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2q24.2

General Information: Available

Organism	Human
Points of Interest	rs1990760
Karyotype Band Location	2q24.2
Chromosomal Location (GRCh37)	Chr2:162960873-163392761
Region Size	0.43 Mb
Orthologous Regions	Mouse: Human 2q24.2 Orthologous Region Rat: Human 2q24.2 Orthologous Region
Genes in Region (5)	FAP, GCA, GCG, IFIH1, KCNH7

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
rs79305438	dbSNP_134	163000583	+	A/T	GCG	2641	164
rs150179526	dbSNP_134	163000601	+	I/V	GCG	2641	158
rs138583535	dbSNP_134	163000652	+	E/K	GCG	2641	141
rs149306780	dbSNP_134	163000664	+	A/T	GCG	2641	137
rs5650	dbSNP_134	163002098	-	A/V	GCG	2641	115
rs35920035	dbSNP_134	163002170	-	R/H	GCG	2641	91
rs11552333	dbSNP_134	163002189	-	R/G	GCG	2641	85
rs11552334	dbSNP_134	163003924	-	Y/H	GCG	2641	65
rs11552338	dbSNP_134	163004005	-	A/T	GCG	2641	38
rs11552337	dbSNP_134	163004013	-	A/V	GCG	2641	35
rs74432317	dbSNP_134	163005655	+	V/L	GCG	2641	12
rs138652824	dbSNP_134	163027550	+	T/M	FAP	2191	741
rs143485547	dbSNP_134	163027560	+	G/S	FAP	2191	738
rs140683015	dbSNP_134	163029725	+	T/A	FAP	2191	681
rs111686380	dbSNP_134	163030280	+	R/G	FAP	2191	663
rs142580939	dbSNP_134	163031377	+	A/T	FAP	2191	657
rs141879753	dbSNP_134	163031461	+	V/I	FAP	2191	629
rs150287336	dbSNP_134	163039940	+	I/K	FAP	2191	618
rs149046822	dbSNP_134	163039961	+	G/D	FAP	2191	611
rs145480126	dbSNP_134	163044770	+	R/X	FAP	2191	575
rs113216329	dbSNP_134	163044781	+	L/S	FAP	2191	571
rs114179274	dbSNP_134	163044806	+	S/G	FAP	2191	563
rs34043219	dbSNP_134	163044863	+	G/G	FAP	2191	543
rs112306496	dbSNP_134	163044868	+	G/D	FAP	2191	542
rs144304958	dbSNP_134	163045645	+	D/E	FAP	2191	529
rs147933561	dbSNP_134	163046188	+	K/N	FAP	2191	509
rs79484073	dbSNP_134	163055344	+	H/R	FAP	2191	442
rs140297886	dbSNP_134	163059568	+	Y/H	FAP	2191	379
rs143208145	dbSNP_134	163070543	+	R/X	FAP	2191	303
rs141855900	dbSNP_134	163070560	+	T/K	FAP	2191	297
rs140779053	dbSNP_134	163072421	+	M/V	FAP	2191	285
rs140132856	dbSNP_134	163072433	+	P/S	FAP	2191	281
rs148803327	dbSNP_134	163072456	+	A/V	FAP	2191	273
rs148466393	dbSNP_134	163072493	+	V/I	FAP	2191	261
rs150161783	dbSNP_134	163074554	+	A/V	FAP	2191	235
rs79793562	dbSNP_134	163074572	+	T/M	FAP	2191	229
rs62001031	dbSNP_134	163074624	+	L/F	FAP	2191	212
rs78722278	dbSNP_134	163075627	+	F/L	FAP	2191	185
rs78632336	dbSNP_134	163076380	+	P/S	FAP	2191	157
rs142146935	dbSNP_134	163076382	+	S/L	FAP	2191	156
rs140351808	dbSNP_134	163076397	+	Q/R	FAP	2191	151
rs141580437	dbSNP_134	163076406	+	R/H	FAP	2191	148
rs138190509	dbSNP_134	163076409	+	P/L	FAP	2191	147
rs149591141	dbSNP_134	163080161	+	Y/H	FAP	2191	124
rs77130311	dbSNP_134	163081002	+	V/I	FAP	2191	112
rs112558928	dbSNP_134	163081994	+	M/T	FAP	2191	95
rs139492630	dbSNP_134	163082046	+	L/I	FAP	2191	78
rs145562225	dbSNP_134	163099429	+	R/H	FAP	2191	27
rs148465982	dbSNP_134	163099460	+	L/F	FAP	2191	17
rs76564309	dbSNP_134	163099483	+	F/S	FAP	2191	9
rs35369989	dbSNP_134	163123746	-	D/E	IFIH1	64135	1014
rs151037370	dbSNP_134	163123788	+	Y/X	IFIH1	64135	1000
rs74162090	dbSNP_134	163123826	-	V/L	IFIH1	64135	988
rs144455277	dbSNP_134	163124024	+	Q/E	IFIH1	64135	955
rs116508532	dbSNP_134	163124026	+	Y/C	IFIH1	64135	954
rs148623633	dbSNP_134	163124029	+	D/G	IFIH1	64135	953
rs77041372	dbSNP_134	163124040	+	K/N	IFIH1	64135	949
rs1990760	dbSNP_134	163124051	+	A/T	IFIH1	64135	946
rs140562355	dbSNP_134	163124619	+	V/I	IFIH1	64135	929
rs35667974	dbSNP_134	163124637	-	I/V	IFIH1	64135	923
rs143054245	dbSNP_134	163128752	+	E/G	IFIH1	64135	867
rs138373022	dbSNP_134	163128791	+	M/R	IFIH1	64135	854
rs3747517	dbSNP_134	163128824	-	H/R	IFIH1	64135	843
rs79324540	dbSNP_134	163128828	+	E/K	IFIH1	64135	842
rs74162087	dbSNP_134	163128893	-	R/H	IFIH1	64135	820
rs144341455	dbSNP_134	163130343	+	R/C	IFIH1	64135	806
rs141366758	dbSNP_134	163130376	+	G/S	IFIH1	64135	795
rs148369169	dbSNP_134	163130397	+	A/T	IFIH1	64135	788
rs72650663	dbSNP_134	163133396	-	T/I	IFIH1	64135	702
rs146300062	dbSNP_134	163134002	+	G/V	IFIH1	64135	656
rs144274375	dbSNP_134	163134004	+	D/E	IFIH1	64135	655
rs145818112	dbSNP_134	163134084	+	F/L	IFIH1	64135	629
rs35744605	dbSNP_134	163134090	-	E/X	IFIH1	64135	627
rs74162084	dbSNP_134	163134185	-	R/H	IFIH1	64135	595
rs145792185	dbSNP_134	163134203	+	A/D	IFIH1	64135	589
rs150760072	dbSNP_134	163134715	+	A/T	IFIH1	64135	589
rs138057665	dbSNP_134	163134757	+	T/A	IFIH1	64135	575
rs111732322	dbSNP_134	163134814	+	E/K	IFIH1	64135	556
rs142348767	dbSNP_134	163136564	+	L/R	IFIH1	64135	528
rs145641024	dbSNP_134	163136589	+	T/A	IFIH1	64135	520
rs147000317	dbSNP_134	163137881	+	G/V	IFIH1	64135	494
rs141748480	dbSNP_134	163137905	+	G/A	IFIH1	64135	486
rs10930046	dbSNP_134	163137983	+	H/R	IFIH1	64135	460
rs147642994	dbSNP_134	163138007	+	A/V	IFIH1	64135	452
rs35329951	dbSNP_134	163138038	-	I/V	IFIH1	64135	442
rs139714761	dbSNP_134	163138050	+	S/P	IFIH1	64135	438
rs74162081	dbSNP_134	163138899	-	E/G	IFIH1	64135	428
rs148540097	dbSNP_134	163138960	+	D/N	IFIH1	64135	408
rs111797285	dbSNP_134	163138971	+	V/A	IFIH1	64135	404
rs138611889	dbSNP_134	163139025	+	R/H	IFIH1	64135	386
rs145520044	dbSNP_134	163139061	+	R/H	IFIH1	64135	374
rs113854430	dbSNP_134	163139062	+	R/C	IFIH1	64135	374
rs140977021	dbSNP_134	163139085	+	V/E	IFIH1	64135	366
rs117608083	dbSNP_134	163144647	+	K/E	IFIH1	64135	365
rs150317197	dbSNP_134	163144674	+	P/T	IFIH1	64135	356
rs35207787	dbSNP_134	163144689	-	K/E	IFIH1	64135	351
rs72650664	dbSNP_134	163144694	-	K/R	IFIH1	64135	349
rs76332728	dbSNP_134	163144721	+	V/G	IFIH1	64135	340
rs141848057	dbSNP_134	163144752	+	P/S	IFIH1	64135	330
rs74162079	dbSNP_134	163144791	-	Q/X	IFIH1	64135	317
rs12470774	dbSNP_134	163150128	+	L/I	IFIH1	64135	274
rs12474918	dbSNP_134	163150170	+	T/S	IFIH1	64135	260
rs138188229	dbSNP_134	163163290	+	L/P	IFIH1	64135	233
rs74162075	dbSNP_134	163167419	-	N/D	IFIH1	64135	160
rs144853750	dbSNP_134	163167430	+	E/A	IFIH1	64135	156
rs74162074	dbSNP_134	163174373	-	R/G	IFIH1	64135	149
rs146721166	dbSNP_134	163174382	+	I/V	IFIH1	64135	146
rs138069411	dbSNP_134	163174405	+	C/F	IFIH1	64135	138
rs138344310	dbSNP_134	163174434	+	K/N	IFIH1	64135	128
rs143910264	dbSNP_134	163174442	+	V/M	IFIH1	64135	126
rs139219083	dbSNP_134	163174445	+	L/M	IFIH1	64135	125
rs150881745	dbSNP_134	163174526	+	E/Q	IFIH1	64135	98
rs147278787	dbSNP_134	163174589	+	R/W	IFIH1	64135	77
rs140882466	dbSNP_134	163204175	+	S/P	GCA	25801	39
rs138275925	dbSNP_134	163204194	+	D/G	GCA	25801	45
rs79565841	dbSNP_134	163208877	+	Q/H	GCA	25801	74
rs11558383	dbSNP_134	163208885	+	L/S	GCA	25801	77
rs17783344	dbSNP_134	163208893	+	S/A	GCA	25801	80
rs11558382	dbSNP_134	163208918	+		GCA	25801	88
rs146161584	dbSNP_134	163215601	+	S/G	GCA	25801	168
rs141572054	dbSNP_134	163215655	+	R/X	GCA	25801	186
rs146185329	dbSNP_134	163216057	+	D/N	GCA	25801	208
rs144025747	dbSNP_134	163228386	+	V/M	KCNH7	90134	1182
rs149916560	dbSNP_134	163228442	+	V/A	KCNH7	90134	1163
rs142210415	dbSNP_134	163228443	+	V/I	KCNH7	90134	1163
rs138263393	dbSNP_134	163228514	+	N/I	KCNH7	90134	1139
rs149607273	dbSNP_134	163228550	+	S/L	KCNH7	90134	1127
rs142248539	dbSNP_134	163228587	+	L/F	KCNH7	90134	1115
rs79262587	dbSNP_134	163230011	+	K/R	KCNH7	90134	1098
rs147827058	dbSNP_134	163230047	+	Q/R	KCNH7	90134	1086
rs148899074	dbSNP_134	163230052	+	I/M	KCNH7	90134	1084
rs139719597	dbSNP_134	163230102	+	P/S	KCNH7	90134	1068
rs148938064	dbSNP_134	163236451	+	A/T	KCNH7	90134	1015
rs6757850	dbSNP_134	163241287	+	G/A	KCNH7	90134	958
rs143881602	dbSNP_134	163250969	+	M/I	KCNH7	90134	880
rs113984295	dbSNP_134	163253311	+	F/S	KCNH7	90134	851
rs139707486	dbSNP_134	163253323	+	M/K	KCNH7	90134	847
rs139632449	dbSNP_134	163256725	+	K/R	KCNH7	90134	794
rs112706514	dbSNP_134	163256732	+	I/V	KCNH7	90134	792
rs34590296	dbSNP_134	163256780	+	C/W	KCNH7	90134	775
rs149070457	dbSNP_134	163291905	+	G/E	KCNH7	90134	579
rs79852917	dbSNP_134	163292047	+	R/G	KCNH7	90134	532
rs142244172	dbSNP_134	163292104	+	T/A	KCNH7	90134	513
rs140040445	dbSNP_134	163302886	+	T/M	KCNH7	90134	392
rs78247304	dbSNP_134	163302901	+	R/H	KCNH7	90134	387
rs140283570	dbSNP_134	163360961	+	V/M	KCNH7	90134	367
rs151139318	dbSNP_134	163361057	+	V/F	KCNH7	90134	335
rs146936771	dbSNP_134	163361131	+	S/F	KCNH7	90134	310
rs41268653	dbSNP_134	163361158	+	N/I	KCNH7	90134	301
rs138611881	dbSNP_134	163374243	+	E/K	KCNH7	90134	297
rs145688877	dbSNP_134	163374269	+	N/S	KCNH7	90134	288
rs139430414	dbSNP_134	163374308	+	S/L	KCNH7	90134	275
rs142897098	dbSNP_134	163374363	+	Q/K	KCNH7	90134	257
rs141867587	dbSNP_134	163374449	+	L/W	KCNH7	90134	228
rs145661878	dbSNP_134	163374564	+	H/Y	KCNH7	90134	190

(Human) GRCh37 - chr2:162960873..163392761 (431.89 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 rs1990760 Chr 2 Position 163124051 Strand P-Value 6.57e-09		N/A	0.5	chr2: 163076146..163336969	FAP GCA IFIH1 KCNH7		LD Region Feature File LD File
		0.4	N/A	chr2: 163076146..163326297	FAP GCA IFIH1 KCNH7
		0.8	N/A	chr2: 163110536..163124051	IFIH1
		1	N/A

Publications: 5

• A large-scale replication study identifies TNIP1, PRDM1, JAZF1, UHRF1BP1 and IL10 as risk loci for systemic lupus erythematosus.
  Gateva V, Sandling JK, Hom G, Taylor KE, Chung SA, Sun X, Ortmann W, Kosoy R, Ferreira RC, Nordmark G, Gunnarsson I, Svenungsson E, Padyukov L, Sturfelt G, Jönsen A, Bengtsson AA, Rantapää-Dahlqvist S, Baechler EC, Brown EE, Alarcón GS, Edberg JC, Ramsey-Goldman R, McGwin G, Reveille JD, Vilá LM, Kimberly RP, Manzi S, Petri MA, Lee A, Gregersen PK, Seldin MF, Rönnblom L, Criswell LA, Syvänen AC, Behrens TW, Graham RR
  Nat Genet. 2009
  PubMed ID: 19838195
   
  
• 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
   
  
• Shared and distinct genetic variants in type 1 diabetes and celiac disease.
  Smyth DJ, Plagnol V, Walker NM, Cooper JD, Downes K, Yang JH, Howson JM, Stevens H, McManus R, Wijmenga C, Heap GA, Dubois PC, Clayton DG, Hunt KA, van Heel DA, Todd JA
  N Engl J Med. 2008
  PubMed ID: 19073967
   
  
• Genomic polymorphism at the interferon-induced helicase (IFIH1) locus contributes to Graves' disease susceptibility.
  Sutherland A, Davies J, Owen CJ, Vaikkakara S, Walker C, Cheetham TD, James RA, Perros P, Donaldson PT, Cordell HJ, Quinton R, Pearce SH
  J Clin Endocrinol Metab. 2007
  PubMed ID: 17535987
   
  
• A genome-wide association study of nonsynonymous SNPs identifies a type 1 diabetes locus in the interferon-induced helicase (IFIH1) region.
  Smyth DJ, Cooper JD, Bailey R, Field S, Burren O, Smink LJ, Guja C, Ionescu-Tirgoviste C, Widmer B, Dunger DB, Savage DA, Walker NM, Clayton DG, Todd JA
  Nat Genet. 2006
  PubMed ID: 16699517
   
  

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

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