Name: rs78861870
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.

rs78861870

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:219210323 (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=0.038351 (10151/264690, TOPMED)
C=0.026697 (6712/251416, GnomAD_exome)
C=0.038788 (5440/140248, GnomAD) (+ 21 more)
C=0.028450 (3452/121336, ExAC)
C=0.02374 (1487/62626, ALFA)
C=0.10246 (2895/28256, 14KJPN)
C=0.10334 (1732/16760, 8.3KJPN)
C=0.03583 (466/13006, GO-ESP)
C=0.0487 (312/6404, 1000G_30x)
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: Reported in ClinVar
Gene : Consequence: ABCB6 : 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	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

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=0.961649	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
Allele Frequency Aggregator	Total	Global	62626	T=0.97626	C=0.02374
Allele Frequency Aggregator	European	Sub	46406	T=0.98479	C=0.01521
Allele Frequency Aggregator	African	Sub	7196	T=0.9198	C=0.0802
Allele Frequency Aggregator	Other	Sub	6604	T=0.9814	C=0.0186
Allele Frequency Aggregator	Latin American 2	Sub	1450	T=0.9931	C=0.0069
Allele Frequency Aggregator	Asian	Sub	502	T=0.890	C=0.110
Allele Frequency Aggregator	Latin American 1	Sub	298	T=0.960	C=0.040
Allele Frequency Aggregator	South Asian	Sub	170	T=0.976	C=0.024
14KJPN	JAPANESE	Study-wide	28256	T=0.89754	C=0.10246
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_30x	Global	Study-wide	6404	T=0.9513	C=0.0487
1000Genomes_30x	African	Sub	1786	T=0.9110	C=0.0890
1000Genomes_30x	Europe	Sub	1266	T=0.9826	C=0.0174
1000Genomes_30x	South Asian	Sub	1202	T=0.9850	C=0.0150
1000Genomes_30x	East Asian	Sub	1170	T=0.9128	C=0.0872
1000Genomes_30x	American	Sub	980	T=0.989	C=0.011
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

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.219210323T>C
GRCh37.p13 chr 2	NC_000002.11:g.220075045T>C
LAN 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

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: C (allele ID: 1233749 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001645437.2	not provided	Benign

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 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
LAN 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

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#.

83 SubSNP, 23 Frequency, 1 ClinVar 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	SYSTEMSBIOZJU	ss2625079126	Nov 08, 2017 (151)
41	ILLUMINA	ss2633741866	Nov 08, 2017 (151)
42	GRF	ss2703871417	Nov 08, 2017 (151)
43	GNOMAD	ss2733343889	Nov 08, 2017 (151)
44	GNOMAD	ss2746883386	Nov 08, 2017 (151)
45	GNOMAD	ss2786531094	Nov 08, 2017 (151)
46	AFFY	ss2985821491	Nov 08, 2017 (151)
47	SWEGEN	ss2991386115	Nov 08, 2017 (151)
48	ILLUMINA	ss3628290529	Oct 11, 2018 (152)
49	ILLUMINA	ss3631701753	Oct 11, 2018 (152)
50	ILLUMINA	ss3636502781	Oct 11, 2018 (152)
51	ILLUMINA	ss3638319810	Oct 11, 2018 (152)
52	ILLUMINA	ss3642156214	Oct 11, 2018 (152)
53	EGCUT_WGS	ss3659281435	Jul 13, 2019 (153)
54	EVA_DECODE	ss3706057066	Jul 13, 2019 (153)
55	ACPOP	ss3729387005	Jul 13, 2019 (153)
56	EVA	ss3758104966	Jul 13, 2019 (153)
57	KHV_HUMAN_GENOMES	ss3802468894	Jul 13, 2019 (153)
58	EVA	ss3823857110	Apr 25, 2020 (154)
59	EVA	ss3825619571	Apr 25, 2020 (154)
60	EVA	ss3827514715	Apr 25, 2020 (154)
61	SGDP_PRJ	ss3854630542	Apr 25, 2020 (154)
62	KRGDB	ss3900354076	Apr 25, 2020 (154)
63	KOGIC	ss3950120509	Apr 25, 2020 (154)
64	FSA-LAB	ss3984202996	Apr 26, 2021 (155)
65	FSA-LAB	ss3984202997	Apr 26, 2021 (155)
66	EVA	ss3986215688	Apr 26, 2021 (155)
67	TOPMED	ss4545266011	Apr 26, 2021 (155)
68	TOMMO_GENOMICS	ss5156576539	Apr 26, 2021 (155)
69	1000G_HIGH_COVERAGE	ss5252094119	Oct 12, 2022 (156)
70	TRAN_CS_UWATERLOO	ss5314404819	Oct 12, 2022 (156)
71	EVA	ss5314809460	Oct 12, 2022 (156)
72	EVA	ss5336150844	Oct 12, 2022 (156)
73	HUGCELL_USP	ss5451699141	Oct 12, 2022 (156)
74	EVA	ss5506802205	Oct 12, 2022 (156)
75	1000G_HIGH_COVERAGE	ss5529473199	Oct 12, 2022 (156)
76	SANFORD_IMAGENETICS	ss5630987241	Oct 12, 2022 (156)
77	TOMMO_GENOMICS	ss5687484763	Oct 12, 2022 (156)
78	YY_MCH	ss5803235851	Oct 12, 2022 (156)
79	EVA	ss5821615520	Oct 12, 2022 (156)
80	EVA	ss5848535557	Oct 12, 2022 (156)
81	EVA	ss5852958284	Oct 12, 2022 (156)
82	EVA	ss5934777880	Oct 12, 2022 (156)
83	EVA	ss5957244674	Oct 12, 2022 (156)
84	1000Genomes	NC_000002.11 - 220075045	Oct 11, 2018 (152)
85	1000Genomes_30x	NC_000002.12 - 219210323	Oct 12, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 220075045	Oct 11, 2018 (152)
87	Genetic variation in the Estonian population	NC_000002.11 - 220075045	Oct 11, 2018 (152)
88	ExAC	NC_000002.11 - 220075045	Oct 11, 2018 (152)
89	FINRISK	NC_000002.11 - 220075045	Apr 25, 2020 (154)
90	gnomAD - Genomes	NC_000002.12 - 219210323	Apr 26, 2021 (155)
91	gnomAD - Exomes	NC_000002.11 - 220075045	Jul 13, 2019 (153)
92	GO Exome Sequencing Project	NC_000002.11 - 220075045	Oct 11, 2018 (152)
93	Genome of the Netherlands Release 5	NC_000002.11 - 220075045	Apr 25, 2020 (154)
94	KOREAN population from KRGDB	NC_000002.11 - 220075045	Apr 25, 2020 (154)
95	Korean Genome Project	NC_000002.12 - 219210323	Apr 25, 2020 (154)
96	Medical Genome Project healthy controls from Spanish population	NC_000002.11 - 220075045	Apr 25, 2020 (154)
97	Northern Sweden	NC_000002.11 - 220075045	Jul 13, 2019 (153)
98	Qatari	NC_000002.11 - 220075045	Apr 25, 2020 (154)
99	SGDP_PRJ	NC_000002.11 - 220075045	Apr 25, 2020 (154)
100	Siberian	NC_000002.11 - 220075045	Apr 25, 2020 (154)
101	8.3KJPN	NC_000002.11 - 220075045	Apr 26, 2021 (155)
102	14KJPN	NC_000002.12 - 219210323	Oct 12, 2022 (156)
103	TopMed	NC_000002.12 - 219210323	Apr 26, 2021 (155)
104	UK 10K study - Twins	NC_000002.11 - 220075045	Oct 11, 2018 (152)
105	A Vietnamese Genetic Variation Database	NC_000002.11 - 220075045	Jul 13, 2019 (153)
106	ALFA	NC_000002.12 - 219210323	Apr 26, 2021 (155)
107	ClinVar	RCV001645437.2	Oct 12, 2022 (156)

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, 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, ss5314809460, ss5336150844, ss5506802205, ss5630987241, ss5821615520, ss5848535557, ss5957244674	NC_000002.11:220075044:T:C	NC_000002.12:219210322:T:C	(self)
RCV001645437.2, 16999134, 91444092, 6498510, 21321867, 349088890, 11613247950, ss2239298347, ss3706057066, ss3802468894, ss3950120509, ss4545266011, ss5252094119, ss5314404819, ss5451699141, ss5529473199, ss5687484763, ss5803235851, ss5852958284, ss5934777880	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)

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

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

rs78861870