2q12.1

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	rs917997
Karyotype Band Location	2q12.1
Chromosomal Location (NCBI36)	Chr2:102221730-102575042
Region Size	0.35 Mb
Genes in Region (5)	IL18R1, IL18RAP, IL1RL1, IL1RL2, SLC9A4

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
rs1041973	dbSNP_130	102321900	+	A/E	IL1RL1	9173	78
rs34210856	dbSNP_130	102321906	-	A/V	IL1RL1	9173	80
rs34225180	dbSNP_130	102323636	-	A/T	IL1RL1	9173	176
rs4988956	dbSNP_130	102334439	+	A/T	IL1RL1	9173	433
rs10192036	dbSNP_130	102334643	+	Q/K	IL1RL1	9173	501
rs10204137	dbSNP_130	102334644	+	Q/R	IL1RL1	9173	501
rs10192157	dbSNP_130	102334788	+	T/I	IL1RL1	9173	549
rs10206753	dbSNP_130	102334794	+	L/S	IL1RL1	9173	551
rs41379550	dbSNP_130	102354889	+	K/R	IL18R1	8809	116
rs34216045	dbSNP_130	102354958	-	T/I	IL18R1	8809	139
rs35292939	dbSNP_130	102358886	+	V/M	IL18R1	8809	186
rs11465635	dbSNP_130	102364515	+	R/H	IL18R1	8809	210
rs56076776	dbSNP_130	102364566	+	V/G	IL18R1	8809	227
rs11465644	dbSNP_130	102367777	+	N/K	IL18R1	8809	232
rs61731174	dbSNP_130	102367859	+	N/D	IL18R1	8809	260
rs11465648	dbSNP_130	102369872	+	S/N	IL18R1	8809	310
rs12619169	dbSNP_130	102377516	+	G/R	IL18R1	8809	423
rs11695455	dbSNP_130	102407134	+	D/G	IL18RAP	8807	136
rs11465716	dbSNP_130	102428208	+	V/I	IL18RAP	8807	350
rs17027275	dbSNP_130	102461819	+	G/S	SLC9A4	389015	116
rs6742280	dbSNP_130	102502769	+	I/V	SLC9A4	389015	581
rs61731274	dbSNP_130	102502782	+	S/F	SLC9A4	389015	585
rs4578881	dbSNP_130	102507933	+	Y/N	SLC9A4	389015	613
rs61731289	dbSNP_130	102508015	+	R/K	SLC9A4	389015	640
rs1014286	dbSNP_130	102515532	-	G/S	SLC9A4	389015	784

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	rs917997
Chr	2
Position	102437000
Strand	-
P-Value	0.360

N/A

0.5

chr2: 102079488..102611457

UNQ9419 IL1R1 SLC9A4 SLC9A2 IL18RAP IL1RL2 IL18R1 IL1RL1

LD Region Feature File

LD File

0.4

N/A

chr2: 102111286..102548705

IL1R1 SLC9A4 IL18RAP IL1RL2 IL18R1 IL1RL1

0.8

N/A

chr2: 102338297..102459675

SLC9A4 IL18RAP IL18R1

N/A

chr2: 102414899..102459513

SLC9A4 IL18RAP

Signal Clouds Top Help

Signal Clouds: Available

Publications Top Help

Publications Associated with this region: 2