3p21.31

Sections: General Information - Query T1DMart for overlapping human marker information - Region Overview - Genes in LD Region - Signal Clouds - Publications

General Information Top Help

General Information: Available

Organism	Human
Points of Interest	rs333,rs11711054
Karyotype Band Location	3p21.31
Chromosomal Location (NCBI36)	Chr3:45955677-46629136
Region Size	0.67 Mb
Genes in Region (12)	CCR1, CCR2, CCR3, CCR5, CCRL2, CXCR6, FYCO1, LRRC2, LTF, RTP3, TDGF1, XCR1

Query T1DMart for overlapping human marker information from T1DMart Top Help

Marker	Marker Source	Start	Strand	Peptide Shift	Gene Symbol (HGNC)	Gene ID (Entrez)	Amino Acid Position
rs2234355	dbSNP_130	45962984	+	E/K	CXCR6	10663	3
rs2234356	dbSNP_130	45963508	+	K/N	CXCR6	10663	177
rs2234357	dbSNP_130	45963693	+	V/A	CXCR6	10663	239
rs41289620	dbSNP_130	45978739	+	R/Q	FYCO1	79443	1140
rs73830668	dbSNP_130	45978836	+	K/E	FYCO1	79443	1108
rs35869281	dbSNP_130	45980857	+	G/G	FYCO1	79443	1081
rs6795530	dbSNP_130	45980867	+	D/E	FYCO1	79443	1078
rs13079478	dbSNP_130	45982827	+	N/K	FYCO1	79443	1001
rs71622515	dbSNP_130	45982827	-	NT/ET	FYCO1	79443	1001
rs13059238	dbSNP_130	45982829	+	N/D	FYCO1	79443	1001
rs34801630	dbSNP_130	45982850	+	E/K	FYCO1	79443	994
rs35450771	dbSNP_130	45983479	+	E/G	FYCO1	79443	784
rs34266136	dbSNP_130	45983536	+	R/H	FYCO1	79443	765
rs36014492	dbSNP_130	45983651	+	H/N	FYCO1	79443	727
rs3796375	dbSNP_130	45983794	+	A/V	FYCO1	79443	679
rs33910087	dbSNP_130	45984491	+	R/C	FYCO1	79443	447
rs72889997	dbSNP_130	45984578	+	E/K	FYCO1	79443	418
rs3733101	dbSNP_130	45984688	-	T/M	FYCO1	79443	381
rs35937665	dbSNP_130	45984767	+	R/W	FYCO1	79443	355
rs3733100	dbSNP_130	45984868	-	G/A	FYCO1	79443	321
rs9875356	dbSNP_130	45984985	+	R/H	FYCO1	79443	282
rs3821885	dbSNP_130	45985077	-	E/D	FYCO1	79443	251
rs4683158	dbSNP_130	45985081	+	R/Q	FYCO1	79443	250
rs61755290	dbSNP_130	46219790	+	S/I	CCR1	1230	340
rs41393844	dbSNP_130	46219938	-	Y/H	CCR1	1230	291
rs61752589	dbSNP_130	46220333	+	A/D	CCR1	1230	159
rs6781048	dbSNP_130	46220781	+	Y/D	CCR1	1230	10
rs4987125	dbSNP_130	46281715	+	G/D	CCR3	1232	21
rs5742906	dbSNP_130	46281769	+	P/L	CCR3	1232	39
rs35272086	dbSNP_130	46281998	+	T/T	CCR3	1232	115
rs56177184	dbSNP_130	46282081	+	R/Q	CCR3	1232	143
rs61738836	dbSNP_130	46282093	+	V/A	CCR3	1232	147
rs56114788	dbSNP_130	46282119	+	V/I	CCR3	1232	156
rs41276533	dbSNP_130	46282138	+	V/G	CCR3	1232	162
rs62243923	dbSNP_130	46282281	+	L/V	CCR3	1232	210
rs41515745	dbSNP_130	46282453	+	I/N	CCR3	1232	267
rs41276535	dbSNP_130	46282476	+	R/W	CCR3	1232	275
rs41409552	dbSNP_130	46282477	+	R/Q	CCR3	1232	275
rs4987052	dbSNP_130	46374155	+	L/V	CCR2	1231	45
rs4987052	dbSNP_130	46374155	+	L/V	FLJ78302	729230	45
rs1799864	dbSNP_130	46374212	+	V/I	CCR2	1231	64
rs1799864	dbSNP_130	46374212	+	V/I	FLJ78302	729230	64
rs34948438	dbSNP_130	46374233	+		CCR2	1231	71
rs34948438	dbSNP_130	46374233	+		FLJ78302	729230	71
rs3918387	dbSNP_130	46376294	+	G/E	CCR2	1231	355
rs3918387	dbSNP_130	46376294	+	G/E	FLJ78302	729230	355
rs1800939	dbSNP_130	46389482	+	A/S	CCR5	1234	29
rs1800939	dbSNP_130	46389482	+	A/S	LOC727797	727797	29
rs56340326	dbSNP_130	46389489	+	R/H	CCR5	1234	31
rs56340326	dbSNP_130	46389489	+	R/H	LOC727797	727797	31
rs41425744	dbSNP_130	46389533	+	V/M	CCR5	1234	46
rs41425744	dbSNP_130	46389533	+	V/M	LOC727797	727797	46
rs1799863	dbSNP_130	46389561	+	L/Q	CCR5	1234	55
rs1799863	dbSNP_130	46389561	+	L/Q	LOC727797	727797	55
rs1800940	dbSNP_130	46389577	+	R/S	CCR5	1234	60
rs1800940	dbSNP_130	46389577	+	R/S	LOC727797	727797	60
rs56198941	dbSNP_130	46389615	+	A/V	CCR5	1234	73
rs56198941	dbSNP_130	46389615	+	A/V	LOC727797	727797	73
rs1800560	dbSNP_130	46389700	+	C/X	CCR5	1234	101
rs1800560	dbSNP_130	46389700	+	C/X	LOC727797	727797	101
rs34418657	dbSNP_130	46389788	+	V/F	CCR5	1234	131
rs34418657	dbSNP_130	46389788	+	V/F	LOC727797	727797	131
rs333	dbSNP_130	46389951	+		CCR5	1234	185
rs333	dbSNP_130	46389951	+		LOC727797	727797	185
rs56030631	dbSNP_130	46389951	+		CCR5	1234	185
rs56030631	dbSNP_130	46389951	+		LOC727797	727797	185
rs56345960	dbSNP_130	46389976	+	F/L	CCR5	1234	193
rs56345960	dbSNP_130	46389976	+	F/L	LOC727797	727797	193
rs62625034	dbSNP_130	46389979	-	Q/H	CCR5	1234	194
rs62625034	dbSNP_130	46389979	-	Q/H	LOC727797	727797	194
rs1800452	dbSNP_130	46390065	+	R/Q	CCR5	1234	223
rs1800452	dbSNP_130	46390065	+	R/Q	LOC727797	727797	223
rs55956105	dbSNP_130	46390257	+	M/R	CCR5	1234	287
rs55956105	dbSNP_130	46390257	+	M/R	LOC727797	727797	287
rs55916127	dbSNP_130	46390298	+	G/R	CCR5	1234	301
rs55916127	dbSNP_130	46390298	+	G/R	LOC727797	727797	301
rs1800943	dbSNP_130	46390299	+	G/V	CCR5	1234	301
rs1800943	dbSNP_130	46390299	+	G/V	LOC727797	727797	301
rs34962689	dbSNP_130	46390385	+	E/R	CCR5	1234	330
rs34962689	dbSNP_130	46390385	+	E/R	LOC727797	727797	330
rs1800944	dbSNP_130	46390401	+	A/V	CCR5	1234	335
rs1800944	dbSNP_130	46390401	+	A/V	LOC727797	727797	335
rs1800945	dbSNP_130	46390413	+	Y/F	CCR5	1234	339
rs1800945	dbSNP_130	46390413	+	Y/F	LOC727797	727797	339
rs11574440	dbSNP_130	46424168	+	M/I	CCRL2	9034
rs11574441	dbSNP_130	46424179	+	R/H	CCRL2	9034	5
rs11574443	dbSNP_130	46424585	+	Y/C	CCRL2	9034	16
rs11574443	dbSNP_130	46424585	+	Y/C	LOC727811	727811	4
rs3204849	dbSNP_130	46425074	+	F/Y	CCRL2	9034	179
rs3204849	dbSNP_130	46425074	+	Y/F	LOC727811	727811	167
rs6441977	dbSNP_130	46425076	+	V/M	CCRL2	9034	180
rs6441977	dbSNP_130	46425076	+	V/M	LOC727811	727811	168
rs56304867	dbSNP_130	46425076	+	V/M	CCRL2	9034	180
rs56127823	dbSNP_130	46425233	+	Y/C	CCRL2	9034	232
rs56127823	dbSNP_130	46425233	+	Y/C	LOC727811	727811	220
rs3204850	dbSNP_130	46425301	+	I/V	CCRL2	9034	255
rs3204850	dbSNP_130	46425301	+	I/V	LOC727811	727811	243
rs66977363	dbSNP_130	46454582	+	F/F	LTF	4057	650
rs66977363	dbSNP_130	46454582	+	F/F	LOC728320	728320	452
rs2073495	dbSNP_130	46455962	+	E/D	LTF	4057	579
rs2073495	dbSNP_130	46455962	+	D/E	LOC728320	728320	381
rs55765065	dbSNP_130	46455962	-	E/D	LTF	4057	579
rs57222564	dbSNP_130	46455962	+	E/D	LTF	4057	579
rs57222564	dbSNP_130	46455962	+	D/E	LOC728320	728320	381
rs17851345	dbSNP_130	46459981	+	V/E	LTF	4057	537
rs17851345	dbSNP_130	46459981	+	V/E	LOC728320	728320	339
rs66892674	dbSNP_130	46459993	+	E/G	LTF	4057	533
rs66892674	dbSNP_130	46459993	+	E/G	LOC728320	728320	335
rs67186015	dbSNP_130	46459999	+	Q/A	LTF	4057	531
rs67186015	dbSNP_130	46459999	+	Q/A	LOC728320	728320	333
rs1803892	dbSNP_130	46461901	-	S/X	LTF	4057	463
rs1803892	dbSNP_130	46461901	-	S/X	LOC728320	728320	265
rs17855463	dbSNP_130	46461923	+	A/T	LTF	4057	456
rs17855463	dbSNP_130	46461923	+	A/T	LOC728320	728320	258
rs61739313	dbSNP_130	46462941	+	V/M	LTF	4057	451
rs61739313	dbSNP_130	46462941	+	V/M	LOC728320	728320	253
rs1042055	dbSNP_130	46463842	-	G/C	LTF	4057	422
rs1042055	dbSNP_130	46463842	-	G/C	LOC728320	728320	224
rs72153807	dbSNP_130	46466493	+	K/K	LTF	4057	304
rs72153807	dbSNP_130	46466493	+	K/K	LOC728320	728320	106
rs61740470	dbSNP_130	46466989	+	Q/H	LTF	4057	294
rs61740470	dbSNP_130	46466989	+	Q/H	LOC728320	728320	96
rs60938611	dbSNP_130	46471858	+	A/V	LTF	4057	193
rs34538438	dbSNP_130	46472330	+	P/P	LTF	4057	153
rs1126479	dbSNP_130	46472346	-	I/T	LTF	4057	148
rs17851991	dbSNP_130	46472376	+	L/R	LTF	4057	138
rs17851346	dbSNP_130	46472401	+	G/C	LTF	4057	130
rs17855496	dbSNP_130	46476209	+	G/R	LTF	4057	50
rs1126478	dbSNP_130	46476217	-	K/R	LTF	4057	47
rs1126477	dbSNP_130	46476272	-	A/T	LTF	4057	29
rs10662431	dbSNP_130	46476288	+	R/KG	LTF	4057	23
rs67658416	dbSNP_130	46476289	+	R/KR	LTF	4057	23
rs55665884	dbSNP_130	46476290	+	R/RE	LTF	4057	22
rs66635520	dbSNP_130	46476291	+	R/KR	LTF	4057	22
rs17855462	dbSNP_130	46476296	+	R/S	LTF	4057	21
rs34529469	dbSNP_130	46538030	+	D/R	LRRC2	79442	351
rs17078944	dbSNP_130	46555595	+	A/E	LRRC2	79442	145
rs34850909	dbSNP_130	46555680	+	L/M	LRRC2	79442	117
rs17286758	dbSNP_130	46561626	+	T/A	LRRC2	79442	83
rs28687398	dbSNP_130	46567991	+	V/A	LRRC2	79442	32
rs34996741	dbSNP_130	46568066	+	V/A	LRRC2	79442	7
rs11130097	dbSNP_130	46595618	+	V/A	TDGF1	6997	22
rs2293025	dbSNP_130	46595764	-	Y/D	TDGF1	6997	43
rs34501971	dbSNP_130	46596340	+	R/G	TDGF1	6997	111

Non-Synonymous SNPs in region dbSNP_130:

Region Overview Top Help

GBrowse Image: Available

An overview of the region is provided by GBrowse. Tracks shown include gene information and study-specific data:
D' (black) and r-squared (red) with genotyped SNP	Calculated using the HapMap CEU Founders population. D' data has been limited to those values where LOD score > 3
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.
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.

Genes in LD Region Top Help

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	rs11711054
Chr	3
Position	46320615
Strand	+
P-Value	1.69e-05

N/A

0.5

chr3: 46249113..46454212

CCR3 CCR5 LTF CCR2 CCRL2

LD Region Feature File

LD File

0.4

N/A

chr3: 46255198..46377022

CCR3 CCR2

0.8

N/A

chr3: 46320615..46374802

CCR2

N/A

chr3: 46320615..46341273

Signal Clouds Top Help

Signal Clouds: Available

Publications Top Help

Publications Associated with this region: 2