Variant report

Variant	rs11569104
Chromosome Location	chr4:110924642-110924643
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:110924600-110924750	HCM	heart:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:110922594..110925099-chr4:111433371..111435082,2	MCF-7	breast:

Variant related genes	Relation type
EGF	TF binding region
ENSG00000138792	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10010695	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1005903	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11098060	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11098061	0.87[EUR][1000 genomes]
rs11569019	1.00[CEU][hapmap]
rs11569020	1.00[CEU][hapmap]
rs11569121	0.88[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs11569126	0.84[TSI][hapmap]
rs17041230	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237053	0.84[CHB][hapmap]
rs2237054	1.00[CEU][hapmap]
rs2282787	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298996	1.00[CEU][hapmap]
rs3733625	0.84[TSI][hapmap]
rs3733626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56339535	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56725761	0.81[EUR][1000 genomes]
rs6825106	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs7653900	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7662362	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7670908	1.00[CEU][hapmap]
rs971695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs971696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9991367	1.00[CEU][hapmap]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11569104	PITX2	cis	brain	seeQTL
rs11569104	NOTUM	trans	brain	seeQTL
rs11569104	COL25A1	cis	brain	seeQTL
rs11569104	ENPEP	cis	brain	seeQTL
rs11569104	FBXL4	trans	brain	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110895000-110928600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:110901000-110929600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:110907000-110932400	Weak transcription	Psoas Muscle	Psoas
4	chr4:110907800-110927400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr4:110910400-110935200	Weak transcription	Pancreas	Pancrea
6	chr4:110910600-110929800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:110910800-110926800	Weak transcription	Fetal Heart	heart
8	chr4:110919000-110935200	Weak transcription	Left Ventricle	heart
9	chr4:110920800-110935800	Strong transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:110921000-110924800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:110921000-110926800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:110921000-110926800	Weak transcription	HepG2	liver
13	chr4:110921000-110927600	Weak transcription	Fetal Intestine Small	intestine
14	chr4:110924600-110925000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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