Variant report

Variant	rs3920049
Chromosome Location	chr4:55716268-55716269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr4:55716019-55716293	MCF-7	breast:	n/a	chr4:55716194-55716203 chr4:55716178-55716198
2	REST	chr4:55716021-55716292	H1-hESC	embryonic stem cell:	n/a	chr4:55716194-55716203 chr4:55716178-55716198
3	REST	chr4:55716013-55716402	HL-60	blood:	n/a	chr4:55716194-55716203 chr4:55716178-55716198
4	REST	chr4:55715952-55716390	HL-60	blood:	n/a	chr4:55716194-55716203 chr4:55716178-55716198

Variant related genes	Relation type
ENSG00000249727	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1391133	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1391134	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1497476	0.87[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs1497493	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1497496	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1497498	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1532460	0.83[AMR][1000 genomes]
rs17084899	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1874645	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1874646	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1874648	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1874652	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1874653	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2173231	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2270674	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28402753	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28435137	0.84[AMR][1000 genomes]
rs28605787	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28720093	0.88[AMR][1000 genomes]
rs4864932	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55841826	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61708640	0.90[AMR][1000 genomes]
rs6554208	0.81[AMR][1000 genomes]
rs6825254	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6827165	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6847687	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7659889	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7677880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs998615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1836939	chr4:55701134-55716601	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55709200-55721600	Weak transcription	Fetal Stomach	stomach
2	chr4:55715600-55717800	Enhancers	Brain Germinal Matrix	brain

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