Variant report

Variant	rs1984473
Chromosome Location	chr3:155811284-155811285
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155811121..155812697-chr4:74123629..74125315,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000250220	Chromatin interaction
ENSG00000132466	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10936024	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11709514	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11716256	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11718399	1.00[CEU][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12493813	0.96[ASN][1000 genomes]
rs13073556	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13078555	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093154	0.83[CHB][hapmap]
rs1386956	0.87[ASN][1000 genomes]
rs1386957	0.86[ASN][1000 genomes]
rs1386958	0.87[ASN][1000 genomes]
rs1488425	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1488426	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1488427	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1825909	0.83[ASN][1000 genomes]
rs1906543	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3936002	0.85[MEX][hapmap]
rs4261831	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4359773	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4359774	0.96[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4580504	0.80[MEX][hapmap]
rs4605502	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4679760	0.87[EUR][1000 genomes]
rs4679761	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4680231	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4680232	1.00[CEU][hapmap];0.98[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4680233	0.95[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4680234	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4680235	0.83[EUR][1000 genomes]
rs4680237	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4680239	0.80[MEX][hapmap]
rs56231269	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6441035	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6441042	0.90[MEX][hapmap]
rs6778035	0.82[CEU][hapmap]
rs6778199	0.96[ASN][1000 genomes]
rs6780500	0.82[EUR][1000 genomes]
rs6788449	0.89[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6793964	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7613000	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7617796	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs7618820	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7633081	0.80[EUR][1000 genomes]
rs7645641	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7652981	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289961	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9683366	0.96[ASN][1000 genomes]
rs9789968	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9814661	0.96[CEU][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9838322	0.83[EUR][1000 genomes]
rs9842620	0.89[CEU][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs9856468	0.96[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs9861320	0.89[CEU][hapmap]
rs9862153	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9882088	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][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	nsv592084	chr3:155751484-155830578	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1984473	MLF1	cis	parietal	SCAN
rs1984473	SCARNA7	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155800200-155811800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:155808800-155811800	Weak transcription	Fetal Brain Male	brain
3	chr3:155811000-155811800	Weak transcription	Liver	Liver

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