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12p13.31

General Information: Available

Organism	Human
Points of Interest	rs4763879
Karyotype Band Location	12p13.31
Chromosomal Location (GRCh37)	Chr12:9621533-9976156
Region Size	0.35 Mb
Orthologous Regions	Mouse: Human 12p13.31 Orthologous Region Mouse: Human 12p13.31 Orthologous Region Rat: Human 12p13.31 Orthologous Region Rat: Human 12p13.31 Orthologous Region
Genes in Region (6)	CD69, CLEC2D, CLECL1, KLRB1, LOC374443, OVOS

View this region in the Human T1D Regions table.

Non-Synonymous SNPs in region dbSNP134:

Marker	Marker Source	Start	Strand	Peptide Shift	Gene Symbol (HGNC)	Gene ID (Entrez)	Amino Acid Position
rs4015230	dbSNP_134	9633258	+	N/S	OVOS	408186	78
rs145843963	dbSNP_134	9684214	+	R/W	OVOS	408186	127
rs2536903	dbSNP_134	9688883	-	E/D	OVOS	408186	231
rs148552111	dbSNP_134	9693830	+	F/C	OVOS	408186	282
rs139614426	dbSNP_134	9695149	+	E/K	OVOS	408186	378
rs116682136	dbSNP_134	9695225	+	R/Q	OVOS	408186	403
rs145577209	dbSNP_134	9695280	+	Q/H	OVOS	408186	421
rs148867665	dbSNP_134	9695296	+	V/L	OVOS	408186	427
rs144689981	dbSNP_134	9697718	+	I/L	OVOS	408186	478
rs3896492	dbSNP_134	9698249	-	C/Y	OVOS	408186	536
rs78132576	dbSNP_134	9698284	+	R/G	OVOS	408186	548
rs3867153	dbSNP_134	9698296	-	R/G	OVOS	408186	552
rs11608392	dbSNP_134	9705114	+	P/L	OVOS2	144203	26
rs11608392	dbSNP_134	9705114	+	P/L	OVOS	408186	651
rs2543171	dbSNP_134	9705156	-	R/H	OVOS	408186	665
rs141710916	dbSNP_134	9707140	+	S/L	OVOS	408186	713
rs138862994	dbSNP_134	9707317	+	V/A	OVOS	408186	772
rs117418135	dbSNP_134	9707329	+	R/L	OVOS	408186	776
rs146295933	dbSNP_134	9707693	+	V/I	OVOS	408186	816
rs72109186	dbSNP_134	9708694	+	K/QK	OVOS2	144203	265
rs2536855	dbSNP_134	9709396	-	Q/K	OVOS	408186	859
rs35005880	dbSNP_134	9711013	-	V/A	OVOS	408186	898
rs140315528	dbSNP_134	9711791	+	L/M	OVOS	408186	917
rs143153363	dbSNP_134	9716912	+	P/T	OVOS	408186	1125
rs147902803	dbSNP_134	9717865	+	R/Q	OVOS	408186	1187
rs138391474	dbSNP_134	9723336	+	D/N	OVOS	408186	1226
rs141653604	dbSNP_134	9723393	+	G/S	OVOS	408186	1245
rs11490334	dbSNP_134	9723444	+	Q/E	LOC100509231	100509231	59
rs11490334	dbSNP_134	9723444	+	Q/E	LOC100509288	100509288	101
rs11490334	dbSNP_134	9723444	+	E/Q	OVOS	408186	1262
rs11051697	dbSNP_134	9727452	+	R/X	LOC100510334	100510334	48
rs4519173	dbSNP_134	9728253	+	A/S	LOC100510334	100510334	84
rs3829324	dbSNP_134	9728268	-	D/N	LOC100510334	100510334	89
rs149065471	dbSNP_134	9728286	+	Q/E	LOC100510334	100510334	95
rs1135816	dbSNP_134	9750669	+	I/T	KLRB1	3820	168
rs146949020	dbSNP_134	9750735	+	R/H	KLRB1	3820	146
rs137930946	dbSNP_134	9750756	+	I/R	KLRB1	3820	139
rs34919993	dbSNP_134	9751127	+	S/G	KLRB1	3820	128
rs138352143	dbSNP_134	9751171	+	N/S	KLRB1	3820	113
rs141057839	dbSNP_134	9751202	+	E/K	KLRB1	3820	103
rs144354266	dbSNP_134	9751231	+	N/S	KLRB1	3820	93
rs142063673	dbSNP_134	9752422	+	Q/R	KLRB1	3820	67
rs149244748	dbSNP_134	9752424	+	I/M	KLRB1	3820	66
rs139525269	dbSNP_134	9754189	+	C/F	KLRB1	3820	31
rs144231382	dbSNP_134	9760381	+	E/K	KLRB1	3820	19
rs146546280	dbSNP_134	9822340	+	S/R	CLEC2D	29121	4
rs16914640	dbSNP_134	9822387	+	N/K	CLEC2D	29121	19
rs3764022	dbSNP_134	9833524	-	L/V	CLEC2D	29121	23
rs145574510	dbSNP_134	9833560	+	I/F	CLEC2D	29121	35
rs146151995	dbSNP_134	9833567	+	R/H	CLEC2D	29121	37
rs140143530	dbSNP_134	9833599	+	I/V	CLEC2D	29121	48
rs138289149	dbSNP_134	9840627	+	R/K	CLEC2D	29121	101
rs142058665	dbSNP_134	9840650	+	D/N	CLEC2D	29121	109
rs145796034	dbSNP_134	9845520	+	T/A	CLEC2D	29121	152
rs150263662	dbSNP_134	9847364	+	I/T	CLEC2D	29121	157
rs138893047	dbSNP_134	9847448	+	S/F	CLEC2D	29121	185
rs142101421	dbSNP_134	9847459	+	I/V	CLEC2D	29121	189
rs146362062	dbSNP_134	9875318	+	K/N	CLECL1	160365	136
rs118152239	dbSNP_134	9875323	+	T/A	CLECL1	160365	135
rs112752598	dbSNP_134	9875347	+	G/X	CLECL1	160365	127
rs144252486	dbSNP_134	9875356	+	V/L	CLECL1	160365	124
rs148708802	dbSNP_134	9875402	+	F/L	CLECL1	160365	108
rs79809727	dbSNP_134	9885578	+	P/S	CLECL1	160365	95
rs139676111	dbSNP_134	9885604	+	A/V	CLECL1	160365	86
rs145268017	dbSNP_134	9885649	+	F/S	CLECL1	160365	71
rs147608426	dbSNP_134	9885653	+	V/I	CLECL1	160365	70
rs144269074	dbSNP_134	9885682	+	D/G	CLECL1	160365	60
rs112979434	dbSNP_134	9885707	+	L/LL	CLECL1	160365	51
rs113575400	dbSNP_134	9885707	+	S/T	CLECL1	160365	52
rs139898935	dbSNP_134	9885707	+		CLECL1	160365	52
rs71929655	dbSNP_134	9885708	+	L/YL	CLECL1	160365	51
rs147873369	dbSNP_134	9885708	+		CLECL1	160365	51
rs113222621	dbSNP_134	9885710	+	Y/YX	CLECL1	160365	50
rs71045297	dbSNP_134	9885712	+	Y/TY	CLECL1	160365	50
rs75915715	dbSNP_134	9885712	+		CLECL1	160365	50
rs72339675	dbSNP_134	9885713	+	I/IL	CLECL1	160365	49
rs148811159	dbSNP_134	9885830	+	V/L	CLECL1	160365	11
rs34201389	dbSNP_134	9885840	+	H/Q	CLECL1	160365	7
rs138470841	dbSNP_134	9885846	+	F/L	CLECL1	160365	5
rs140715648	dbSNP_134	9906088	+	P/S	CD69	969	197
rs113155724	dbSNP_134	9907187	+	N/D	CD69	969	163
rs144700824	dbSNP_134	9907223	+	H/D	CD69	969	151
rs142870511	dbSNP_134	9907268	+	A/T	CD69	969	136
rs150634267	dbSNP_134	9907698	+	H/R	CD69	969	116
rs138724350	dbSNP_134	9907773	+	G/D	CD69	969	91
rs3176798	dbSNP_134	9907786	-	E/K	CD69	969	87
rs144675038	dbSNP_134	9908916	+	I/T	CD69	969	55
rs139793479	dbSNP_134	9908952	+	C/Y	CD69	969	43
rs145286917	dbSNP_134	9908955	+	L/Q	CD69	969	42
rs147196303	dbSNP_134	9909009	+	A/D	CD69	969	24

(Human) GRCh37 - chr12:9621533..9976156 (354.62 kb)  View in Genome Browser

An overview of the region is provided by GBrowse. Tracks shown include gene information and study-specific data:
Immune Disease Associated Variants	Variants shown to be associated with different auto-immune diseases
P-values, -log(p)	1 degree of freedom p-values, stratified by geographic location. Generated using snpMatrix with data from the T1DGC Meta-analysis study.
HapMap Recobination Data	Genome-wide recombination rate from Phase 2 HapMap estimated from phased haplotypes in HapMap Release 22 (NCBI 36). Units are in cM/Mb, coordinates have been projected to the current build.

Genes in LD Region: Available

Summary data derived from GWA meta analysis Barrett et al. LD regions were calculated using different r² and D' threshold values, and these regions were then examined for genes. The definition of a gene location includes a 3kb flanking region either side of the gene.

Marker Data		Region Data					Links
		r2 Threshold	D' Threshold	Region	Genes
Marker rs4763879 Chr 12 Position 9910164 Strand P-Value 2.78e-07		N/A	0.5	chr12: 9761291..9947703	CLECL1 CLEC2D LOC374443 CD69		LD Region Feature File LD File
		0.4	N/A	chr12: 9824138..9939224	CLECL1 CLEC2D CD69
		0.8	N/A	chr12: 9905851..9910449	CD69
		1	N/A	chr12: 9905851..9910449	CD69

Publications: 1

• Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes.
  Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS, The Type 1 Diabetes Genetics Consortium
  Nat Genet. 2009
  PubMed ID: 19430480
   
  

Signal Clouds: Available

Genotype data for collections is plotted to give a visual sense of the quality of clustering. The two homozygous and the heterozygous genotypes are represented by different colours; a clear separation between the clouds is indicative of good clustering.

Source: ImmunoChip

Source: T1DGC 4K-4K Study - 2008

Source: WTCCC

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Printed on Fri February 10, 2012