Variant report

Variant	rs3913899
Chromosome Location	chr4:142031168-142031169
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:141865472..141867411-chr4:142030563..142032115,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10008705	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10519584	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12509440	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1395668	1.00[EUR][1000 genomes]
rs1395669	1.00[EUR][1000 genomes]
rs1873370	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4267811	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4386678	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4629541	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4637487	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4956512	0.96[EUR][1000 genomes]
rs4956513	1.00[EUR][1000 genomes]
rs4956514	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs4956517	0.86[GIH][hapmap]
rs4956518	0.86[GIH][hapmap];0.82[MEX][hapmap]
rs62324901	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62324902	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6537030	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6817313	1.00[EUR][1000 genomes]
rs6826231	1.00[EUR][1000 genomes]
rs6831578	1.00[EUR][1000 genomes]
rs6856997	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7658695	0.93[EUR][1000 genomes]
rs7683490	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7697519	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9790672	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9790673	1.00[CEU][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880167	chr4:141616979-142092124	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv880169	chr4:142005573-142038481	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3913899	MGST2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142000800-142031600	Weak transcription	Right Ventricle	heart
2	chr4:142013000-142040400	Weak transcription	Psoas Muscle	Psoas
3	chr4:142024200-142031200	Weak transcription	Colon Smooth Muscle	Colon
4	chr4:142026200-142039200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:142028000-142031200	Weak transcription	Left Ventricle	heart
6	chr4:142028200-142032400	Enhancers	Fetal Heart	heart
7	chr4:142028600-142042400	Weak transcription	Stomach Smooth Muscle	stomach

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