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Variant13 AnnotaHon UsingRegulomeDB and HaploReg
Jill E MooreWeng Lab
University of MassachuseJs Medical SchoolJune13 29 2015
MoHvaHon
bull The majority of variants report13 by GWAS are in noncodingregions of the genome
bull The variant13 reported in the GWAS (leadtagged variant) maynot13 be causal but13 is in high linkage disequilibrium with thecasual variant13
bull Using data13 from ENCODE we can annotate noncoding regionsof the genome and predict13 the funcHon of disease associatednoncoding variants
Variant13 AnnotaHon Tools
hJpwwwregulomedborg
hJpwwwbroadinsHtuteorgmammalshaploreghaploregphp
rs17293632 is Associated with IBD and Crohnrsquos Disease
NHGRI13 GWAS Database hJpswwwgenomegov2652538413
rs17293632 is Associated with IBD and Crohnrsquos Disease
bull rs17293632 is upstream of SMAD3 transcript13 variant13 4 and in the introns of transcript13 variants 1 2 and 3
Backup Slides
hJpregulomestanfordeduGWAS13
Analyzing rs17293632 with RegulomeDB
Analyzing rs17293632 with RegulomeDB
ldquoLikely to Affect13 BindingrdquoTF binding + matched TF moHf + matched DNase footprint13 + DNase peak
MoHvaHon
bull The majority of variants report13 by GWAS are in noncodingregions of the genome
bull The variant13 reported in the GWAS (leadtagged variant) maynot13 be causal but13 is in high linkage disequilibrium with thecasual variant13
bull Using data13 from ENCODE we can annotate noncoding regionsof the genome and predict13 the funcHon of disease associatednoncoding variants
Variant13 AnnotaHon Tools
hJpwwwregulomedborg
hJpwwwbroadinsHtuteorgmammalshaploreghaploregphp
rs17293632 is Associated with IBD and Crohnrsquos Disease
NHGRI13 GWAS Database hJpswwwgenomegov2652538413
rs17293632 is Associated with IBD and Crohnrsquos Disease
bull rs17293632 is upstream of SMAD3 transcript13 variant13 4 and in the introns of transcript13 variants 1 2 and 3
Backup Slides
hJpregulomestanfordeduGWAS13
Analyzing rs17293632 with RegulomeDB
Analyzing rs17293632 with RegulomeDB
ldquoLikely to Affect13 BindingrdquoTF binding + matched TF moHf + matched DNase footprint13 + DNase peak
Variant13 AnnotaHon Tools
hJpwwwregulomedborg
hJpwwwbroadinsHtuteorgmammalshaploreghaploregphp
rs17293632 is Associated with IBD and Crohnrsquos Disease
NHGRI13 GWAS Database hJpswwwgenomegov2652538413
rs17293632 is Associated with IBD and Crohnrsquos Disease
bull rs17293632 is upstream of SMAD3 transcript13 variant13 4 and in the introns of transcript13 variants 1 2 and 3
Backup Slides
hJpregulomestanfordeduGWAS13
Analyzing rs17293632 with RegulomeDB
Analyzing rs17293632 with RegulomeDB
ldquoLikely to Affect13 BindingrdquoTF binding + matched TF moHf + matched DNase footprint13 + DNase peak
rs17293632 is Associated with IBD and Crohnrsquos Disease
NHGRI13 GWAS Database hJpswwwgenomegov2652538413
rs17293632 is Associated with IBD and Crohnrsquos Disease
bull rs17293632 is upstream of SMAD3 transcript13 variant13 4 and in the introns of transcript13 variants 1 2 and 3
Backup Slides
hJpregulomestanfordeduGWAS13
Analyzing rs17293632 with RegulomeDB
Analyzing rs17293632 with RegulomeDB
ldquoLikely to Affect13 BindingrdquoTF binding + matched TF moHf + matched DNase footprint13 + DNase peak
rs17293632 is Associated with IBD and Crohnrsquos Disease
bull rs17293632 is upstream of SMAD3 transcript13 variant13 4 and in the introns of transcript13 variants 1 2 and 3
Backup Slides
hJpregulomestanfordeduGWAS13
Analyzing rs17293632 with RegulomeDB
Analyzing rs17293632 with RegulomeDB
ldquoLikely to Affect13 BindingrdquoTF binding + matched TF moHf + matched DNase footprint13 + DNase peak
Backup Slides
hJpregulomestanfordeduGWAS13
Analyzing rs17293632 with RegulomeDB
Analyzing rs17293632 with RegulomeDB
ldquoLikely to Affect13 BindingrdquoTF binding + matched TF moHf + matched DNase footprint13 + DNase peak
hJpregulomestanfordeduGWAS13
Analyzing rs17293632 with RegulomeDB
Analyzing rs17293632 with RegulomeDB
ldquoLikely to Affect13 BindingrdquoTF binding + matched TF moHf + matched DNase footprint13 + DNase peak
Analyzing rs17293632 with RegulomeDB
Analyzing rs17293632 with RegulomeDB
ldquoLikely to Affect13 BindingrdquoTF binding + matched TF moHf + matched DNase footprint13 + DNase peak
Analyzing rs17293632 with RegulomeDB
ldquoLikely to Affect13 BindingrdquoTF binding + matched TF moHf + matched DNase footprint13 + DNase peak
