Variant report

Variant	rs39311
Chromosome Location	chr7:116954117-116954118
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	7:115847372-115857098..7:116949919-116957096	GM12878	blood:
2	7:116434729-116454408..7:116949919-116957096	H1-hESC	embryonic stem cell:	embryo
3	7:115861595-115870968..7:116949919-116957096	Hela-S3	cervix:
4	7:116604327-116608063..7:116949919-116957096	H1-hESC	embryonic stem cell:	embryo
5	7:115890993-115892266..7:116949919-116957096	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000198898	Chromatin interaction
ENSG00000228368	Chromatin interaction
ENSG00000135269	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10230259	0.88[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10237017	1.00[ASN][1000 genomes]
rs10242827	0.88[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1025342	1.00[ASN][1000 genomes]
rs10255092	0.92[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258791	0.89[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10264450	0.96[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10278953	0.92[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10487364	1.00[ASN][1000 genomes]
rs12536356	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17139821	1.00[ASN][1000 genomes]
rs17450482	1.00[ASN][1000 genomes]
rs17544734	1.00[ASN][1000 genomes]
rs17545644	1.00[ASN][1000 genomes]
rs17547485	1.00[ASN][1000 genomes]
rs177071	1.00[ASN][1000 genomes]
rs1800503	1.00[ASN][1000 genomes]
rs2518872	1.00[ASN][1000 genomes]
rs254537	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs254538	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs34268361	1.00[ASN][1000 genomes]
rs34420782	1.00[ASN][1000 genomes]
rs34654194	1.00[ASN][1000 genomes]
rs35003065	1.00[ASN][1000 genomes]
rs35130797	1.00[ASN][1000 genomes]
rs35415299	1.00[ASN][1000 genomes]
rs35715578	1.00[ASN][1000 genomes]
rs35820454	1.00[ASN][1000 genomes]
rs35987553	1.00[ASN][1000 genomes]
rs36082161	1.00[ASN][1000 genomes]
rs39308	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39309	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39310	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39314	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39320	0.92[CEU][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39321	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39322	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs39325	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4285411	0.96[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466610	0.96[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6943509	1.00[ASN][1000 genomes]
rs6961545	1.00[ASN][1000 genomes]
rs6963669	0.96[CEU][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73480763	1.00[ASN][1000 genomes]
rs7779160	0.88[EUR][1000 genomes]
rs7795896	1.00[ASN][1000 genomes]
rs7802924	1.00[ASN][1000 genomes]
rs916727	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916728	0.96[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9886209	0.92[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv608256	chr7:116928371-117040117	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs39311	WNT2	cis	intralobular white matter	BrainEAC

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:116931800-116961600	Weak transcription	Placenta	Placenta
2	chr7:116937000-116954800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:116945200-116954400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:116952400-116960600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:116952600-116954200	Weak transcription	Fetal Lung	lung
6	chr7:116953000-116954400	Enhancers	Liver	Liver
7	chr7:116953800-116954200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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