Variant report

Variant	rs3733626
Chromosome Location	chr4:110925492-110925493
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRIT3-4	chr4:110925403-110925778	NONHSAT097802

Extended variants
information (count: 29 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10010695	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1005903	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10857004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098060	0.88[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11098061	0.86[EUR][1000 genomes]
rs11569019	1.00[CEU][hapmap]
rs11569020	1.00[CEU][hapmap]
rs11569104	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]
rs11569121	0.88[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs11569126	0.92[TSI][hapmap]
rs17041230	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2074392	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237053	0.84[CHB][hapmap]
rs2237054	1.00[CEU][hapmap]
rs2255355	0.81[MEX][hapmap]
rs2282787	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2298996	1.00[CEU][hapmap]
rs2299001	0.84[TSI][hapmap]
rs3733625	0.92[TSI][hapmap]
rs56339535	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56725761	0.84[EUR][1000 genomes]
rs6825106	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs7653900	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661968	0.84[TSI][hapmap]
rs7662362	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7670908	1.00[CEU][hapmap]
rs971695	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs971696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9991367	1.00[CEU][hapmap]

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3733626	NOTUM	trans	brain	seeQTL
rs3733626	LRIT3	cis	brain	seeQTL
rs3733626	COL25A1	cis	brain	seeQTL
rs3733626	ENPEP	cis	brain	seeQTL
rs3733626	PITX2	cis	brain	seeQTL
rs3733626	GAS7	trans	brain	seeQTL

Chromatin state (count:13 , 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	chr4:110921000-110926800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr4:110921000-110926800	Weak transcription	HepG2	liver
12	chr4:110921000-110927600	Weak transcription	Fetal Intestine Small	intestine
13	chr4:110924800-110925600	Enhancers	Fetal Intestine Large	intestine

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