Name: rs1060081
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.

rs1060081

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:32579004 (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=0.36442 (33172/91028, GnomAD)
C=0.12279 (10949/89172, GnomAD_exome)
C=0.36255 (10036/27682, 14KJPN) (+ 10 more)
C=0.18827 (4113/21846, ExAC)
C=0.31702 (5312/16756, 8.3KJPN)
C=0.35577 (5836/16404, ALFA)
C=0.4021 (2575/6404, 1000G_30x)
C=0.3372 (988/2930, KOREAN)
C=0.028 (15/534, MGP)
T=0.493 (205/416, SGDP_PRJ)
C=0.315 (63/200, Qatari)
T=0.50 (21/42, Siberian)
C=0.50 (21/42, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: HLA-DRB1 : 3 Prime UTR 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	16404	T=0.64423	C=0.35577
European	Sub	12128	T=0.66029	C=0.33971
African	Sub	2830	T=0.5788	C=0.4212
African Others	Sub	108	T=0.611	C=0.389
African American	Sub	2722	T=0.5775	C=0.4225
Asian	Sub	108	T=0.676	C=0.324
East Asian	Sub	84	T=0.63	C=0.37
Other Asian	Sub	24	T=0.83	C=0.17
Latin American 1	Sub	146	T=0.664	C=0.336
Latin American 2	Sub	610	T=0.621	C=0.379
South Asian	Sub	94	T=0.68	C=0.32
Other	Sub	488	T=0.633	C=0.367

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
gnomAD - Genomes	Global	Study-wide	91028	T=0.63558	C=0.36442
gnomAD - Genomes	European	Sub	50326	T=0.66622	C=0.33378
gnomAD - Genomes	African	Sub	27434	T=0.57852	C=0.42148
gnomAD - Genomes	American	Sub	7542	T=0.6449	C=0.3551
gnomAD - Genomes	Ashkenazi Jewish	Sub	2308	T=0.6330	C=0.3670
gnomAD - Genomes	East Asian	Sub	2092	T=0.6157	C=0.3843
gnomAD - Genomes	Other	Sub	1326	T=0.6365	C=0.3635
gnomAD - Exomes	Global	Study-wide	89172	T=0.87721	C=0.12279
gnomAD - Exomes	European	Sub	49970	T=0.89582	C=0.10418
gnomAD - Exomes	Asian	Sub	17454	T=0.85241	C=0.14759
gnomAD - Exomes	American	Sub	10520	T=0.85276	C=0.14724
gnomAD - Exomes	Ashkenazi Jewish	Sub	4582	T=0.7992	C=0.2008
gnomAD - Exomes	African	Sub	4250	T=0.9111	C=0.0889
gnomAD - Exomes	Other	Sub	2396	T=0.8664	C=0.1336
14KJPN	JAPANESE	Study-wide	27682	T=0.63745	C=0.36255
ExAC	Global	Study-wide	21846	T=0.81173	C=0.18827
ExAC	Europe	Sub	11508	T=0.84107	C=0.15893
ExAC	Asian	Sub	7510	T=0.7659	C=0.2341
ExAC	African	Sub	2194	T=0.8040	C=0.1960
ExAC	American	Sub	400	T=0.838	C=0.163
ExAC	Other	Sub	234	T=0.868	C=0.132
8.3KJPN	JAPANESE	Study-wide	16756	T=0.68298	C=0.31702
Allele Frequency Aggregator	Total	Global	16404	T=0.64423	C=0.35577
Allele Frequency Aggregator	European	Sub	12128	T=0.66029	C=0.33971
Allele Frequency Aggregator	African	Sub	2830	T=0.5788	C=0.4212
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.621	C=0.379
Allele Frequency Aggregator	Other	Sub	488	T=0.633	C=0.367
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.664	C=0.336
Allele Frequency Aggregator	Asian	Sub	108	T=0.676	C=0.324
Allele Frequency Aggregator	South Asian	Sub	94	T=0.68	C=0.32
1000Genomes_30x	Global	Study-wide	6404	T=0.5979	C=0.4021
1000Genomes_30x	African	Sub	1786	T=0.4978	C=0.5022
1000Genomes_30x	Europe	Sub	1266	T=0.6256	C=0.3744
1000Genomes_30x	South Asian	Sub	1202	T=0.6847	C=0.3153
1000Genomes_30x	East Asian	Sub	1170	T=0.6197	C=0.3803
1000Genomes_30x	American	Sub	980	T=0.612	C=0.388
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.6628	C=0.3372
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	T=0.972	C=0.028
SGDP_PRJ	Global	Study-wide	416	T=0.493	C=0.507
Qatari	Global	Study-wide	200	T=0.685	C=0.315
Siberian	Global	Study-wide	42	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 6	NC_000006.12:g.32579004T>C
GRCh37.p13 chr 6	NC_000006.11:g.32546781T>C
DR51 genomic region	NG_002432.1:g.126272T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.3998282T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.3998388T>C
DR52 genomic region	NG_002392.2:g.124492T>C
HLA-DRB1 RefSeqGene	NG_029921.1:g.18166A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.3779241T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.3784837T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.3814775T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.3820360T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.3989183T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.3994803T>C

Gene: HLA-DRB1, major histocompatibility complex, class II, DR beta 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
HLA-DRB1 transcript variant 1	NM_002124.4:c.*87=	N/A	3 Prime UTR 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 6	NC_000006.12:g.32579004=	NC_000006.12:g.32579004T>C
GRCh37.p13 chr 6	NC_000006.11:g.32546781=	NC_000006.11:g.32546781T>C
DR51 genomic region	NG_002432.1:g.126272=	NG_002432.1:g.126272T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.3:g.3998282=	NT_113891.3:g.3998282T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1	NT_113891.2:g.3998388=	NT_113891.2:g.3998388T>C
DR52 genomic region	NG_002392.2:g.124492=	NG_002392.2:g.124492T>C
HLA-DRB1 RefSeqGene	NG_029921.1:g.18166=	NG_029921.1:g.18166A>G
HLA-DRB1 transcript variant 1	NM_002124.4:c.*87=	NM_002124.4:c.*87A>G
HLA-DRB1 transcript variant 1	NM_002124.3:c.*87=	NM_002124.3:c.*87A>G
HLA-DRB1 transcript variant 2	NM_001243965.1:c.*86=	NM_001243965.1:c.*86A>G
HLA-DRB1 transcript variant 4	NM_001359194.1:c.*87=	NM_001359194.1:c.*87A>G
HLA-DRB1 transcript variant 3	NM_001359193.1:c.*87=	NM_001359193.1:c.*87A>G
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.2:g.3779241=	NT_167248.2:g.3779241T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1	NT_167248.1:g.3784837=	NT_167248.1:g.3784837T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.2:g.3814775=	NT_167245.2:g.3814775T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1	NT_167245.1:g.3820360=	NT_167245.1:g.3820360T>C
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.2:g.3989183=	NT_167246.2:g.3989183T>C
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1	NT_167246.1:g.3994803=	NT_167246.1:g.3994803T>C
HLA-DRB1 transcript variant X1	XM_024452553.2:c.*86=	XM_024452553.2:c.*86A>G
HLA-DRB1 transcript variant X3	XM_024452553.1:c.*86=	XM_024452553.1:c.*86A>G
HLA-DRB2 transcript	NM_001037638.1:c.*87=	NM_001037638.1:c.*87A>G
HLA-DRB1 transcript variant X2	XM_047443024.1:c.*86=	XM_047443024.1:c.*86A>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#.

49 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	LEE	ss1543224	Oct 05, 2000 (86)
2	LEE	ss4435635	May 29, 2002 (106)
3	SEQUENOM	ss24813253	Sep 20, 2004 (126)
4	SI_MHC_SNP	ss52085252	Oct 18, 2006 (130)
5	ILLUMINA-UK	ss116399253	Feb 14, 2009 (130)
6	BUSHMAN	ss201641113	Jul 04, 2010 (132)
7	1000GENOMES	ss210641171	Jul 14, 2010 (132)
8	1000GENOMES	ss211815301	Jul 14, 2010 (132)
9	1000GENOMES	ss222311652	Jul 14, 2010 (132)
10	1000GENOMES	ss233408443	Jul 14, 2010 (132)
11	1000GENOMES	ss240476783	Jul 15, 2010 (132)
12	BL	ss254201944	May 09, 2011 (134)
13	GMI	ss278735616	May 04, 2012 (137)
14	SSMP	ss653046162	Apr 25, 2013 (138)
15	EVA-GONL	ss982779311	Aug 21, 2014 (142)
16	EVA_EXAC	ss1688257517	Apr 01, 2015 (144)
17	EVA_MGP	ss1711123474	Apr 01, 2015 (144)
18	HAMMER_LAB	ss1804363683	Sep 08, 2015 (146)
19	YSAMUELS	ss1849944502	Feb 12, 2016 (147)
20	WEILL_CORNELL_DGM	ss1926034692	Feb 12, 2016 (147)
21	JJLAB	ss2023650399	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2151823436	Dec 20, 2016 (150)
23	SYSTEMSBIOZJU	ss2626312885	Nov 08, 2017 (151)
24	GRF	ss2707417172	Nov 08, 2017 (151)
25	ILLUMINA	ss2711071405	Nov 08, 2017 (151)
26	GNOMAD	ss2735691441	Nov 08, 2017 (151)
27	GNOMAD	ss2747594164	Nov 08, 2017 (151)
28	GNOMAD	ss2837507206	Nov 08, 2017 (151)
29	SWEGEN	ss2998826961	Nov 08, 2017 (151)
30	BIOINF_KMB_FNS_UNIBA	ss3025613977	Nov 08, 2017 (151)
31	OMUKHERJEE_ADBS	ss3646336084	Oct 12, 2018 (152)
32	EVA_DECODE	ss3716929523	Jul 13, 2019 (153)
33	EVA	ss3764838889	Jul 13, 2019 (153)
34	EVA	ss3829842557	Apr 26, 2020 (154)
35	SGDP_PRJ	ss3864288219	Apr 26, 2020 (154)
36	KRGDB	ss3911066091	Apr 26, 2020 (154)
37	EVA	ss3986034922	Apr 26, 2021 (155)
38	TOMMO_GENOMICS	ss5176892613	Apr 26, 2021 (155)
39	EVA	ss5237190765	Apr 26, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5553635914	Oct 17, 2022 (156)
41	EVA	ss5623935949	Oct 17, 2022 (156)
42	SANFORD_IMAGENETICS	ss5640117951	Oct 17, 2022 (156)
43	TOMMO_GENOMICS	ss5714760709	Oct 17, 2022 (156)
44	EVA	ss5800055800	Oct 17, 2022 (156)
45	YY_MCH	ss5807331718	Oct 17, 2022 (156)
46	EVA	ss5842043168	Oct 17, 2022 (156)
47	EVA	ss5848653408	Oct 17, 2022 (156)
48	EVA	ss5936531051	Oct 17, 2022 (156)
49	EVA	ss5968611778	Oct 17, 2022 (156)
50	1000Genomes_30x	NC_000006.12 - 32579004	Oct 17, 2022 (156)
51	ExAC	NC_000006.11 - 32546781	Oct 12, 2018 (152)
52	gnomAD - Genomes	NC_000006.12 - 32579004	Apr 26, 2021 (155)
53	gnomAD - Exomes	NC_000006.11 - 32546781	Jul 13, 2019 (153)
54	KOREAN population from KRGDB	NC_000006.11 - 32546781	Apr 26, 2020 (154)
55	Medical Genome Project healthy controls from Spanish population	NC_000006.11 - 32546781	Apr 26, 2020 (154)
56	Qatari	NC_000006.11 - 32546781	Apr 26, 2020 (154)
57	SGDP_PRJ	NC_000006.11 - 32546781	Apr 26, 2020 (154)
58	Siberian	NC_000006.11 - 32546781	Apr 26, 2020 (154)
59	8.3KJPN	NC_000006.11 - 32546781	Apr 26, 2021 (155)
60	14KJPN	NC_000006.12 - 32579004	Oct 17, 2022 (156)
61	ALFA	NC_000006.12 - 32579004	Apr 26, 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).

Associated ID	History Updated (Build)
rs3205666	Jul 03, 2002 (106)
rs16822525	Oct 17, 2006 (127)
rs41287202	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1543224, ss4435635, ss24813253, ss116399253, ss201641113, ss210641171, ss211815301, ss254201944, ss278735616	NC_000006.10:32654758:T:C	NC_000006.12:32579003:T:C	(self)
8284818, 4833375, 18243485, 239234, 8076622, 16305199, 4339790, 34861920, ss222311652, ss233408443, ss240476783, ss653046162, ss982779311, ss1688257517, ss1711123474, ss1804363683, ss1849944502, ss1926034692, ss2023650399, ss2151823436, ss2626312885, ss2707417172, ss2711071405, ss2735691441, ss2747594164, ss2837507206, ss2998826961, ss3646336084, ss3764838889, ss3829842557, ss3864288219, ss3911066091, ss3986034922, ss5176892613, ss5623935949, ss5640117951, ss5800055800, ss5842043168, ss5848653408, ss5936531051, ss5968611778	NC_000006.11:32546780:T:C	NC_000006.12:32579003:T:C	(self)
41161849, 221402953, 48597813, 14621831136, ss3025613977, ss3716929523, ss5237190765, ss5553635914, ss5714760709, ss5807331718	NC_000006.12:32579003:T:C	NC_000006.12:32579003:T:C	(self)
ss52085252	NT_007592.15:32486780:T:C	NC_000006.12:32579003: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 rs1060081

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

rs1060081