Oct 11, 2018 (152)
90 A Vietnamese Genetic Variation Database NC_000002.11 - 220075045 Jul 13, 2019 (153)
91 ALFA NC_000002.12 - 219210323 Apr 26, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss159845996, ss276903975, ss484016397, ss491800498, ss1558284888, ss1587433640 NC_000002.10:219783288:T:C NC_000002.12:219210322:T:C (self)
12823252, 7093121, 5019683, 6647907, 20468, 2411079, 315513, 3109768, 7531470, 113869, 2671870, 3265380, 6647522, 1738317, 14545846, 7093121, 1541315, ss219822477, ss239050237, ss479154418, ss480563170, ss489853058, ss533815159, ss556231154, ss649896690, ss712488637, ss779765040, ss781262024, ss832615414, ss833206103, ss835240384, ss974445786, ss977977968, ss1067445466, ss1069954236, ss1301715456, ss1428916099, ss1584024007, ss1605831101, ss1648825134, ss1686742828, ss1710997330, ss1798386185, ss1921223450, ss2021159560, ss2149221963, ss2405756851, ss2625079126, ss2633741866, ss2703871417, ss2733343889, ss2746883386, ss2786531094, ss2985821491, ss2991386115, ss3628290529, ss3631701753, ss3636502781, ss3638319810, ss3642156214, ss3659281435, ss3729387005, ss3758104966, ss3823857110, ss3825619571, ss3827514715, ss3854630542, ss3900354076, ss3984202996, ss3984202997, ss3986215688, ss5156576539 NC_000002.11:220075044:T:C NC_000002.12:219210322:T:C (self)
91444092, 6498510, 217906739, 349088890, 11613247950, ss2239298347, ss3338865495, ss3706057066, ss3802468894, ss3950120509, ss4545266011 NC_000002.12:219210322:T:C NC_000002.12:219210322:T:C (self)
ss152536309, ss159102618, ss168870693 NT_005403.17:70284462:T:C NC_000002.12:219210322: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 rs78861870

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