1p13.2

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	rs2476601
Karyotype Band Location	1p13.2
Chromosomal Location (NCBI36)	Chr1:113620000-114460000
Region Size	0.84 Mb
Genes in Region (10)	AP4B1, BCL2L15, DCLRE1B, HIPK1, MAGI3, OLFML3, PHTF1, PTPN22, RSBN1, SYT6

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
rs41283512	dbSNP_130	113967008	+	R/Q	MAGI3	260425	410
rs72990405	dbSNP_130	114026384	+	Y/S	MAGI3	260425	1119
rs1141014	dbSNP_130	114050120	-	L/W	PHTF1	10745	529
rs36076018	dbSNP_130	114054529	+	D/R	PHTF1	10745	380
rs61730007	dbSNP_130	114057498	+	Q/K	PHTF1	10745	237
rs61817585	dbSNP_130	114070572	+	R/L	PHTF1	10745	160
rs35311195	dbSNP_130	114070678	+	I/V	PHTF1	10745	125
rs3211282	dbSNP_130	114110132	-	S/Y	RSBN1	54665	801
rs34462362	dbSNP_130	114121485	+	P/P	RSBN1	54665	509
rs41283514	dbSNP_130	114142025	+	R/H	RSBN1	54665	287
rs41313296	dbSNP_130	114163748	+	N/I	PTPN22	26191	778
rs56048322	dbSNP_130	114173737	-	K/N	PTPN22	26191	750
rs74163663	dbSNP_130	114173745	-	R/G	PTPN22	26191	748
rs74111772	dbSNP_130	114177270	+	R/Q	PTPN22	26191	680
rs74163661	dbSNP_130	114178529	-	I/M	PTPN22	26191	650
rs74163660	dbSNP_130	114179084	-	P/R	PTPN22	26191	622
rs2476601	dbSNP_130	114179091	+	R/W	PTPN22	26191	620
rs61757796	dbSNP_130	114181764	+	S/L	PTPN22	26191	594
rs74163659	dbSNP_130	114181818	-	S/C	PTPN22	26191	576
rs74163657	dbSNP_130	114181962	-	Y/C	PTPN22	26191	528
rs72650672	dbSNP_130	114182179	-	Q/E	PTPN22	26191	456
rs74163655	dbSNP_130	114182215	-	I/L	PTPN22	26191	444
rs72650671	dbSNP_130	114182437	-	H/N	PTPN22	26191	370
rs72483511	dbSNP_130	114192771	-	E/X	PTPN22	26191	277
rs72650670	dbSNP_130	114196204	-	R/W	PTPN22	26191	266
rs33996649	dbSNP_130	114196212	+	R/Q	PTPN22	26191	263
rs61738614	dbSNP_130	114199118	+	L/H	PTPN22	26191	206
rs74163647	dbSNP_130	114199133	-	S/F	PTPN22	26191	201
rs34590413	dbSNP_130	114199188	+	R/X	PTPN22	26191	183
rs74163642	dbSNP_130	114203208	-	V/A	PTPN22	26191	71
rs1217381	dbSNP_130	114226124	+	D/N	BCL2L15	440603	90
rs11349	dbSNP_130	114239260	+	I/F	AP4B1	10717	724
rs71744623	dbSNP_130	114239640	+		AP4B1	10717	597
rs1217401	dbSNP_130	114240474	+	L/S	AP4B1	10717	480
rs28381069	dbSNP_130	114249868	+	R/L	DCLRE1B	64858	46
rs11552449	dbSNP_130	114249912	+	H/Y	DCLRE1B	64858	61
rs11102700	dbSNP_130	114251145	+	S/F	DCLRE1B	64858	65
rs11552448	dbSNP_130	114251165	+	L/M	DCLRE1B	64858	72
rs11552447	dbSNP_130	114251193	+	P/H	DCLRE1B	64858	81
rs34762757	dbSNP_130	114252180	+		DCLRE1B	64858	128
rs28381079	dbSNP_130	114256121	+	D/N	DCLRE1B	64858	462
rs35183203	dbSNP_130	114256229	+	R/E	DCLRE1B	64858	498
rs35397235	dbSNP_130	114256265	+	N/Y	DCLRE1B	64858	510
rs35324789	dbSNP_130	114284545	+	Q/R	HIPK1	204851	6
rs34335651	dbSNP_130	114285456	+	G/C	HIPK1	204851	310
rs57585637	dbSNP_130	114302257	+	S/F	HIPK1	204851	601
rs17853139	dbSNP_130	114307590	+	P/Q	HIPK1	204851	721
rs12568463	dbSNP_130	114316121	+	L/F	HIPK1	204851	1056
rs56401016	dbSNP_130	114316166	+	L/V	HIPK1	204851	1071
rs17853522	dbSNP_130	114317185	+	A/V	HIPK1	204851	660
rs34966241	dbSNP_130	114317491	+	V/A	HIPK1	204851	762
rs11553080	dbSNP_130	114324500	+	D/E	OLFML3	56944	46
rs11553081	dbSNP_130	114325227	+	D/E	OLFML3	56944	178
rs35317518	dbSNP_130	114325252	+	R/S	OLFML3	56944	187

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	rs2476601
Chr	1
Position	114179091
Strand	+
P-Value	8.49e-85

N/A

0.5

chr1: 113896862..114428238

AP4B1 PHTF1 HIPK1 MAGI3 PTPN22 BCL2L15 RSBN1 OLFML3 DCLRE1B

LD Region Feature File

LD File

0.4

N/A

chr1: 113962639..114333980

AP4B1 PHTF1 HIPK1 MAGI3 PTPN22 BCL2L15 RSBN1 OLFML3 DCLRE1B

0.8

N/A

chr1: 114105331..114179091

PTPN22 RSBN1

N/A

chr1: 114105331..114179091

PTPN22 RSBN1

Signal Clouds Top Help

Signal Clouds: Available

Publications Top Help

Publications Associated with this region: 3