2q24.2

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	rs1990760
Karyotype Band Location	2q24.2
Chromosomal Location (NCBI36)	Chr2:162669119-163101007
Region Size	0.43 Mb
Genes in Region (5)	FAP, GCA, GCG, IFIH1, KCNH7

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
rs5650	dbSNP_130	162710344	-	A/V	GCG	2641	115
rs35920035	dbSNP_130	162710416	-	R/H	GCG	2641	91
rs11552333	dbSNP_130	162712110	-	R/G	GCG	2641	85
rs11552334	dbSNP_130	162712170	-	Y/H	GCG	2641	65
rs11552338	dbSNP_130	162712251	-	A/T	GCG	2641	38
rs11552337	dbSNP_130	162712259	-	A/V	GCG	2641	35
rs34043219	dbSNP_130	162753109	+	G/G	FAP	2191	543
rs62001030	dbSNP_130	162763541	+	Y/X	FAP	2191	458
rs62001031	dbSNP_130	162782870	+	L/I	FAP	2191	212
rs35369989	dbSNP_130	162831992	-	D/E	IFIH1	64135	1014
rs74162090	dbSNP_130	162832072	-	V/L	IFIH1	64135	988
rs1990760	dbSNP_130	162832297	+	A/T	IFIH1	64135	946
rs35667974	dbSNP_130	162832883	-	I/V	IFIH1	64135	923
rs3747517	dbSNP_130	162837070	-	H/R	IFIH1	64135	843
rs74162087	dbSNP_130	162837139	-	R/H	IFIH1	64135	820
rs72650663	dbSNP_130	162841642	-	T/I	IFIH1	64135	702
rs35744605	dbSNP_130	162842336	-	E/X	IFIH1	64135	627
rs74162084	dbSNP_130	162842431	-	R/H	IFIH1	64135	595
rs10930046	dbSNP_130	162846229	+	H/R	IFIH1	64135	460
rs35329951	dbSNP_130	162846284	-	I/V	IFIH1	64135	442
rs74162081	dbSNP_130	162847145	-	E/G	IFIH1	64135	428
rs35207787	dbSNP_130	162852935	-	K/E	IFIH1	64135	351
rs72650664	dbSNP_130	162852940	-	K/R	IFIH1	64135	349
rs74162079	dbSNP_130	162853037	-	Q/X	IFIH1	64135	317
rs12470774	dbSNP_130	162858374	+	L/I	IFIH1	64135	274
rs12474918	dbSNP_130	162858416	+	T/S	IFIH1	64135	260
rs74162075	dbSNP_130	162875665	-	N/D	IFIH1	64135	160
rs74162074	dbSNP_130	162882619	-	R/G	IFIH1	64135	149
rs11558383	dbSNP_130	162917131	+	L/S	GCA	25801	77
rs17783344	dbSNP_130	162917139	+	S/A	GCA	25801	80
rs6757850	dbSNP_130	162949533	+	G/A	KCNH7	90134	958
rs34590296	dbSNP_130	162965026	+	C/W	KCNH7	90134	775
rs41268653	dbSNP_130	163069404	+	N/I	KCNH7	90134	308

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	rs1990760
Chr	2
Position	162832297
Strand	+
P-Value	6.57e-09

N/A

0.5

chr2: 162784392..162968937

FAP GCA IFIH1 KCNH7

LD Region Feature File

LD File

0.4

N/A

chr2: 162784392..162945636

FAP GCA IFIH1 KCNH7

0.8

N/A

chr2: 162818782..162832297

IFIH1

N/A

Signal Clouds Top Help

Signal Clouds: Available

Publications Top Help

Publications Associated with this region: 2