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6q25.3

General Information: Available

Organism	Human
Points of Interest	rs1738074
Karyotype Band Location	6q25.3
Chromosomal Location (GRCh37)	Chr6:159317512-159526689
Region Size	0.21 Mb
Orthologous Regions	Mouse: Human 6q25.3 Orthologous Region Rat: Human 6q25.3 Orthologous Region
Genes in Region (3)	C6orf99, RSPH3, TAGAP

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
rs144193169	dbSNP_134	159331066	+	G/S	C6orf99	100130967	67
rs140020446	dbSNP_134	159331198	+		C6orf99	100130967	111
rs140821356	dbSNP_134	159398620	+	D/N	RSPH3	83861	545
rs144678437	dbSNP_134	159398691	+	Q/R	RSPH3	83861	521
rs3756987	dbSNP_134	159398700	-	G/D	RSPH3	83861	518
rs150432556	dbSNP_134	159398721	+	R/Q	RSPH3	83861	511
rs138781661	dbSNP_134	159398745	+	L/R	RSPH3	83861	503
rs147001164	dbSNP_134	159398788	+	G/C	RSPH3	83861	489
rs12204826	dbSNP_134	159398803	+	E/K	RSPH3	83861	484
rs78116655	dbSNP_134	159398835	+	H/P	RSPH3	83861	473
rs147880570	dbSNP_134	159398871	+	R/H	RSPH3	83861	461
rs768994	dbSNP_134	159399348	-	M/T	RSPH3	83861	439
rs141178332	dbSNP_134	159401853	+	F/S	RSPH3	83861	413
rs150750790	dbSNP_134	159401874	+	A/V	RSPH3	83861	406
rs10455840	dbSNP_134	159401898	+	R/Q	RSPH3	83861	398
rs140204620	dbSNP_134	159401947	+	W/R	RSPH3	83861	382
rs149769974	dbSNP_134	159401964	+	R/Q	RSPH3	83861	376
rs145688686	dbSNP_134	159403554	+	R/Q	RSPH3	83861	362
rs148930620	dbSNP_134	159403577	+	N/K	RSPH3	83861	354
rs142857859	dbSNP_134	159403612	+	R/W	RSPH3	83861	343
rs147697861	dbSNP_134	159403642	+	V/I	RSPH3	83861	333
rs141317681	dbSNP_134	159403661	+	I/M	RSPH3	83861	326
rs138202910	dbSNP_134	159404717	+	A/P	RSPH3	83861	299
rs147211320	dbSNP_134	159407347	+	P/R	RSPH3	83861	246
rs138365743	dbSNP_134	159407351	+	E/K	RSPH3	83861	245
rs41267751	dbSNP_134	159407416	+	R/Q	RSPH3	83861	223
rs34582178	dbSNP_134	159407446	-	R/Q	RSPH3	83861	213
rs41267753	dbSNP_134	159407447	+	R/W	RSPH3	83861	213
rs141552246	dbSNP_134	159414888	+	L/V	RSPH3	83861	205
rs16889320	dbSNP_134	159414899	+	N/S	RSPH3	83861	201
rs139235571	dbSNP_134	159414919	+	D/E	RSPH3	83861	194
rs147688147	dbSNP_134	159420485	+	R/Q	RSPH3	83861	175
rs140867286	dbSNP_134	159420512	+	A/V	RSPH3	83861	166
rs61750776	dbSNP_134	159420545	+	P/R	RSPH3	83861	155
rs61750777	dbSNP_134	159420548	+	A/V	RSPH3	83861	154
rs143166491	dbSNP_134	159420592	+	Q/H	RSPH3	83861	139
rs151230376	dbSNP_134	159420630	+	C/S	RSPH3	83861	127
rs140068249	dbSNP_134	159420702	+	L/I	RSPH3	83861	103
rs145292281	dbSNP_134	159420708	+	P/T	RSPH3	83861	101
rs41267755	dbSNP_134	159420735	+	P/S	RSPH3	83861	92
rs138878442	dbSNP_134	159420783	+	A/P	RSPH3	83861	76
rs144832123	dbSNP_134	159420807	+	A/T	RSPH3	83861	68
rs148593164	dbSNP_134	159420866	+	R/Q	RSPH3	83861	48
rs143832203	dbSNP_134	159420938	+	G/A	RSPH3	83861	24
rs147256615	dbSNP_134	159420965	+	L/R	RSPH3	83861	15
rs140715430	dbSNP_134	159420966	+	L/F	RSPH3	83861	15
rs144691673	dbSNP_134	159456881	+	Y/C	TAGAP	117289	725
rs144830124	dbSNP_134	159456938	+	R/Q	TAGAP	117289	706
rs148570036	dbSNP_134	159457034	+	H/R	TAGAP	117289	674
rs139559821	dbSNP_134	159457161	+	C/G	TAGAP	117289	632
rs142920707	dbSNP_134	159457244	+	A/V	TAGAP	117289	604
rs148912994	dbSNP_134	159457293	+	E/K	TAGAP	117289	588
rs145572935	dbSNP_134	159457395	+	V/M	TAGAP	117289	554
rs116639718	dbSNP_134	159457430	+	G/D	TAGAP	117289	542
rs144641395	dbSNP_134	159457502	+	K/T	TAGAP	117289	518
rs148229333	dbSNP_134	159457523	+	F/S	TAGAP	117289	511
rs141510073	dbSNP_134	159457562	+	G/D	TAGAP	117289	498
rs150468963	dbSNP_134	159457680	+	A/P	TAGAP	117289	459
rs138323645	dbSNP_134	159457773	+	P/S	TAGAP	117289	428
rs144047559	dbSNP_134	159457826	+	G/A	TAGAP	117289	410
rs75182303	dbSNP_134	159457869	+	T/S	TAGAP	117289	396
rs144719803	dbSNP_134	159457979	+	V/G	TAGAP	117289	359
rs148545546	dbSNP_134	159458006	+	A/D	TAGAP	117289	350
rs112777023	dbSNP_134	159458016	+	P/T	TAGAP	117289	347
rs35263580	dbSNP_134	159458018	-	G/D	TAGAP	117289	346
rs139309613	dbSNP_134	159458022	+	A/T	TAGAP	117289	345
rs61753626	dbSNP_134	159458024	+	S/N	TAGAP	117289	344
rs146522698	dbSNP_134	159458112	+	P/A	TAGAP	117289	315
rs112913154	dbSNP_134	159459194	+	H/Y	TAGAP	117289	284
rs146899715	dbSNP_134	159460285	+	V/A	TAGAP	117289	215
rs34649601	dbSNP_134	159460290	+	V/G	TAGAP	117289	213
rs139378811	dbSNP_134	159461768	+	E/K	TAGAP	117289	192
rs142994072	dbSNP_134	159461781	+	E/D	TAGAP	117289	187
rs41267765	dbSNP_134	159462424	+	E/K	TAGAP	117289	147
rs149576847	dbSNP_134	159462471	+	R/H	TAGAP	117289	131
rs144116675	dbSNP_134	159462511	+	T/A	TAGAP	117289	118
rs151132746	dbSNP_134	159463225	+	L/H	TAGAP	117289	67
rs140113362	dbSNP_134	159463270	+	K/T	TAGAP	117289	52
rs140990019	dbSNP_134	159464639	+	S/R	TAGAP	117289	44
rs34834201	dbSNP_134	159464669	+	H/H	TAGAP	117289	33

(Human) GRCh37 - chr6:159317512..159526689 (209.18 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 rs1738074 Chr 6 Position 159465977 Strand P-Value 6.02e-03		N/A	0.5	chr6: 159323833..159540213	C6orf99 TAGAP RSPH3		LD Region Feature File LD File
		0.4	N/A	chr6: 159343182..159515077	TAGAP RSPH3
		0.8	N/A	chr6: 159465977..159470058	TAGAP
		1	N/A

Publications: 3

• Multiple common variants for celiac disease influencing immune gene expression.
  Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, Curtotti A, Zhernakova A, Heap GA, Adány R, Aromaa A, Bardella MT, van den Berg LH, Bockett NA, de la Concha EG, Dema B, Fehrmann RS, Fernández-Arquero M, Fiatal S, Grandone E, Green PM, Groen HJ, Gwilliam R, Houwen RH, Hunt SE, Kaukinen K, Kelleher D, Korponay-Szabo I, Kurppa K, MacMathuna P, Mäki M, Mazzilli MC, McCann OT, Mearin ML, Mein CA, Mirza MM, Mistry V, Mora B, Morley KI, Mulder CJ, Murray JA, Núñez C, Oosterom E, Ophoff RA, Polanco I, Peltonen L, Platteel M, Rybak A, Salomaa V, Schweizer JJ, Sperandeo MP, Tack GJ, Turner G, Veldink JH, Verbeek WH, Weersma RK, Wolters VM, Urcelay E, Cukrowska B, Greco L, Neuhausen SL, McManus R, Barisani D, Deloukas P, Barrett JC, Saavalainen P, Wijmenga C, van Heel DA
  Nat Genet. 2010
  PubMed ID: 20190752
   
  
• 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
   
  

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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