Crohn's disease data

Description

The data set consist of 103 common (>5% minor allele frequency) SNPs genotyped in 129 trios from an European-derived population. These SNPs are in a 500-kb region on human chromosome 5q31 implicated as containing a genetic risk factor for Crohn disease.

The positions, names and haplotype blocks reported are as follows,

274044   IGR1118a_1	BLOCK 1
274541   IGR1119a_1	*
286593   IGR1143a_1	*
287261   IGR1144a_1	*
299755   IGR1169a_2	*
324341   IGR1218a_2	*
324379   IGR1219a_2	*
358048   IGR1286a_1	BLOCK 1
366811	 TSC0101718
395079   IGR1373a_1	BLOCK 2
396353   IGR1371a_1	*
397334   IGR1369a_2	*
397381   IGR1369a_1	*
398352   IGR1367a_1	BLOCK 2
411823   IGR2008a_2
411873   IGR2008a_1	BLOCK 3
412456   IGR2010a_3	*
413233   IGR2011b_1	*
415579   IGR2016a_1	*
417617   IGR2020a_15	*
419845   IGR2025a_2	*
424283   IGR2033a_1	*
425376   IGR2036a_2	*
425549   IGR2036a_1	BLOCK 3
433467   IGR2052a_1	BLOCK 4
435282   IGR2055a_1	*
437682   IGR2060a_1	*
438883   IGR2063b_1	*
443565   IGR2072a_2	*
443750   IGR2073a_1	*
445337   IGR2076a_1	*
447791   IGR2081a_1	*
449895   IGR2085a_2	*
455246   IGR2096a_1	*
463136   IGR2111a_3	BLOCK 4
482171   IGR2150a_1	BLOCK 5
485828   IGR2157a_1	*
495082   IGR2175a_2	*
506266   IGR2198a_1	*
506890   IGR2199a_1	BLOCK 5
507208   IGR2200a_1	BLOCK 6
508338   IGR2202a_1	*
508858   IGR2203a_1	*
510951   IGR2207a_1	*
518478   IGR2222a_2	BLOCK 6
519387   IGR2224a_2	BLOCK 7
519962   IGR2225a_1	*
520521   IGR2226a_3	*
522600   IGR2230a_1	*
525243   IGR2236a_1	*	
529556   IGR2244a_4	*
532363   IGR2250a_4	*
545062   IGR2276a_1	*
553189   IGR2292a_1	*
570978   IGR3005a_1	*
571022   IGR3005a_2	*
576586   IGR3016a_1	*
577141   IGR3018a_2	*
577838   IGR3019a_2	*
578122   IGR3020a_1	*
579217   IGR3022a_1	*
579529   IGR3023a_1	*
579818   IGR3023a_3	*
582651   IGR3029a_1	*
582948   IGR3029a_2	*
583131   IGR3030a_1	*
587836   IGR3039a_1	*
590425   IGR3044a_1	*
590585   IGR3045a_1	*
594115   IGR3051a_1	*
594812   IGR3053a_1	*
598805   IGR3061a_1	*
601294   IGR3066a_1	*
608759   IGR3081a_1	*
610447   IGR3084a_1	*
611177   IGR3086a_1	BLOCK 7
613488   IGR3090a_1
616241   IGR3096a_1	BLOCK 8
616763   IGR3097a_1	*
617299   IGR3098a_1	*
626881   IGR3117a_1	*
633786   IGR3131a_1	*
635072   IGR3134a_1	*
637441   IGR3138a_1	BLOCK 8
648564   IGR3161a_1
649061   IGR3162a_1	BLOCK 9
649903   IGR3163a_1	*
657234   IGR3178a_1	*
662077   IGR3188a_1	*
662819   IGR3189a_2	*
676688   IGRX100a_1	BLOCK 9
683387   IGR3230a_1	BLOCK 10
686249   IGR3236a_1	*
692320   IGR3248a_1	*
718291   IGR3300a_2	*
730313   IGR3324a_1	*
731025   IGR3326a_1	*
738461   IGR3340a_1	BLOCK 10
871978   GENS021ex1_2	BLOCK 11
877571   GENS020ex3_3	*
877671   GENS020ex3_2	*
877809   GENS020ex3_1	*
890710   GENS020ex1_1	BLOCK 11

However it has been updated after the paper was published (posted on http://www.broad.mit.edu/humgen/IBD5/haplodata.html)

An example use of the data is with the following paper, Kelly M. Burkett, Celia M. T. Greenwood, BradMcNeney, Jinko Graham. Gene genealogies for genetic association mapping, with application to Crohn's disease. Fron Genet 2013, 4(260) doi: 10.3389/fgene.2013.00260

Usage

data(crohn)

Format

A data frame containing 387 rows and 212 columns

Source

MJ Daly, JD Rioux, SF Schaffner, TJ Hudson, ES Lander (2001) High-resolution haplotype structure in the human genome Nature Genetics 29:229-232