Variant report

Variant	rs6534321
Chromosome Location	chr4:122692023-122692024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10002280	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10024445	0.89[ASN][1000 genomes]
rs10857086	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11098647	0.93[ASN][1000 genomes]
rs11726779	0.89[ASN][1000 genomes]
rs11732582	0.88[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12499222	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28665553	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4240261	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4342205	0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4370153	0.83[CEU][hapmap];0.89[MEX][hapmap];0.80[TSI][hapmap];0.91[EUR][1000 genomes]
rs4496602	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs4519820	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4629472	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs4833774	0.95[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6534317	0.89[EUR][1000 genomes]
rs6534319	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6534325	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6815050	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6819870	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6823686	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6830128	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6835864	0.90[ASN][1000 genomes]
rs6836290	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7661641	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7665098	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7672640	0.81[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7690991	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817261	chr4:122085173-123020068	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv997539	chr4:122544104-123274266	Genic enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv530157	chr4:122557302-123248756	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv461635	chr4:122633535-122720999	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv595357	chr4:122633535-122720999	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	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
rs6534321	CCNA2	cis	cerebellum	SCAN
rs6534321	FGF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:122687600-122695200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:122689400-122695400	Weak transcription	Fetal Heart	heart
3	chr4:122692000-122692200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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