Variant report

Variant	rs16824992
Chromosome Location	chr3:155167027-155167028
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MME-3	chr3:155166973-155167214	ENSG00000239508.1

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11918635	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11925808	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11927163	0.91[MKK][hapmap]
rs11928539	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16824956	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs16824961	0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs16824962	0.90[YRI][hapmap];0.89[AFR][1000 genomes]
rs16824965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16824986	1.00[ASW][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16825048	1.00[CEU][hapmap]
rs28503947	1.00[ASN][1000 genomes]
rs34828234	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302412	1.00[ASN][1000 genomes]
rs4352412	1.00[ASN][1000 genomes]
rs4352413	1.00[ASN][1000 genomes]
rs4392458	1.00[ASN][1000 genomes]
rs4630983	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs57461710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57825069	1.00[ASN][1000 genomes]
rs57951243	0.89[AFR][1000 genomes]
rs57985049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58523386	1.00[ASN][1000 genomes]
rs6440982	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6440983	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6440984	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6764943	1.00[CEU][hapmap]
rs6777732	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6791188	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6791222	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs6802130	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6802336	1.00[ASN][1000 genomes]
rs6805227	1.00[ASN][1000 genomes]
rs73009787	0.89[AFR][1000 genomes]
rs73009792	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73009795	0.89[AFR][1000 genomes]
rs73011503	0.89[AFR][1000 genomes]
rs73011509	0.89[AFR][1000 genomes]
rs73011512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73011513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73011515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73011519	0.89[AFR][1000 genomes]
rs73011523	0.85[AFR][1000 genomes]
rs73011525	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73011526	0.87[AFR][1000 genomes]
rs73011527	0.87[AFR][1000 genomes]
rs73011528	0.94[AFR][1000 genomes]
rs73873187	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637223	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1000753	chr3:154848433-155207022	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv536773	chr3:154848433-155207022	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv877679	chr3:155128968-155204939	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16824992	WWTR1	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155155600-155167400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:155165600-155172400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:155166400-155167200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:155166400-155167200	Enhancers	Left Ventricle	heart
5	chr3:155166400-155167200	Enhancers	Right Atrium	heart
6	chr3:155166600-155168600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:155166800-155167200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:155166800-155167200	Weak transcription	Osteobl	bone
9	chr3:155166800-155178800	Weak transcription	Pancreas	Pancrea

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