Name: rs2228479
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.

rs2228479

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:89919532 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.064287 (17016/264690, TOPMED)
A=0.084032 (19678/234174, ALFA)
A=0.065204 (9145/140252, GnomAD) (+ 21 more)
A=0.06700 (5272/78690, PAGE_STUDY)
A=0.09220 (2605/28254, 14KJPN)
A=0.09525 (1596/16756, 8.3KJPN)
A=0.0765 (490/6404, 1000G_30x)
A=0.0797 (399/5008, 1000G)
A=0.1042 (467/4480, Estonian)
A=0.0913 (352/3854, ALSPAC)
A=0.1076 (399/3708, TWINSUK)
A=0.1407 (411/2922, KOREAN)
A=0.1370 (251/1832, Korea1K)
A=0.0741 (126/1700, HapMap)
A=0.098 (98/998, GoNL)
A=0.179 (141/788, PRJEB37584)
A=0.358 (219/612, Vietnamese)
A=0.105 (63/600, NorthernSweden)
A=0.072 (22/304, FINRISK)
A=0.005 (1/216, Qatari)
G=0.38 (30/80, SGDP_PRJ)
A=0.11 (8/76, Ancient Sardinia)
G=0.50 (6/12, Siberian)
A=0.50 (6/12, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: MC1R : Missense Variant
Publications: 28 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	250634	G=0.917094	A=0.082906
European	Sub	206852	G=0.915742	A=0.084258
African	Sub	15296	G=0.98411	A=0.01589
African Others	Sub	520	G=0.998	A=0.002
African American	Sub	14776	G=0.98362	A=0.01638
Asian	Sub	3688	G=0.7495	A=0.2505
East Asian	Sub	2340	G=0.7530	A=0.2470
Other Asian	Sub	1348	G=0.7433	A=0.2567
Latin American 1	Sub	1034	G=0.9642	A=0.0358
Latin American 2	Sub	2276	G=0.9495	A=0.0505
South Asian	Sub	190	G=0.979	A=0.021
Other	Sub	21298	G=0.90483	A=0.09517

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	G=0.935713	A=0.064287
Allele Frequency Aggregator	Total	Global	234174	G=0.915968	A=0.084032
Allele Frequency Aggregator	European	Sub	196680	G=0.916031	A=0.083969
Allele Frequency Aggregator	Other	Sub	19846	G=0.90346	A=0.09654
Allele Frequency Aggregator	African	Sub	10460	G=0.98403	A=0.01597
Allele Frequency Aggregator	Asian	Sub	3688	G=0.7495	A=0.2505
Allele Frequency Aggregator	Latin American 2	Sub	2276	G=0.9495	A=0.0505
Allele Frequency Aggregator	Latin American 1	Sub	1034	G=0.9642	A=0.0358
Allele Frequency Aggregator	South Asian	Sub	190	G=0.979	A=0.021
gnomAD - Genomes	Global	Study-wide	140252	G=0.934796	A=0.065204
gnomAD - Genomes	European	Sub	75944	G=0.91324	A=0.08676
gnomAD - Genomes	African	Sub	42048	G=0.98385	A=0.01615
gnomAD - Genomes	American	Sub	13664	G=0.95528	A=0.04472
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.9374	A=0.0626
gnomAD - Genomes	East Asian	Sub	3120	G=0.7090	A=0.2910
gnomAD - Genomes	Other	Sub	2152	G=0.9303	A=0.0697
The PAGE Study	Global	Study-wide	78690	G=0.93300	A=0.06700
The PAGE Study	AfricanAmerican	Sub	32512	G=0.98053	A=0.01947
The PAGE Study	Mexican	Sub	10810	G=0.95291	A=0.04709
The PAGE Study	Asian	Sub	8314	G=0.8559	A=0.1441
The PAGE Study	PuertoRican	Sub	7918	G=0.9588	A=0.0412
The PAGE Study	NativeHawaiian	Sub	4532	G=0.5351	A=0.4649
The PAGE Study	Cuban	Sub	4228	G=0.9544	A=0.0456
The PAGE Study	Dominican	Sub	3828	G=0.9768	A=0.0232
The PAGE Study	CentralAmerican	Sub	2450	G=0.9743	A=0.0257
The PAGE Study	SouthAmerican	Sub	1982	G=0.9763	A=0.0237
The PAGE Study	NativeAmerican	Sub	1260	G=0.9310	A=0.0690
The PAGE Study	SouthAsian	Sub	856	G=0.977	A=0.023
14KJPN	JAPANESE	Study-wide	28254	G=0.90780	A=0.09220
8.3KJPN	JAPANESE	Study-wide	16756	G=0.90475	A=0.09525
1000Genomes_30x	Global	Study-wide	6404	G=0.9233	A=0.0765, C=0.0002
1000Genomes_30x	African	Sub	1786	G=0.9961	A=0.0039, C=0.0000
1000Genomes_30x	Europe	Sub	1266	G=0.9336	A=0.0656, C=0.0008
1000Genomes_30x	South Asian	Sub	1202	G=0.9792	A=0.0208, C=0.0000
1000Genomes_30x	East Asian	Sub	1170	G=0.7017	A=0.2983, C=0.0000
1000Genomes_30x	American	Sub	980	G=0.973	A=0.027, C=0.000
1000Genomes	Global	Study-wide	5008	G=0.9203	A=0.0797
1000Genomes	African	Sub	1322	G=0.9962	A=0.0038
1000Genomes	East Asian	Sub	1008	G=0.7113	A=0.2887
1000Genomes	Europe	Sub	1006	G=0.9314	A=0.0686
1000Genomes	South Asian	Sub	978	G=0.982	A=0.018
1000Genomes	American	Sub	694	G=0.977	A=0.023
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.8958	A=0.1042
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9087	A=0.0913
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8924	A=0.1076
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.8593	A=0.1407
Korean Genome Project	KOREAN	Study-wide	1832	G=0.8630	A=0.1370
HapMap	Global	Study-wide	1700	G=0.9259	A=0.0741
HapMap	American	Sub	764	G=0.898	A=0.102
HapMap	African	Sub	508	G=0.994	A=0.006
HapMap	Asian	Sub	252	G=0.869	A=0.131
HapMap	Europe	Sub	176	G=0.932	A=0.068
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.902	A=0.098
CNV burdens in cranial meningiomas	Global	Study-wide	788	G=0.821	A=0.179
CNV burdens in cranial meningiomas	CRM	Sub	788	G=0.821	A=0.179
A Vietnamese Genetic Variation Database	Global	Study-wide	612	G=0.642	A=0.358
Northern Sweden	ACPOP	Study-wide	600	G=0.895	A=0.105
FINRISK	Finnish from FINRISK project	Study-wide	304	G=0.928	A=0.072
Qatari	Global	Study-wide	216	G=0.995	A=0.005
SGDP_PRJ	Global	Study-wide	80	G=0.38	A=0.62
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	76	G=0.89	A=0.11
Siberian	Global	Study-wide	12	G=0.50	A=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 16	NC_000016.10:g.89919532G>A
GRCh38.p14 chr 16	NC_000016.10:g.89919532G>C
GRCh37.p13 chr 16	NC_000016.9:g.89985940G>A
GRCh37.p13 chr 16	NC_000016.9:g.89985940G>C
TUBB3 RefSeqGene	NG_027810.1:g.2524G>A
TUBB3 RefSeqGene	NG_027810.1:g.2524G>C
MC1R RefSeqGene	NG_012026.1:g.6654G>A
MC1R RefSeqGene	NG_012026.1:g.6654G>C

Gene: MC1R, melanocortin 1 receptor (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MC1R transcript	NM_002386.4:c.274G>A	V [GTG] > M [ATG]	Coding Sequence Variant
melanocyte-stimulating hormone receptor	NP_002377.4:p.Val92Met	V (Val) > M (Met)	Missense Variant
MC1R transcript	NM_002386.4:c.274G>C	V [GTG] > L [CTG]	Coding Sequence Variant
melanocyte-stimulating hormone receptor	NP_002377.4:p.Val92Leu	V (Val) > L (Leu)	Missense 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: A (allele ID: 29347 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000015378.29	Skin/hair/eye pigmentation 2, red hair/fair skin	Association
RCV000015379.29	Skin/hair/eye pigmentation 2, blond hair/fair skin	Association
RCV000247471.1	not specified	Benign
RCV000278283.7	Melanoma, cutaneous malignant, susceptibility to, 5	Benign
RCV001707509.1	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	G=	A	C
GRCh38.p14 chr 16	NC_000016.10:g.89919532=	NC_000016.10:g.89919532G>A	NC_000016.10:g.89919532G>C
GRCh37.p13 chr 16	NC_000016.9:g.89985940=	NC_000016.9:g.89985940G>A	NC_000016.9:g.89985940G>C
TUBB3 RefSeqGene	NG_027810.1:g.2524=	NG_027810.1:g.2524G>A	NG_027810.1:g.2524G>C
MC1R RefSeqGene	NG_012026.1:g.6654=	NG_012026.1:g.6654G>A	NG_012026.1:g.6654G>C
MC1R transcript	NM_002386.4:c.274=	NM_002386.4:c.274G>A	NM_002386.4:c.274G>C
MC1R transcript	NM_002386.3:c.274=	NM_002386.3:c.274G>A	NM_002386.3:c.274G>C
melanocyte-stimulating hormone receptor	NP_002377.4:p.Val92=	NP_002377.4:p.Val92Met	NP_002377.4:p.Val92Leu

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#.

131 SubSNP, 27 Frequency, 5 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	WIAF-CSNP	ss3173167	Aug 15, 2001 (98)
2	PGA-UW-FHCRC	ss4472755	Jul 03, 2002 (106)
3	CSHL-HAPMAP	ss16697812	Feb 27, 2004 (120)
4	ABI	ss40647778	Mar 13, 2006 (126)
5	SNP500CANCER	ss48295622	Mar 13, 2006 (126)
6	RIKENSNPRC	ss49848775	Mar 13, 2006 (126)
7	ILLUMINA	ss74900011	Dec 07, 2007 (129)
8	ILLUMINA	ss160517278	Dec 01, 2009 (131)
9	ENSEMBL	ss161821088	Dec 01, 2009 (131)
10	ILLUMINA	ss173192590	Jul 04, 2010 (132)
11	1000GENOMES	ss237150928	Jul 15, 2010 (132)
12	1000GENOMES	ss243467201	Jul 15, 2010 (132)
13	OMICIA	ss244239407	May 27, 2010 (132)
14	OMIM-CURATED-RECORDS	ss275515487	Nov 24, 2010 (133)
15	GMI	ss282656951	May 04, 2012 (137)
16	ILLUMINA	ss480471838	May 04, 2012 (137)
17	ILLUMINA	ss480486170	May 04, 2012 (137)
18	ILLUMINA	ss481283413	Sep 08, 2015 (146)
19	ILLUMINA	ss485033394	May 04, 2012 (137)
20	EXOME_CHIP	ss491513792	May 04, 2012 (137)
21	CLINSEQ_SNP	ss491725585	May 04, 2012 (137)
22	ILLUMINA	ss537057490	Sep 08, 2015 (146)
23	SSMP	ss660892025	Apr 25, 2013 (138)
24	NHLBI-ESP	ss713334828	Apr 25, 2013 (138)
25	ILLUMINA	ss778699398	Sep 08, 2015 (146)
26	ILLUMINA	ss780722550	Sep 08, 2015 (146)
27	ILLUMINA	ss782962943	Sep 08, 2015 (146)
28	ILLUMINA	ss783398378	Sep 08, 2015 (146)
29	ILLUMINA	ss783924990	Sep 08, 2015 (146)
30	ILLUMINA	ss832219180	Sep 08, 2015 (146)
31	ILLUMINA	ss834158305	Sep 08, 2015 (146)
32	EVA-GONL	ss992830727	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1067565420	Aug 21, 2014 (142)
34	JMKIDD_LAB	ss1080869835	Aug 21, 2014 (142)
35	1000GENOMES	ss1357561431	Aug 21, 2014 (142)
36	EVA_FINRISK	ss1584102409	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1635117232	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1678111265	Apr 01, 2015 (144)
39	EVA_EXAC	ss1692487434	Apr 01, 2015 (144)
40	EVA_EXAC	ss1692487435	Apr 01, 2015 (144)
41	EVA_DECODE	ss1696872306	Apr 01, 2015 (144)
42	EVA_SVP	ss1713563807	Apr 01, 2015 (144)
43	ILLUMINA	ss1752213133	Sep 08, 2015 (146)
44	ILLUMINA	ss1752213134	Sep 08, 2015 (146)
45	ILLUMINA	ss1917911984	Feb 12, 2016 (147)
46	WEILL_CORNELL_DGM	ss1936272971	Feb 12, 2016 (147)
47	ILLUMINA	ss1946424245	Feb 12, 2016 (147)
48	ILLUMINA	ss1959711631	Feb 12, 2016 (147)
49	AMU	ss1971464519	Jul 19, 2016 (147)
50	JJLAB	ss2028926295	Sep 14, 2016 (149)
51	ILLUMINA	ss2095070733	Dec 20, 2016 (150)
52	USC_VALOUEV	ss2157367874	Dec 20, 2016 (150)
53	HUMAN_LONGEVITY	ss2214824161	Dec 20, 2016 (150)
54	SYSTEMSBIOZJU	ss2628953374	Nov 08, 2017 (151)
55	ILLUMINA	ss2633363337	Nov 08, 2017 (151)
56	ILLUMINA	ss2635067379	Nov 08, 2017 (151)
57	GRF	ss2701904641	Nov 08, 2017 (151)
58	GNOMAD	ss2742271273	Nov 08, 2017 (151)
59	GNOMAD	ss2749635765	Nov 08, 2017 (151)
60	GNOMAD	ss2946702198	Nov 08, 2017 (151)
61	AFFY	ss2985080445	Nov 08, 2017 (151)
62	AFFY	ss2985718375	Nov 08, 2017 (151)
63	SWEGEN	ss3015041387	Nov 08, 2017 (151)
64	ILLUMINA	ss3021742085	Nov 08, 2017 (151)
65	BIOINF_KMB_FNS_UNIBA	ss3028280823	Nov 08, 2017 (151)
66	CSHL	ss3351606488	Nov 08, 2017 (151)
67	ILLUMINA	ss3627602938	Oct 12, 2018 (152)
68	ILLUMINA	ss3627602939	Oct 12, 2018 (152)
69	ILLUMINA	ss3631346731	Oct 12, 2018 (152)
70	ILLUMINA	ss3633132162	Oct 12, 2018 (152)
71	ILLUMINA	ss3633838990	Oct 12, 2018 (152)
72	ILLUMINA	ss3634658681	Oct 12, 2018 (152)
73	ILLUMINA	ss3634658682	Oct 12, 2018 (152)
74	ILLUMINA	ss3635527015	Oct 12, 2018 (152)
75	ILLUMINA	ss3636350093	Oct 12, 2018 (152)
76	ILLUMINA	ss3637278510	Oct 12, 2018 (152)
77	ILLUMINA	ss3638143981	Oct 12, 2018 (152)
78	ILLUMINA	ss3640366001	Oct 12, 2018 (152)
79	ILLUMINA	ss3640366002	Oct 12, 2018 (152)
80	ILLUMINA	ss3643123675	Oct 12, 2018 (152)
81	ILLUMINA	ss3644677326	Oct 12, 2018 (152)
82	OMUKHERJEE_ADBS	ss3646500355	Oct 12, 2018 (152)
83	ILLUMINA	ss3652154483	Oct 12, 2018 (152)
84	ILLUMINA	ss3652154484	Oct 12, 2018 (152)
85	ILLUMINA	ss3653852542	Oct 12, 2018 (152)
86	EGCUT_WGS	ss3682019185	Jul 13, 2019 (153)
87	EVA_DECODE	ss3699905741	Jul 13, 2019 (153)
88	ILLUMINA	ss3725591483	Jul 13, 2019 (153)
89	ACPOP	ss3741791956	Jul 13, 2019 (153)
90	ILLUMINA	ss3744436933	Jul 13, 2019 (153)
91	ILLUMINA	ss3744959044	Jul 13, 2019 (153)
92	ILLUMINA	ss3744959045	Jul 13, 2019 (153)
93	EVA	ss3754343116	Jul 13, 2019 (153)
94	PAGE_CC	ss3771903545	Jul 13, 2019 (153)
95	ILLUMINA	ss3772457150	Jul 13, 2019 (153)
96	ILLUMINA	ss3772457151	Jul 13, 2019 (153)
97	KHV_HUMAN_GENOMES	ss3819613402	Jul 13, 2019 (153)
98	EVA	ss3825053866	Apr 27, 2020 (154)
99	EVA	ss3825887450	Apr 27, 2020 (154)
100	EVA	ss3834732215	Apr 27, 2020 (154)
101	SGDP_PRJ	ss3885136846	Apr 27, 2020 (154)
102	KRGDB	ss3934702342	Apr 27, 2020 (154)
103	KOGIC	ss3978222948	Apr 27, 2020 (154)
104	FSA-LAB	ss3984102668	Apr 27, 2021 (155)
105	EVA	ss3984718270	Apr 27, 2021 (155)
106	EVA	ss3985776302	Apr 27, 2021 (155)
107	EVA	ss3986072009	Apr 27, 2021 (155)
108	EVA	ss3986703905	Apr 27, 2021 (155)
109	TOPMED	ss5026622668	Apr 27, 2021 (155)
110	TOMMO_GENOMICS	ss5221067054	Apr 27, 2021 (155)
111	EVA	ss5236937438	Apr 27, 2021 (155)
112	EVA	ss5237570267	Apr 27, 2021 (155)
113	EVA	ss5237667445	Oct 16, 2022 (156)
114	1000G_HIGH_COVERAGE	ss5302107346	Oct 16, 2022 (156)
115	TRAN_CS_UWATERLOO	ss5314445947	Oct 16, 2022 (156)
116	EVA	ss5315865843	Oct 16, 2022 (156)
117	EVA	ss5425824602	Oct 16, 2022 (156)
118	HUGCELL_USP	ss5495328307	Oct 16, 2022 (156)
119	1000G_HIGH_COVERAGE	ss5605329350	Oct 16, 2022 (156)
120	SANFORD_IMAGENETICS	ss5624389590	Oct 16, 2022 (156)
121	SANFORD_IMAGENETICS	ss5659545416	Oct 16, 2022 (156)
122	TOMMO_GENOMICS	ss5776520250	Oct 16, 2022 (156)
123	EVA	ss5799967744	Oct 16, 2022 (156)
124	YY_MCH	ss5816253031	Oct 16, 2022 (156)
125	EVA	ss5846860253	Oct 16, 2022 (156)
126	EVA	ss5847783822	Oct 16, 2022 (156)
127	EVA	ss5848435441	Oct 16, 2022 (156)
128	EVA	ss5851702271	Oct 16, 2022 (156)
129	EVA	ss5900402858	Oct 16, 2022 (156)
130	EVA	ss5950960229	Oct 16, 2022 (156)
131	EVA	ss5979496598	Oct 16, 2022 (156)
132	1000Genomes	NC_000016.9 - 89985940	Oct 12, 2018 (152)
133	1000Genomes_30x	NC_000016.10 - 89919532	Oct 16, 2022 (156)
134	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 89985940	Oct 12, 2018 (152)
135	Genetic variation in the Estonian population	NC_000016.9 - 89985940	Oct 12, 2018 (152)
136	ExAC Submission ignored due to conflicting rows: Row 2907889 (NC_000016.9:89985939:G:G 110686/119838, NC_000016.9:89985939:G:A 9152/119838) Row 2907890 (NC_000016.9:89985939:G:G 119837/119838, NC_000016.9:89985939:G:C 1/119838)	-	Oct 12, 2018 (152)
137	ExAC Submission ignored due to conflicting rows: Row 2907889 (NC_000016.9:89985939:G:G 110686/119838, NC_000016.9:89985939:G:A 9152/119838) Row 2907890 (NC_000016.9:89985939:G:G 119837/119838, NC_000016.9:89985939:G:C 1/119838)	-	Oct 12, 2018 (152)
138	FINRISK	NC_000016.9 - 89985940	Apr 27, 2020 (154)
139	gnomAD - Genomes	NC_000016.10 - 89919532	Apr 27, 2021 (155)
140	gnomAD - Exomes Submission ignored due to conflicting rows: Row 11564149 (NC_000016.9:89985939:G:G 228927/248326, NC_000016.9:89985939:G:A 19399/248326) Row 11564150 (NC_000016.9:89985939:G:G 248325/248326, NC_000016.9:89985939:G:C 1/248326)	-	Jul 13, 2019 (153)
141	gnomAD - Exomes Submission ignored due to conflicting rows: Row 11564149 (NC_000016.9:89985939:G:G 228927/248326, NC_000016.9:89985939:G:A 19399/248326) Row 11564150 (NC_000016.9:89985939:G:G 248325/248326, NC_000016.9:89985939:G:C 1/248326)	-	Jul 13, 2019 (153)
142	Genome of the Netherlands Release 5	NC_000016.9 - 89985940	Apr 27, 2020 (154)
143	HapMap	NC_000016.10 - 89919532	Apr 27, 2020 (154)
144	KOREAN population from KRGDB	NC_000016.9 - 89985940	Apr 27, 2020 (154)
145	Korean Genome Project	NC_000016.10 - 89919532	Apr 27, 2020 (154)
146	Northern Sweden	NC_000016.9 - 89985940	Jul 13, 2019 (153)
147	The PAGE Study	NC_000016.10 - 89919532	Jul 13, 2019 (153)
148	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000016.9 - 89985940	Apr 27, 2021 (155)
149	CNV burdens in cranial meningiomas	NC_000016.9 - 89985940	Apr 27, 2021 (155)
150	Qatari	NC_000016.9 - 89985940	Apr 27, 2020 (154)
151	SGDP_PRJ	NC_000016.9 - 89985940	Apr 27, 2020 (154)
152	Siberian	NC_000016.9 - 89985940	Apr 27, 2020 (154)
153	8.3KJPN	NC_000016.9 - 89985940	Apr 27, 2021 (155)
154	14KJPN	NC_000016.10 - 89919532	Oct 16, 2022 (156)
155	TopMed	NC_000016.10 - 89919532	Apr 27, 2021 (155)
156	UK 10K study - Twins	NC_000016.9 - 89985940	Oct 12, 2018 (152)
157	A Vietnamese Genetic Variation Database	NC_000016.9 - 89985940	Jul 13, 2019 (153)
158	ALFA	NC_000016.10 - 89919532	Apr 27, 2021 (155)
159	ClinVar	RCV000015378.29	Oct 12, 2018 (152)
160	ClinVar	RCV000015379.29	Oct 12, 2018 (152)
161	ClinVar	RCV000247471.1	Oct 12, 2018 (152)
162	ClinVar	RCV000278283.7	Oct 16, 2022 (156)
163	ClinVar	RCV001707509.1	Oct 16, 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
ss282656951, ss480471838, ss491725585, ss1696872306, ss1713563807, ss2635067379, ss3643123675	NC_000016.8:88513440:G:A	NC_000016.10:89919531:G:A	(self)
70762794, 39253501, 27757433, 98870, 17497974, 41879736, 15076821, 1002229, 267809, 18314893, 37153826, 9884228, 79036361, 39253501, 8697220, ss237150928, ss243467201, ss480486170, ss481283413, ss485033394, ss491513792, ss537057490, ss660892025, ss713334828, ss778699398, ss780722550, ss782962943, ss783398378, ss783924990, ss832219180, ss834158305, ss992830727, ss1067565420, ss1080869835, ss1357561431, ss1584102409, ss1635117232, ss1678111265, ss1692487434, ss1752213133, ss1752213134, ss1917911984, ss1936272971, ss1946424245, ss1959711631, ss1971464519, ss2028926295, ss2095070733, ss2157367874, ss2628953374, ss2633363337, ss2701904641, ss2742271273, ss2749635765, ss2946702198, ss2985080445, ss2985718375, ss3015041387, ss3021742085, ss3351606488, ss3627602938, ss3627602939, ss3631346731, ss3633132162, ss3633838990, ss3634658681, ss3634658682, ss3635527015, ss3636350093, ss3637278510, ss3638143981, ss3640366001, ss3640366002, ss3644677326, ss3646500355, ss3652154483, ss3652154484, ss3653852542, ss3682019185, ss3741791956, ss3744436933, ss3744959044, ss3744959045, ss3754343116, ss3772457150, ss3772457151, ss3825053866, ss3825887450, ss3834732215, ss3885136846, ss3934702342, ss3984102668, ss3984718270, ss3985776302, ss3986072009, ss3986703905, ss5221067054, ss5237570267, ss5315865843, ss5425824602, ss5624389590, ss5659545416, ss5799967744, ss5846860253, ss5847783822, ss5848435441, ss5950960229, ss5979496598	NC_000016.9:89985939:G:A	NC_000016.10:89919531:G:A	(self)
RCV000015378.29, RCV000015379.29, RCV000247471.1, RCV000278283.7, RCV001707509.1, 92855285, 498997305, 1443714, 34600949, 1125014, 110357354, 242168329, 1622692412, ss244239407, ss275515487, ss2214824161, ss3028280823, ss3699905741, ss3725591483, ss3771903545, ss3819613402, ss3978222948, ss5026622668, ss5236937438, ss5237667445, ss5302107346, ss5314445947, ss5495328307, ss5605329350, ss5776520250, ss5816253031, ss5851702271, ss5900402858	NC_000016.10:89919531:G:A	NC_000016.10:89919531:G:A	(self)
ss16697812	NT_010542.14:1541845:G:A	NC_000016.10:89919531:G:A	(self)
ss3173167, ss4472755, ss40647778, ss48295622, ss49848775, ss74900011, ss160517278, ss161821088, ss173192590	NT_010542.15:1546556:G:A	NC_000016.10:89919531:G:A	(self)
ss1692487435, ss2742271273	NC_000016.9:89985939:G:C	NC_000016.10:89919531:G:C	(self)
92855285, ss5605329350	NC_000016.10:89919531:G:C	NC_000016.10:89919531:G:C

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

28 citations for rs2228479

PMID	Title	Author	Year	Journal
7581459	Variants of the melanocyte-stimulating hormone receptor gene are associated with red hair and fair skin in humans.	Valverde P et al.	1995	Nature genetics
8944016	Val92Met variant of the melanocyte stimulating hormone receptor gene.	Xu X et al.	1996	Nature genetics
8990005	Identification of common polymorphisms in the coding sequence of the human MSH receptor (MCIR) with possible biological effects.	Koppula SV et al.	1997	Human mutation
11487574	The melanocortin-1-receptor gene is the major freckle gene.	Bastiaens M et al.	2001	Human molecular genetics
16463023	Identification of novel functional variants of the melanocortin 1 receptor gene originated from Asians.	Nakayama K et al.	2006	Human genetics
17999355	A genomewide association study of skin pigmentation in a South Asian population.	Stokowski RP et al.	2007	American journal of human genetics
19710684	Multiple pigmentation gene polymorphisms account for a substantial proportion of risk of cutaneous malignant melanoma.	Duffy DL et al.	2010	The Journal of investigative dermatology
20042077	Genetic determinants of hair and eye colours in the Scottish and Danish populations.	Mengel-From J et al.	2009	BMC genetics
20158590	Predicting phenotype from genotype: normal pigmentation.	Valenzuela RK et al.	2010	Journal of forensic sciences
20670983	The Multiple Sclerosis Severity Score: associations with MC1R single nucleotide polymorphisms and host response to ultraviolet radiation.	Strange RC et al.	2010	Multiple sclerosis (Houndmills, Basingstoke, England)
21052032	Sequence polymorphisms of MC1R gene and their association with depression and antidepressant response.	Wu GS et al.	2011	Psychiatric genetics
21197618	Model-based prediction of human hair color using DNA variants.	Branicki W et al.	2011	Human genetics
22629401	Evaluation of genetic markers as instruments for Mendelian randomization studies on vitamin D.	Berry DJ et al.	2012	PloS one
23744330	[Association study of MC1R gene polymorphisms with freckles in Chinese Han population from Chengdu].	Cao L et al.	2013	Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics
25741868	Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.	Richards S et al.	2015	Genetics in medicine
25945350	Variants of SCARB1 and VDR Involved in Complex Genetic Interactions May Be Implicated in the Genetic Susceptibility to Clear Cell Renal Cell Carcinoma.	Pośpiech E et al.	2015	BioMed research international
26482799	MC1R diversity in Northern Island Melanesia has not been constrained by strong purifying selection and cannot explain pigmentation phenotype variation in the region.	Norton HL et al.	2015	BMC genetics
26547235	Crowdsourced direct-to-consumer genomic analysis of a family quartet.	Corpas M et al.	2015	BMC genomics
26826707	The Effects of Sequence Variation on Genome-wide NRF2 Binding--New Target Genes and Regulatory SNPs.	Kuosmanen SM et al.	2016	Nucleic acids research
27084066	MC1R variants in Chinese Han patients with sporadic Parkinson's disease.	Shi CH et al.	2016	Neurobiology of aging
28059796	A Common Variant in the MC1R Gene (p.V92M) is associated with Alzheimer's Disease Risk.	Tell-Marti G et al.	2017	Journal of Alzheimer's disease
30657907	A study in scarlet: MC1R as the main predictor of red hair and exemplar of the flip-flop effect.	Zorina-Lichtenwalter K et al.	2019	Human molecular genetics
32835660	GWAS Analysis of 17,019 Korean Women Identifies the Variants Associated with Facial Pigmented Spots.	Shin JG et al.	2021	The Journal of investigative dermatology
33907405	Association Analysis of Polymorphisms in BIN1, MC1R, STARD6 and PVRL2 with Mild Cognitive Impairment in Elderly Carrying APOE ε4 Allele.	Wu Y et al.	2021	Neuropsychiatric disease and treatment
34698109	MC1R Is a Prognostic Marker and Its Expression Is Correlated with MSI in Colorectal Cancer.	Peng L et al.	2021	Current issues in molecular biology
35176104	Unveiling forensically relevant biogeographic, phenotype and Y-chromosome SNP variation in Pakistani ethnic groups using a customized hybridisation enrichment forensic intelligence panel.	Rauf S et al.	2022	PloS one
35188998	MC1R diversity and its role in skin pigmentation variation in West Maharashtra, India.	Jonnalagadda M et al.	2022	American journal of human biology
35955479	Implication of Melanocortin Receptor Genes in the Familial Comorbidity of Type 2 Diabetes and Depression.	Amin M et al.	2022	International journal of molecular sciences

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

rs2228479